Mercurial > repos > iuc > meme_fimo

annotate test-data/meme_output_test2.html @ 20:613c75eee7bd draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
author iuc
date Mon, 14 Jul 2025 21:33:56 +0000
parents c5209f38700d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1 * See http://stackoverflow.com/a/5450113/66387
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2 * Does string multiplication like the perl x operator.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4 function string_mult(pattern, count) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5 if (count < 1) return '';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6 var result = '';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7 while (count > 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8 if (count & 1) result += pattern;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9 count >>= 1, pattern += pattern;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
10 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
11 return result + pattern;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
12 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
13
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
14 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
15 * See http://stackoverflow.com/questions/814613/how-to-read-get-data-from-a-url-using-javascript
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
16 * Slightly modified with information from
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
17 * https://developer.mozilla.org/en/DOM/window.location
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
18 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
19 function parse_params() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
20 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
21 var search, queryStart, queryEnd, query, params, nvPairs, i, nv, n, v;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
22 search = window.location.search;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
23 queryStart = search.indexOf("?") + 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
24 queryEnd = search.indexOf("#") + 1 || search.length + 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
25 query = search.slice(queryStart, queryEnd - 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
26
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
27 if (query === search || query === "") return {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
28
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
29 params = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
30 nvPairs = query.replace(/\+/g, " ").split("&");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
31
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
32 for (i = 0; i < nvPairs.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
33 nv = nvPairs[i].split("=");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
34 n = decodeURIComponent(nv[0]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
35 v = decodeURIComponent(nv[1]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
36 // allow a name to be used multiple times
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
37 // storing each value in the array
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
38 if (!(n in params)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
39 params[n] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
40 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
41 params[n].push(nv.length === 2 ? v : null);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
42 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
43 return params;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
44 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
45
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
46 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
47 * coords
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
48 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
49 * Calculates the x and y offset of an element.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
50 * From http://www.quirksmode.org/js/findpos.html
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
51 * with alterations to take into account scrolling regions
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
52 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
53 function coords(elem) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
54 var myX = myY = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
55 if (elem.getBoundingClientRect) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
56 var rect;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
57 rect = elem.getBoundingClientRect();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
58 myX = rect.left + ((typeof window.pageXOffset !== "undefined") ?
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
59 window.pageXOffset : document.body.scrollLeft);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
60 myY = rect.top + ((typeof window.pageYOffset !== "undefined") ?
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
61 window.pageYOffset : document.body.scrollTop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
62 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
63 // this fall back doesn't properly handle absolutely positioned elements
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
64 // inside a scrollable box
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
65 var node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
66 if (elem.offsetParent) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
67 // subtract all scrolling
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
68 node = elem;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
69 do {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
70 myX -= node.scrollLeft ? node.scrollLeft : 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
71 myY -= node.scrollTop ? node.scrollTop : 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
72 } while (node = node.parentNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
73 // this will include the page scrolling (which is unwanted) so add it back on
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
74 myX += (typeof window.pageXOffset !== "undefined") ? window.pageXOffset : document.body.scrollLeft;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
75 myY += (typeof window.pageYOffset !== "undefined") ? window.pageYOffset : document.body.scrollTop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
76 // sum up offsets
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
77 node = elem;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
78 do {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
79 myX += node.offsetLeft;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
80 myY += node.offsetTop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
81 } while (node = node.offsetParent);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
82 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
83 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
84 return [myX, myY];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
85 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
86
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
87 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
88 * position_popup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
89 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
90 * Positions a popup relative to an anchor element.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
91 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
92 * The available positions are:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
93 * 0 - Centered below the anchor.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
94 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
95 function position_popup(anchor, popup, position) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
96 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
97 var a_x, a_y, a_w, a_h, p_x, p_y, p_w, p_h;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
98 var a_xy, spacer, margin, scrollbar, page_w;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
99 // define constants
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
100 spacer = 5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
101 margin = 15;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
102 scrollbar = 15;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
103 // define the positions and widths
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
104 a_xy = coords(anchor);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
105 a_x = a_xy[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
106 a_y = a_xy[1];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
107 a_w = anchor.offsetWidth;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
108 a_h = anchor.offsetHeight;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
109 p_w = popup.offsetWidth;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
110 p_h = popup.offsetHeight;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
111 page_w = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
112 if (window.innerWidth) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
113 page_w = window.innerWidth;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
114 } else if (document.body) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
115 page_w = document.body.clientWidth;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
116 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
117 // check the position type is defined
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
118 if (typeof position !== "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
119 position = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
120 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
121 // calculate the popup position
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
122 switch (position) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
123 case 1:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
124 p_x = a_x + a_w + spacer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
125 p_y = a_y + (a_h / 2) - (p_h / 2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
126 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
127 case 0:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
128 default:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
129 p_x = a_x + (a_w / 2) - (p_w / 2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
130 p_y = a_y + a_h + spacer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
131 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
132 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
133 // constrain the popup position
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
134 if (p_x < margin) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
135 p_x = margin;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
136 } else if (page_w != null && (p_x + p_w) > (page_w - margin - scrollbar)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
137 p_x = page_w - margin - scrollbar - p_w;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
138 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
139 if (p_y < margin) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
140 p_y = margin;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
141 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
142 // position the popup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
143 popup.style.left = p_x + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
144 popup.style.top = p_y + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
145 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
146
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
147 function lookup_help_popup(popup_id) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
148 var _body, pop, info;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
149 pop = document.getElementById(popup_id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
150 if (pop == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
151 _body = document.getElementsByTagName("body")[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
152 pop = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
153 pop.className = "pop_content";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
154 pop.id = popup_id;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
155 pop.style.backgroundColor = "#FFC";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
156 pop.style.borderColor = "black";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
157 info = document.createElement("p");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
158 info.style.fontWeight = "bold";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
159 info.appendChild(document.createTextNode("Error: No popup for topic \"" + popup_id + "\"."));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
160 pop.appendChild(info);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
161 // this might cause problems with the menu, but as this only happens
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
162 // when something is already wrong I don't think that's too much of a problem
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
163 _body.insertBefore(pop, _body.firstChild);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
164 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
165 if (document.getElementsByTagName('body')[0].hasAttribute("data-autobtns")) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
166 if (!/\bauto_buttons\b/.test(pop.className)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
167 pop.className += " auto_buttons";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
168 var back_btn_sec = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
169 back_btn_sec.className = "nested_only pop_back_sec";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
170 var back_btn = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
171 back_btn.className = "pop_back";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
172 back_btn.appendChild(document.createTextNode("<< back"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
173 back_btn.addEventListener("click", function(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
174 help_return();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
175 }, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
176 back_btn_sec.appendChild(back_btn);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
177 pop.insertBefore(back_btn_sec, pop.firstChild);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
178 var close_btn_sec = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
179 close_btn_sec.className = "pop_close_sec";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
180 var close_btn = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
181 close_btn.className = "pop_close";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
182 close_btn.appendChild(document.createTextNode("close"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
183 close_btn.addEventListener("click", function(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
184 help_popup();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
185 }, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
186 close_btn_sec.appendChild(close_btn);
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diff changeset
187 pop.appendChild(close_btn_sec);
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188 }
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189 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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190 return pop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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191 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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192
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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193 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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194 * help_popup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
195 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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196 * Moves around help pop-ups so they appear
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
197 * below an activator.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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198 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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199 function help_popup(activator, popup_id) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
200 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
201 var pop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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202 // set default values
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
203 if (typeof help_popup.popup === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
204 help_popup.popup = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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205 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
206 if (typeof help_popup.activator === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
207 help_popup.activator = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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208 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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209 var last_pop = (help_popup.popup.length > 0 ? help_popup.popup[help_popup.popup.length - 1] : null);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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210 if (typeof(activator) == "undefined") { // no activator so hide
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
211 if (last_pop != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
212 last_pop.style.display = 'none';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
213 help_popup.popup = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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214 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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215 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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216 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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217 pop = lookup_help_popup(popup_id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
218 if (pop == last_pop) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
219 if (activator == help_popup.activator) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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220 //hide popup (as we've already shown it for the current help button)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
221 last_pop.style.display = 'none';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
222 help_popup.popup = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
223 return; // toggling complete!
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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224 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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225 } else if (last_pop != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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226 //activating different popup so hide current one
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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227 last_pop.style.display = 'none';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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228 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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229 help_popup.popup = [pop];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
230 help_popup.activator = activator;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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231 toggle_class(pop, "nested", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
232 //must make the popup visible to measure it or it has zero width
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diff changeset
233 pop.style.display = 'block';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
234 position_popup(activator, pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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235 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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236
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
237 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
238 * help_refine
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
239 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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240 * Intended for links within a help popup. Stores a stack of state so
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
241 * you can go back.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
242 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
243 function help_refine(popup_id) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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244 if (help_popup.popup == null || help_popup.popup.length == 0 || help_popup.activator == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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245 //throw new Error("Cannot refine a help popup when one is not shown!");
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246 var pop = lookup_help_popup(popup_id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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247 var act_id = popup_id + '_act';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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248 var activator = document.getElementById(act_id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
249 help_popup(activator, popup_id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
250 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
251 var pop = lookup_help_popup(popup_id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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252 var last_pop = help_popup.popup[help_popup.popup.length - 1];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
253 if (pop == last_pop) return; // slightly odd, but no real cause for alarm
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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254 help_popup.popup.push(pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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255 toggle_class(pop, "nested", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
256 last_pop.style.display = "none";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
257 //must make the popup visible to measure it or it has zero width
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258 pop.style.display = "block";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
259 position_popup(help_popup.activator, pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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260 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
261
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
262 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
263 * help_return
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
264 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
265 * Intended for links within a help popup. Stores a stack of state so
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
266 * you can go back.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
267 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
268 function help_return() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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269 if (help_popup.popup == null || help_popup.popup.length == 0 || help_popup.activator == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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270 throw new Error("Can not return to a earlier help popup when one is not shown!");
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diff changeset
271 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
272 var last_pop = help_popup.popup.pop();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
273 last_pop.style.display = "none";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
274 var pop = (help_popup.popup.length > 0 ? help_popup.popup[help_popup.popup.length - 1] : null);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
275 if (pop != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
276 toggle_class(pop, "nested", help_popup.popup.length > 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
277 pop.style.display = "block";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
278 position_popup(help_popup.activator, pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
279 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
280 help_popup.activator = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
281 }
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diff changeset
282 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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283
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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parents: 18
diff changeset
284 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
285 * update_scroll_pad
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
286 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
287 * Creates padding at the bottom of the page to allow
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
288 * scrolling of anything into view.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
289 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
290 function update_scroll_pad() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
291 var page, pad;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
292 page = (document.compatMode === "CSS1Compat") ? document.documentElement : document.body;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
293 pad = $("scrollpad");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
294 if (pad === null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
295 pad = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
296 pad.id = 'scrollpad';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
297 document.getElementsByTagName('body')[0].appendChild(pad);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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298 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
299 pad.style.height = Math.abs(page.clientHeight - 100) + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
300 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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301
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
302 function substitute_classes(node, remove, add) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
303 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
304 var list, all, i, cls, classes;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
305 list = node.className.split(/\s+/);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
306 all = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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parents: 18
diff changeset
307 for (i = 0; i < list.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
308 if (list[i].length > 0) all[list[i]] = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
309 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
310 for (i = 0; i < remove.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
311 if (all.hasOwnProperty(remove[i])) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
312 delete all[remove[i]];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
313 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
314 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
315 for (i = 0; i < add.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
316 all[add[i]] = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
317 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
318 classes = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
319 for (cls in all) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
320 classes += cls + " ";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
321 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
322 node.className = classes;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
323 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
324
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
325 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
326 * toggle_class
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
327 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
328 * Adds or removes a class from the node. If the parameter 'enabled' is not
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
329 * passed then the existence of the class will be toggled, otherwise it will be
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
330 * included if enabled is true.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
331 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
332 function toggle_class(node, cls, enabled) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
333 var classes = node.className;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
334 var list = classes.replace(/^\s+/, '').replace(/\s+$/, '').split(/\s+/);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
335 var found = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
336 for (var i = 0; i < list.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
337 if (list[i] == cls) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
338 list.splice(i, 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
339 i--;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
340 found = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
341 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
342 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
343 if (typeof enabled == "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
344 if (!found) list.push(cls);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
345 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
346 if (enabled) list.push(cls);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
347 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
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diff changeset
348 node.className = list.join(" ");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
349 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
350
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
351 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
352 * find_child
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
353 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
354 * Searches child nodes in depth first order and returns the first it finds
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
355 * with the className specified.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
356 * TODO replace with querySelector
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
357 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
358 function find_child(node, className) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
359 var pattern;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
360 if (node == null || typeof node !== "object") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
361 return null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
362 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
363 if (typeof className === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
364 pattern = new RegExp("\\b" + className + "\\b");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
365 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
366 pattern = className;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
367 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
368 if (node.nodeType == Node.ELEMENT_NODE &&
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
369 pattern.test(node.className)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
370 return node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
371 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
372 var result = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
373 for (var i = 0; i < node.childNodes.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
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diff changeset
374 result = find_child(node.childNodes[i], pattern);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
375 if (result != null) break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
376 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
377 return result;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
378 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
379 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
380
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
381 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
382 * find_parent
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
383 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
384 * Searches parent nodes outwards from the node and returns the first it finds
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
385 * with the className specified.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
386 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
387 function find_parent(node, className) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
388 var pattern;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
389 pattern = new RegExp("\\b" + className + "\\b");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
390 do {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
391 if (node.nodeType == Node.ELEMENT_NODE &&
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
392 pattern.test(node.className)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
393 return node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
394 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
395 } while (node = node.parentNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
396 return null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
397 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
398
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
399 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
400 * find_parent_tag
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
401 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
402 * Searches parent nodes outwards from the node and returns the first it finds
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
403 * with the tag name specified. HTML tags should be specified in upper case.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
404 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
405 function find_parent_tag(node, tag_name) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
406 do {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
407 if (node.nodeType == Node.ELEMENT_NODE && node.tagName == tag_name) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
408 return node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
409 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
410 } while (node = node.parentNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
411 return null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
412 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
413
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
414 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
415 * __toggle_help
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
416 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
417 * Uses the 'topic' property of the this object to
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
418 * toggle display of a help topic.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
419 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
420 * This function is not intended to be called directly.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
421 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
422 function __toggle_help(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
423 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
424 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
425 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
426 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
427 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
428 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
429 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
430 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
431
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
432 help_popup(this, this.getAttribute("data-topic"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
433 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
434
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
435 function setup_help_button(button) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
436 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
437 var topic;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
438 if (button.hasAttribute("data-topic")) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
439 topic = button.getAttribute("data-topic");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
440 if (document.getElementById(topic) != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
441 button.tabIndex = "0"; // make keyboard selectable
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
442 button.addEventListener("click", function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
443 help_popup(button, topic);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
444 }, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
445 button.addEventListener("keydown", function(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
446 // toggle only on Enter or Spacebar, let other keys do their thing
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
447 if (e.keyCode !== 13 && e.keyCode !== 32) return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
448 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
449 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
450 help_popup(button, topic);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
451 }, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
452 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
453 button.style.visibility = "hidden";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
454 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
455 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
456 button.className += " active";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
457 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
458
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
459 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
460 * help_button
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
461 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
462 * Makes a help button for the passed topic.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
463 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
464 function help_button(topic) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
465 var btn = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
466 btn.className = "help";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
467 btn.setAttribute("data-topic", topic);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
468 setup_help_button(btn);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
469 return btn;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
470 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
471
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
472 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
473 * prepare_download
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
474 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
475 * Sets the attributes of a link to setup a file download using the given content.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
476 * If no link is provided then create one and click it.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
477 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
478 function prepare_download(content, mimetype, filename, link) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
479 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
480 // if no link is provided then create one and click it
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
481 var click_link = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
482 if (!link) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
483 link = document.createElement("a");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
484 click_link = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
485 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
486 try {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
487 // Use a BLOB to convert the text into a data URL.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
488 // We could do this manually with a base 64 conversion.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
489 // This will only be supported on modern browsers,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
490 // hence the try block.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
491 var blob = new Blob([content], {type: mimetype});
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
492 var reader = new FileReader();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
493 reader.onloadend = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
494 // If we're lucky the browser will also support the download
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
495 // attribute which will let us suggest a file name to save the link.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
496 // Otherwise it is likely that the filename will be unintelligible.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
497 link.setAttribute("download", filename);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
498 link.href = reader.result;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
499 if (click_link) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
500 // must add the link to click it
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
501 document.body.appendChild(link);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
502 link.click();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
503 document.body.removeChild(link);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
504 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
505 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
506 reader.readAsDataURL(blob);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
507 } catch (error) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
508 if (console && console.log) console.log(error);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
509 // probably an old browser
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
510 link.href = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
511 link.visible = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
512 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
513 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
514
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
515 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
516 * add_cell
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
517 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
518 * Add a cell to the table row.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
519 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
520 function add_cell(row, node, cls, click_action) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
521 var cell = row.insertCell(row.cells.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
522 if (node) cell.appendChild(node);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
523 if (cls && cls !== "") cell.className = cls;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
524 if (click_action) cell.addEventListener("click", click_action, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
525 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
526
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
527 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
528 * add_header_cell
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
529 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
530 * Add a header cell to the table row.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
531 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
532 function add_header_cell(row, node, help_topic, cls, colspan, is_new) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
533 var th = document.createElement("th");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
534 if (node) th.appendChild(node);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
535 if (help_topic && help_topic !== "") th.appendChild(help_button(help_topic));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
536 if (is_new && is_new !== "") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
537 var br = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
538 br.innerHTML = "<br>";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
539 th.appendChild(br);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
540 var new_icon = document.createElement("img");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
541 new_icon.src = new_icon_src;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
542 new_icon.alt = "NEW";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
543 th.appendChild(new_icon);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
544 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
545 if (cls && cls !== "") th.className = cls;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
546 if (typeof colspan == "number" && colspan > 1) th.colSpan = colspan;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
547 row.appendChild(th);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
548 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
549
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
550 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
551 * add_text_cell
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
552 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
553 * Add a text cell to the table row.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
554 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
555 function add_text_cell(row, text, cls, action) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
556 var node = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
557 if (typeof(text) != 'undefined') node = document.createTextNode(text);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
558 add_cell(row, node, cls, action);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
559 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
560
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
561 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
562 * add_text_header_cell
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
563 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
564 * Add a text header cell to the table row.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
565 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
566 function add_text_header_cell(row, text, help_topic, cls, action, colspan, is_new) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
567 var node = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
568 if (typeof(text) != 'undefined') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
569 var nbsp = (help_topic ? "\u00A0" : "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
570 var str = "" + text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
571 var parts = str.split(/\n/);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
572 if (parts.length === 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
573 if (action) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
574 node = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
575 node.appendChild(document.createTextNode(str + nbsp));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
576 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
577 node = document.createTextNode(str + nbsp);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
578 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
579 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
580 node = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
581 for (var i = 0; i < parts.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
582 if (i !== 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
583 node.appendChild(document.createElement("br"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
584 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
585 node.appendChild(document.createTextNode(parts[i]));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
586 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
587 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
588 if (action) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
589 node.addEventListener("click", action, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
590 node.style.cursor = "pointer";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
591 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
592 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
593 add_header_cell(row, node, help_topic, cls, colspan, is_new);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
594 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
595
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
596 function setup_help() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
597 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
598 var help_buttons, i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
599 help_buttons = document.querySelectorAll(".help:not(.active)");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
600 for (i = 0; i < help_buttons.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
601 setup_help_button(help_buttons[i]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
602 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
603 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
604
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
605 function setup_scrollpad() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
606 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
607 if (document.getElementsByTagName('body')[0].hasAttribute("data-scrollpad") && document.getElementById("scrollpad") == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
608 window.addEventListener("resize", update_scroll_pad, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
609 update_scroll_pad();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
610 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
611 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
612
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
613 // anon function to avoid polluting global scope
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
614 (function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
615 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
616 window.addEventListener("load", function load(evt) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
617 window.removeEventListener("load", load, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
618 setup_help();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
619 setup_scrollpad();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
620 }, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
621 })();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
622
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
623 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
624 * make_link
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
625 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
626 * Creates a text node and if a URL is specified it surrounds it with a link.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
627 * If the URL doesn't begin with "http://" it automatically adds it, as
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
628 * relative links don't make much sense in this context.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
629 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
630 function make_link(text, url) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
631 var textNode = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
632 var link = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
633 if (typeof text !== "undefined" && text !== null) textNode = document.createTextNode(text);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
634 if (typeof url === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
635 if (url.indexOf("//") == -1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
636 url = "http://" + url;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
637 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
638 link = document.createElement('a');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
639 link.href = url;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
640 if (textNode) link.appendChild(textNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
641 return link;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
642 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
643 return textNode;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
644 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
645
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
646 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
647 // Function to create an HTML paragraph describing the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
648 // MEME Suite background model source.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
649 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
650 function make_background_source(title, source, text) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
651 var paraNode = document.createElement("P");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
652 var titleNode = document.createElement("B");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
653 var textNode1 = document.createTextNode("\u00A0\u00A0\u00A0\u00A0" + title + ": ");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
654 titleNode.appendChild(textNode1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
655 var source_text = ((source == "--motif--") ? "the (first) motif file" : (source == "--nrdb--") ? "an old version of the NCBI non-redundant database" : (source == "--uniform--") ? "the uniform model" : (source == "--query--") ? "the query file" : (source == "--sequences--") ? "built from the (primary) sequences" : (source == "--control--") ? "built from the control (negative) sequences" : ((source == "--negatives--") ? "built from the negative (control) sequences" : "the file '" + source + "'"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
656 if (text) { return source_text; }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
657 var textNode2 = document.createTextNode(source_text);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
658 paraNode.appendChild(titleNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
659 paraNode.appendChild(textNode2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
660 return paraNode;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
661 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
662
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
663 // Function to create a help button
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
664 function make_help_button(container, help_topic) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
665 container.appendChild(help_button(help_topic));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
666 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
667
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
668 // Function to toggle display.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
669 function change_display(id) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
670 var element=document.getElementById(id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
671 element.style.display=(element.style.display=='none') ? element.style.display='inline' : element.style.display='none';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
672 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
673 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
674 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
675 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
676 // return true if any part of the passed element is visible in the viewport
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
677 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
678 function element_in_viewport(elem) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
679 var rect;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
680 try {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
681 rect = elem.getBoundingClientRect();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
682 } catch (e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
683 return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
684 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
685 return (
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
686 rect.top < (window.innerHeight || document.body.clientHeight) &&
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
687 rect.bottom > 0 &&
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
688 rect.left < (window.innerWidth || document.body.clientWidth) &&
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
689 rect.right > 0
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
690 );
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
691 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
692
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
693 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
694 // Functions to delay a drawing task until it is required or it would not lag the display to do so
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
695 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
696
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
697 // a list of items still to be drawn
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
698 var drawable_list = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
699 // the delay between drawing objects that are not currently visible
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
700 var draw_delay = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
701 // the delay after a user interaction
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
702 var user_delay = 300;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
703 // the delay after a user has stopped scrolling and is viewing the stuff drawn on the current page
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
704 var stop_delay = 300;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
705 // the timer handle; allows resetting of the timer after user interactions
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
706 var draw_timer = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
707
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
708 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
709 // Drawable
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
710 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
711 // elem - a page element which defines the position on the page that drawing is to be done
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
712 // task - an object with the method run which takes care of painting the object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
713 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
714 var Drawable = function(elem, task) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
715 this.elem = elem;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
716 this.task = task;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
717 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
718
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
719 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
720 // Drawable.is_visible
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
721 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
722 // Determines if the element is visible in the viewport
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
723 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
724 Drawable.prototype.is_visible = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
725 return element_in_viewport(this.elem);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
726 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
727
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
728 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
729 // Drawable.run
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
730 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
731 // Run the task held by the drawable
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
732 Drawable.prototype.run = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
733 if (this.task) this.task.run();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
734 this.task = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
735 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
736
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
737 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
738 // Drawable.run
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
739 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
740 // Run the task iff visible
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
741 // returns true if the task ran or has already run
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
742 Drawable.prototype.run_visible = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
743 if (this.task) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
744 if (element_in_viewport(this.elem)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
745 this.task.run();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
746 this.task = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
747 return true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
748 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
749 return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
750 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
751 return true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
752 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
753 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
754
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
755 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
756 // draw_on_screen
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
757 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
758 // Checks each drawable object and draws those on screen.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
759 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
760 function draw_on_screen() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
761 var found = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
762 for (var i = 0; i < drawable_list.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
763 if (drawable_list[i].run_visible()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
764 drawable_list.splice(i--, 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
765 found = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
766 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
767 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
768 return found;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
769 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
770
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
771 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
772 // process_draw_tasks
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
773 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
774 // Called on a delay to process the next available
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
775 // draw task.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
776 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
777 function process_draw_tasks() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
778 var delay = draw_delay;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
779 draw_timer = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
780 if (drawable_list.length == 0) return; //no more tasks
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
781 if (draw_on_screen()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
782 delay = stop_delay; //give the user a chance to scroll
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
783 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
784 //get next task
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
785 var drawable = drawable_list.shift();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
786 drawable.task.run();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
787 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
788 //allow UI updates between tasks
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
789 draw_timer = window.setTimeout("process_draw_tasks()", delay);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
790 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
791
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
792 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
793 // delayed_process_draw_tasks
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
794 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
795 // Call process_draw_tasks after a short delay.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
796 // The delay serves to group multiple redundant events.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
797 // Should be set as event handler for onscroll and onresize.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
798 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
799 function delayed_process_draw_tasks() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
800 //reset the timer
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
801 if (drawable_list.length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
802 if (draw_timer != null) clearTimeout(draw_timer);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
803 draw_timer = window.setTimeout("process_draw_tasks()", user_delay);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
804 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
805 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
806
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
807 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
808 // add_draw_task
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
809 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
810 // Add a drawing task to be called immediately if it is
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
811 // visible, or to be called on a delay to reduce stuttering
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
812 // effect on the web browser.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
813 function add_draw_task(elem, task) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
814 drawable = new Drawable(elem, task);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
815 if (drawable.is_visible()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
816 task.run();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
817 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
818 drawable_list.push(drawable);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
819 //reset timer
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
820 if (draw_timer != null) clearTimeout(draw_timer);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
821 draw_timer = window.setTimeout("process_draw_tasks()", user_delay);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
822 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
823 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
824
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
825 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
826 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
827 function motif_logo_template(inputs) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
828 function _input(name) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
829 if (typeof inputs[name] === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
830 throw new Error("Missing template variable: " + name);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
831 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
832 return inputs[name];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
833 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
834 return (
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
835 "%!PS-Adobe-3.0 EPSF-3.0\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
836 "%%Title: Sequence Logo : " + _input("TITLE") + "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
837 "%%Creator: " + _input("CREATOR") + "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
838 "%%CreationDate: " + _input("CREATIONDATE") + "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
839 "%%BoundingBox: 0 0 " + _input("BOUNDINGWIDTH") + " " + _input("BOUNDINGHEIGHT") + " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
840 "%%Pages: 0\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
841 "%%DocumentFonts: \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
842 "%%EndComments\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
843 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
844 "% ---- CONSTANTS ----\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
845 "\/cmfactor 72 2.54 div def % defines points -> cm conversion\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
846 "\/cm {cmfactor mul} bind def % defines centimeters\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
847 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
848 "% ---- VARIABLES ----\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
849 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
850 "% NA = Nucleic Acid, AA = Amino Acid\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
851 "\/logoType (" + _input("LOGOTYPE") + ") def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
852 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
853 "\/logoTitle (" + _input("TITLE") + ") def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
854 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
855 "% Dimensions in cm\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
856 "\/logoWidth " + _input("LOGOWIDTH") + " cm def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
857 "\/logoHeight " + _input("LOGOLINEHEIGHT") + " cm def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
858 "\/totalHeight " + _input("LOGOHEIGHT") + " cm def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
859 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
860 "\/yaxis " + _input("YAXIS") + " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
861 "\/yaxisLabel (" + _input("YAXISLABEL") + ") def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
862 "\/yaxisBits " + _input("BARBITS") + " def % bits\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
863 "\/yaxisTicBits " + _input("TICBITS") + " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
864 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
865 "\/xaxis " + _input("NUMBERING") + " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
866 "\/xaxisLabel (" + _input("XAXISLABEL") + ") def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
867 "\/showEnds (" + _input("SHOWENDS") + ") def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
868 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
869 "\/showFineprint true def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
870 "\/fineprint (" + _input("FINEPRINT") + ") def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
871 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
872 "\/charsPerLine " + _input("CHARSPERLINE") + " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
873 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
874 "\/showingBox " + _input("SHOWINGBOX") + " def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
875 "\/shrinking false def % true falses\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
876 "\/shrink 1.0 def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
877 "\/outline " + _input("OUTLINE") + " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
878 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
879 "\/IbeamFraction " + _input("ERRORBARFRACTION") + " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
880 "\/IbeamGray 0.50 def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
881 "\/IbeamLineWidth 0.5 def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
882 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
883 "\/fontsize " + _input("FONTSIZE") + " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
884 "\/titleFontsize " + _input("TITLEFONTSIZE") + " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
885 "\/smallFontsize " + _input("SMALLFONTSIZE") + " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
886 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
887 "\/topMargin " + _input("TOPMARGIN") + " cm def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
888 "\/bottomMargin " + _input("BOTTOMMARGIN") + " cm def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
889 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
890 "\/defaultColor [0 0 0] def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
891 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
892 _input("COLORDICT") + "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
893 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
894 "\/colorDict fullColourDict def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
895 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
896 "% ---- DERIVED PARAMETERS ----\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
897 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
898 "\/leftMargin\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
899 " fontsize 3.5 mul\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
900 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
901 "def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
902 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
903 "\/rightMargin \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
904 " %Add extra room if showing ends\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
905 " showEnds (false) eq { fontsize}{fontsize 1.5 mul} ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
906 "def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
907 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
908 "\/yaxisHeight \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
909 " logoHeight \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
910 " bottomMargin sub \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
911 " topMargin sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
912 "def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
913 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
914 "\/ticWidth fontsize 2 div def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
915 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
916 "\/pointsPerBit yaxisHeight yaxisBits div def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
917 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
918 "\/stackMargin 1 def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
919 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
920 "% Do not add space aroung characters if characters are boxed\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
921 "\/charRightMargin \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
922 " showingBox { 0.0 } {stackMargin} ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
923 "def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
924 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
925 "\/charTopMargin \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
926 " showingBox { 0.0 } {stackMargin} ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
927 "def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
928 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
929 "\/charWidth\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
930 " logoWidth\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
931 " leftMargin sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
932 " rightMargin sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
933 " charsPerLine div\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
934 " charRightMargin sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
935 "def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
936 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
937 "\/charWidth4 charWidth 4 div def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
938 "\/charWidth2 charWidth 2 div def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
939 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
940 "\/stackWidth \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
941 " charWidth charRightMargin add\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
942 "def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
943 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
944 "\/numberFontsize \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
945 " fontsize charWidth lt {fontsize}{charWidth} ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
946 "def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
947 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
948 "% movements to place 5'\/N and 3'\/C symbols\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
949 "\/leftEndDeltaX fontsize neg def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
950 "\/leftEndDeltaY fontsize 1.5 mul neg def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
951 "\/rightEndDeltaX fontsize 0.25 mul def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
952 "\/rightEndDeltaY leftEndDeltaY def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
953 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
954 "% Outline width is proporional to charWidth, \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
955 "% but no less that 1 point\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
956 "\/outlinewidth \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
957 " charWidth 32 div dup 1 gt {}{pop 1} ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
958 "def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
959 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
960 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
961 "% ---- PROCEDURES ----\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
962 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
963 "\/StartLogo { \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
964 " % Save state\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
965 " save \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
966 " gsave \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
967 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
968 " % Print Logo Title, top center \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
969 " gsave \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
970 " SetStringFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
971 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
972 " logoWidth 2 div\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
973 " logoTitle\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
974 " stringwidth pop 2 div sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
975 " totalHeight\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
976 " titleFontsize sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
977 " moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
978 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
979 " logoTitle\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
980 " show\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
981 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
982 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
983 " % Print X-axis label, bottom center\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
984 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
985 " SetStringFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
986 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
987 " logoWidth 2 div\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
988 " xaxisLabel\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
989 " stringwidth pop 2 div sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
990 " 0\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
991 " titleFontsize 3 div\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
992 " add\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
993 " moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
994 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
995 " xaxisLabel\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
996 " show\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
997 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
998 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
999 " % Show Fine Print\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1000 " showFineprint {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1001 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1002 " SetSmallFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1003 " logoWidth\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1004 " fineprint stringwidth pop sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1005 " smallFontsize sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1006 " smallFontsize 3 div\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1007 " moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1008 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1009 " fineprint show\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1010 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1011 " } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1012 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1013 " % Move to lower left corner of last line, first stack\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1014 " leftMargin bottomMargin translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1015 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1016 " % Move above first line ready for StartLine \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1017 " 0 totalHeight translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1018 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1019 " SetLogoFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1020 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1021 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1022 "\/EndLogo { \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1023 " grestore \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1024 " showpage \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1025 " restore \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1026 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1027 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1028 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1029 "\/StartLine { \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1030 " % move down to the bottom of the line:\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1031 " 0 logoHeight neg translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1032 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1033 " gsave \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1034 " yaxis { MakeYaxis } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1035 " xaxis { showEnds (true) eq {ShowLeftEnd} if } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1036 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1037 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1038 "\/EndLine{ \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1039 " xaxis { showEnds (true) eq {ShowRightEnd} if } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1040 " grestore \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1041 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1042 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1043 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1044 "\/MakeYaxis {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1045 " gsave \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1046 " stackMargin neg 0 translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1047 " ShowYaxisBar\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1048 " ShowYaxisLabel\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1049 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1050 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1051 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1052 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1053 "\/ShowYaxisBar { \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1054 " gsave \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1055 " SetStringFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1056 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1057 " \/str 10 string def % string to hold number \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1058 " \/smallgap stackMargin 2 div def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1059 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1060 " % Draw first tic and bar\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1061 " gsave \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1062 " ticWidth neg 0 moveto \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1063 " ticWidth 0 rlineto \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1064 " 0 yaxisHeight rlineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1065 " stroke\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1066 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1067 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1068 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1069 " % Draw the tics\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1070 " % initial increment limit proc for\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1071 " 0 yaxisTicBits yaxisBits abs %cvi\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1072 " {\/loopnumber exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1073 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1074 " % convert the number coming from the loop to a string\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1075 " % and find its width\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1076 " loopnumber 10 str cvrs\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1077 " \/stringnumber exch def % string representing the number\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1078 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1079 " stringnumber stringwidth pop\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1080 " \/numberwidth exch def % width of number to show\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1081 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1082 " \/halfnumberheight\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1083 " stringnumber CharBoxHeight 2 div\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1084 " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1085 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1086 " numberwidth % move back width of number\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1087 " neg loopnumber pointsPerBit mul % shift on y axis\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1088 " halfnumberheight sub % down half the digit\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1089 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1090 " moveto % move back the width of the string\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1091 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1092 " ticWidth neg smallgap sub % Move back a bit more \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1093 " 0 rmoveto % move back the width of the tic \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1094 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1095 " stringnumber show\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1096 " smallgap 0 rmoveto % Make a small gap \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1097 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1098 " % now show the tic mark\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1099 " 0 halfnumberheight rmoveto % shift up again\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1100 " ticWidth 0 rlineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1101 " stroke\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1102 " } for\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1103 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1104 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1105 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1106 "\/ShowYaxisLabel {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1107 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1108 " SetStringFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1109 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1110 " % How far we move left depends on the size of\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1111 " % the tic labels.\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1112 " \/str 10 string def % string to hold number \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1113 " yaxisBits yaxisTicBits div cvi yaxisTicBits mul \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1114 " str cvs stringwidth pop\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1115 " ticWidth 1.5 mul add neg \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1116 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1117 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1118 " yaxisHeight\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1119 " yaxisLabel stringwidth pop\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1120 " sub 2 div\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1121 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1122 " translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1123 " 90 rotate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1124 " 0 0 moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1125 " yaxisLabel show\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1126 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1127 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1128 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1129 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1130 "\/StartStack { % <stackNumber> startstack\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1131 " xaxis {MakeNumber}{pop} ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1132 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1133 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1134 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1135 "\/EndStack {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1136 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1137 " stackWidth 0 translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1138 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1139 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1140 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1141 "% Draw a character whose height is proportional to symbol bits\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1142 "\/MakeSymbol{ % charbits character MakeSymbol\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1143 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1144 " \/char exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1145 " \/bits exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1146 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1147 " \/bitsHeight \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1148 " bits pointsPerBit mul \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1149 " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1150 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1151 " \/charHeight \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1152 " bitsHeight charTopMargin sub\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1153 " dup \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1154 " 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1155 " def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1156 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1157 " charHeight 0.0 gt {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1158 " char SetColor\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1159 " charWidth charHeight char ShowChar\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1160 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1161 " showingBox { % Unfilled box\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1162 " 0 0 charWidth charHeight false ShowBox\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1163 " } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1164 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1165 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1166 " } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1167 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1168 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1169 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1170 " 0 bitsHeight translate \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1171 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1172 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1173 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1174 "\/ShowChar { % <width> <height> <char> ShowChar\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1175 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1176 " \/tc exch def % The character\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1177 " \/ysize exch def % the y size of the character\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1178 " \/xsize exch def % the x size of the character\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1179 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1180 " \/xmulfactor 1 def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1181 " \/ymulfactor 1 def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1182 " \/limmulfactor 0.01 def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1183 " \/drawable true def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1184 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1185 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1186 " % if ysize is negative, make everything upside down!\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1187 " ysize 0 lt {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1188 " % put ysize normal in this orientation\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1189 " \/ysize ysize abs def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1190 " xsize ysize translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1191 " 180 rotate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1192 " } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1193 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1194 " shrinking {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1195 " xsize 1 shrink sub 2 div mul\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1196 " ysize 1 shrink sub 2 div mul translate \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1197 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1198 " shrink shrink scale\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1199 " } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1200 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1201 " % Calculate the font scaling factors\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1202 " % Loop twice to catch small correction due to first scaling\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1203 " 2 {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1204 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1205 " xmulfactor ymulfactor scale\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1206 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1207 " ysize % desired size of character in points\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1208 " tc CharBoxHeight \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1209 " dup 0.0 ne {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1210 " div % factor by which to scale up the character\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1211 " \/ymulfactor exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1212 " } % end if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1213 " {pop pop}\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1214 " ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1215 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1216 " xsize % desired size of character in points\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1217 " tc CharBoxWidth \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1218 " dup 0.0 ne {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1219 " div % factor by which to scale up the character\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1220 " \/xmulfactor exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1221 " } % end if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1222 " {pop pop}\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1223 " ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1224 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1225 " % if the multiplication factors get too small we need to avoid a crash\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1226 " xmulfactor limmulfactor lt {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1227 " \/xmulfactor 1 def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1228 " \/drawable false def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1229 " } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1230 " ymulfactor limmulfactor lt {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1231 " \/ymulfactor 1 def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1232 " \/drawable false def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1233 " } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1234 " } repeat\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1235 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1236 " % Adjust horizontal position if the symbol is an I\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1237 " tc (I) eq {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1238 " charWidth 2 div % half of requested character width\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1239 " tc CharBoxWidth 2 div % half of the actual character\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1240 " sub 0 translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1241 " % Avoid x scaling for I \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1242 " \/xmulfactor 1 def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1243 " } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1244 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1245 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1246 " % ---- Finally, draw the character\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1247 " drawable { \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1248 " newpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1249 " xmulfactor ymulfactor scale\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1250 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1251 " % Move lower left corner of character to start point\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1252 " tc CharBox pop pop % llx lly : Lower left corner\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1253 " exch neg exch neg\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1254 " moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1255 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1256 " outline { % outline characters:\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1257 " outlinewidth setlinewidth\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1258 " tc true charpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1259 " gsave 1 setgray fill grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1260 " clip stroke\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1261 " } { % regular characters\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1262 " tc show\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1263 " } ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1264 " } if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1265 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1266 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1267 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1268 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1269 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1270 "\/ShowBox { % x1 y1 x2 y2 filled ShowBox\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1271 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1272 " \/filled exch def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1273 " \/y2 exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1274 " \/x2 exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1275 " \/y1 exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1276 " \/x1 exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1277 " newpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1278 " x1 y1 moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1279 " x2 y1 lineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1280 " x2 y2 lineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1281 " x1 y2 lineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1282 " closepath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1283 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1284 " clip\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1285 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1286 " filled {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1287 " fill\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1288 " }{ \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1289 " 0 setgray stroke \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1290 " } ifelse\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1291 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1292 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1293 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1294 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1295 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1296 "\/MakeNumber { % number MakeNumber\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1297 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1298 " SetNumberFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1299 " stackWidth 0 translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1300 " 90 rotate % rotate so the number fits\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1301 " dup stringwidth pop % find the length of the number\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1302 " neg % prepare for move\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1303 " stackMargin sub % Move back a bit\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1304 " charWidth (0) CharBoxHeight % height of numbers\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1305 " sub 2 div %\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1306 " moveto % move back to provide space\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1307 " show\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1308 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1309 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1310 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1311 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1312 "\/Ibeam{ % heightInBits Ibeam\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1313 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1314 " % Make an Ibeam of twice the given height in bits\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1315 " \/height exch pointsPerBit mul def \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1316 " \/heightDRAW height IbeamFraction mul def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1317 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1318 " IbeamLineWidth setlinewidth\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1319 " IbeamGray setgray \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1320 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1321 " charWidth2 height neg translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1322 " ShowIbar\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1323 " newpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1324 " 0 0 moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1325 " 0 heightDRAW rlineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1326 " stroke\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1327 " newpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1328 " 0 height moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1329 " 0 height rmoveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1330 " currentpoint translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1331 " ShowIbar\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1332 " newpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1333 " 0 0 moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1334 " 0 heightDRAW neg rlineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1335 " currentpoint translate\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1336 " stroke\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1337 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1338 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1339 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1340 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1341 "\/ShowIbar { % make a horizontal bar\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1342 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1343 " newpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1344 " charWidth4 neg 0 moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1345 " charWidth4 0 lineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1346 " stroke\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1347 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1348 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1349 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1350 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1351 "\/ShowLeftEnd {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1352 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1353 " SetStringFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1354 " leftEndDeltaX leftEndDeltaY moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1355 " logoType (NA) eq {(5) show ShowPrime} if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1356 " logoType (AA) eq {(N) show} if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1357 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1358 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1359 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1360 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1361 "\/ShowRightEnd { \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1362 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1363 " SetStringFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1364 " rightEndDeltaX rightEndDeltaY moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1365 " logoType (NA) eq {(3) show ShowPrime} if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1366 " logoType (AA) eq {(C) show} if\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1367 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1368 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1369 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1370 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1371 "\/ShowPrime {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1372 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1373 " SetPrimeFont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1374 " (\\242) show \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1375 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1376 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1377 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1378 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1379 "\/SetColor{ % <char> SetColor\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1380 " dup colorDict exch known {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1381 " colorDict exch get aload pop setrgbcolor\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1382 " } {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1383 " pop\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1384 " defaultColor aload pop setrgbcolor\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1385 " } ifelse \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1386 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1387 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1388 "% define fonts\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1389 "\/SetTitleFont {\/Times-Bold findfont titleFontsize scalefont setfont} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1390 "\/SetLogoFont {\/Helvetica-Bold findfont charWidth scalefont setfont} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1391 "\/SetStringFont{\/Helvetica-Bold findfont fontsize scalefont setfont} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1392 "\/SetPrimeFont {\/Symbol findfont fontsize scalefont setfont} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1393 "\/SetSmallFont {\/Helvetica findfont smallFontsize scalefont setfont} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1394 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1395 "\/SetNumberFont {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1396 " \/Helvetica-Bold findfont \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1397 " numberFontsize\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1398 " scalefont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1399 " setfont\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1400 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1401 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1402 "%Take a single character and return the bounding box\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1403 "\/CharBox { % <char> CharBox <lx> <ly> <ux> <uy>\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1404 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1405 " newpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1406 " 0 0 moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1407 " % take the character off the stack and use it here:\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1408 " true charpath \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1409 " flattenpath \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1410 " pathbbox % compute bounding box of 1 pt. char => lx ly ux uy\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1411 " % the path is here, but toss it away ...\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1412 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1413 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1414 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1415 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1416 "% The height of a characters bounding box\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1417 "\/CharBoxHeight { % <char> CharBoxHeight <num>\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1418 " CharBox\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1419 " exch pop sub neg exch pop\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1420 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1421 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1422 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1423 "% The width of a characters bounding box\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1424 "\/CharBoxWidth { % <char> CharBoxHeight <num>\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1425 " CharBox\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1426 " pop exch pop sub neg \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1427 "} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1428 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1429 "% Set the colour scheme to be faded to indicate trimming\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1430 "\/MuteColour {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1431 " \/colorDict mutedColourDict def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1432 "} def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1433 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1434 "% Restore the colour scheme to the normal colours\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1435 "\/RestoreColour {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1436 " \/colorDict fullColourDict def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1437 "} def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1438 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1439 "% Draw the background for a trimmed section\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1440 "% takes the number of columns as a parameter\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1441 "\/DrawTrimBg { % <num> DrawTrimBox\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1442 " \/col exch def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1443 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1444 " \/boxwidth \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1445 " col stackWidth mul \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1446 " def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1447 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1448 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1449 " 0.97 setgray\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1450 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1451 " newpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1452 " 0 0 moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1453 " boxwidth 0 rlineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1454 " 0 yaxisHeight rlineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1455 " 0 yaxisHeight lineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1456 " closepath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1457 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1458 " fill\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1459 " grestore\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1460 "} def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1461 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1462 "\/DrawTrimEdge {\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1463 " gsave\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1464 " 0.2 setgray\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1465 " [2] 0 setdash\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1466 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1467 " newpath\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1468 " 0 0 moveto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1469 " 0 yaxisHeight lineto\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1470 " \n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1471 " stroke\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1472 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1473 "} def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1474 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1475 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1476 "% Deprecated names\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1477 "\/startstack {StartStack} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1478 "\/endstack {EndStack} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1479 "\/makenumber {MakeNumber} bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1480 "\/numchar { MakeSymbol } bind def\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1481 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1482 "%%EndProlog\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1483 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1484 "%%Page: 1 1\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1485 "StartLogo\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1486 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1487 _input("DATA") + "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1488 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1489 "EndLogo\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1490 "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1491 "%%EOF\n"
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1492 );
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1493 }</script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1494 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1495 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1496 // start Alphabet object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1497 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1498 var Alphabet = function(alphabet, background) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1499 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1500 var i, j, sym, aliases, complement, comp_e_sym, ambigs, generate_background;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1501 generate_background = (background == null);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1502 if (generate_background) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1503 background = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1504 for (i = 0; i < alphabet.ncore; i++) background[i] = 1.0 / alphabet.ncore;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1505 } else if (alphabet.ncore != background.length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1506 throw new Error("The background length does not match the alphabet length.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1507 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1508 this.name = alphabet.name;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1509 this.like = (alphabet.like != null ? alphabet.like.toUpperCase() : null);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1510 this.ncore = alphabet.ncore;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1511 this.symbols = alphabet.symbols;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1512 this.background = background;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1513 this.genbg = generate_background;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1514 this.encode = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1515 this.encode2core = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1516 this.complement = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1517 // check if all symbols are same case
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1518 var seen_uc = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1519 var seen_lc = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1520 var check_case = function (syms) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1521 var s, sym;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1522 if (typeof syms === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1523 for (s = 0; s < syms.length; s++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1524 sym = syms.charAt(s);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1525 if (sym >= 'a' && sym <= 'z') seen_lc = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1526 else if (sym >= 'A' && sym <= 'Z') seen_uc = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1527 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1528 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1529 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1530 for (i = 0; i < this.symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1531 check_case(this.symbols[i].symbol);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1532 check_case(this.symbols[i].aliases);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1533 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1534 // now map symbols to indexes
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1535 var update_array = function(array, syms, index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1536 var s, sym;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1537 if (typeof syms === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1538 for (s = 0; s < syms.length; s++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1539 sym = syms.charAt(s);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1540 array[sym] = index;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1541 // when only a single case is used, then encode as case insensitive
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1542 if (seen_uc != seen_lc) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1543 if (sym >= 'a' && sym <= 'z') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1544 array[sym.toUpperCase()] = index;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1545 } else if (sym >= 'A' && sym <= 'Z') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1546 array[sym.toLowerCase()] = index;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1547 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1548 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1549 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1550 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1551 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1552 // map core symbols to index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1553 for (i = 0; i < this.ncore; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1554 update_array(this.encode2core, this.symbols[i].symbol, i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1555 update_array(this.encode, this.symbols[i].symbol, i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1556 update_array(this.encode2core, this.symbols[i].aliases, i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1557 update_array(this.encode, this.symbols[i].aliases, i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1558 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1559 // map ambiguous symbols to index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1560 ambigs = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1561 for (i = this.ncore; i < this.symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1562 update_array(this.encode, this.symbols[i].symbol, i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1563 update_array(this.encode, this.symbols[i].aliases, i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1564 ambigs[this.symbols[i].equals] = i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1565 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1566 // determine complements
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1567 for (i = 0; i < this.ncore; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1568 complement = this.symbols[i].complement;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1569 if (typeof complement === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1570 this.complement[i] = this.encode2core[complement];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1571 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1572 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1573 next_symbol:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1574 for (i = this.ncore; i < this.symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1575 complement = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1576 for (j = 0; j < this.symbols[i].equals.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1577 comp_e_sym = this.complement[this.encode2core[this.symbols[i].equals.charAt(j)]];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1578 if (typeof comp_e_sym !== "number") continue next_symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1579 complement += this.symbols[comp_e_sym].symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1580 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1581 complement = complement.split("").sort().join("");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1582 if (typeof ambigs[complement] === "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1583 this.complement[i] = ambigs[complement];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1584 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1585 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1586 // determine case insensitivity
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1587 this.case_insensitive = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1588 if (seen_uc == seen_lc) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1589 // when there is a mixture of cases it probably won't
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1590 // be case insensitive but we still need to check
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1591 loop:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1592 for (i = 0; i < this.symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1593 sym = this.symbols[i].symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1594 if (sym >= 'A' && sym <= 'Z') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1595 if (this.encode[sym.toLowerCase()] != i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1596 this.case_insensitive = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1597 break loop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1598 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1599 } else if (sym >= 'a' && sym <= 'z') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1600 if (this.encode[sym.toUpperCase()] != i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1601 this.case_insensitive = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1602 break loop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1603 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1604 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1605 aliases = this.symbols[i].aliases;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1606 if (aliases != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1607 for (j = 0; j < aliases.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1608 sym = aliases.charAt(j);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1609 if (sym >= 'A' && sym <= 'Z') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1610 if (this.encode[sym.toLowerCase()] != i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1611 this.case_insensitive = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1612 break loop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1613 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1614 } else if (sym >= 'a' && sym <= 'z') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1615 if (this.encode[sym.toUpperCase()] != i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1616 this.case_insensitive = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1617 break loop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1618 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1619 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1620 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1621 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1622 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1623 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1624 // normalise aliases to remove the prime symbol and eliminate
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1625 // the alternate cases when the alphabet is case insensitive
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1626 var seen, out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1627 for (i = 0; i < this.symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1628 sym = this.symbols[i].symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1629 aliases = this.symbols[i].aliases;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1630 if (typeof aliases != "string") aliases = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1631 seen = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1632 out = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1633 if (this.case_insensitive) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1634 sym = sym.toUpperCase();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1635 aliases = aliases.toUpperCase();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1636 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1637 seen[sym] = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1638 for (j = 0; j < aliases.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1639 if (!seen[aliases.charAt(j)]) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1640 seen[aliases.charAt(j)] = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1641 out.push(aliases.charAt(j));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1642 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1643 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1644 this.symbols[i].aliases = out.sort().join("");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1645 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1646 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1647 // return the name of the alphabet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1648 Alphabet.prototype.get_alphabet_name = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1649 return this.name;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1650 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1651 // return if the alphabet can be complemented
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1652 Alphabet.prototype.has_complement = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1653 return (typeof this.symbols[0].complement === "string");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1654 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1655 // return true if an uppercase letter has the same meaning as the lowercase form
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1656 Alphabet.prototype.is_case_insensitive = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1657 return this.case_insensitive;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1658 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1659 // return the information content of an alphabet letter
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1660 Alphabet.prototype.get_ic = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1661 return Math.log(this.ncore) / Math.LN2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1662 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1663 // return the count of the core alphabet symbols
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1664 Alphabet.prototype.get_size_core = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1665 return this.ncore;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1666 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1667 // return the count of all alphabet symbols
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1668 Alphabet.prototype.get_size_full = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1669 return this.symbols.length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1670 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1671 // return the symbol for the given alphabet index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1672 Alphabet.prototype.get_symbol = function(alph_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1673 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1674 if (alph_index < 0 || alph_index >= this.symbols.length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1675 throw new Error("Alphabet index out of bounds");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1676 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1677 return this.symbols[alph_index].symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1678 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1679 // return the aliases for the given alphabet index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1680 Alphabet.prototype.get_aliases = function(alph_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1681 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1682 if (alph_index < 0 || alph_index >= this.symbols.length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1683 throw new Error("Alphabet index out of bounds");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1684 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1685 var sym_obj = this.symbols[alph_index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1686 return (sym_obj.aliases != null ? sym_obj.aliases : "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1687 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1688 // return the name for the given alphabet index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1689 Alphabet.prototype.get_name = function(alph_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1690 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1691 var sym;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1692 if (alph_index < 0 || alph_index >= this.symbols.length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1693 throw new Error("Alphabet index out of bounds");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1694 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1695 sym = this.symbols[alph_index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1696 return (typeof sym.name === "string" ? sym.name : sym.symbol);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1697 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1698 // return the alphabet it is like or null
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1699 Alphabet.prototype.get_like = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1700 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1701 return this.like;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1702 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1703 // return the index of the complement for the given alphabet index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1704 Alphabet.prototype.get_complement = function(alph_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1705 var comp_e_sym = this.complement[alph_index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1706 if (typeof comp_e_sym === "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1707 return comp_e_sym;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1708 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1709 return -1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1710 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1711 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1712 // return a string containing the core symbols
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1713 Alphabet.prototype.get_symbols = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1714 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1715 var i, core_symbols;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1716 core_symbols = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1717 for (i = 0; i < this.ncore; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1718 core_symbols += this.symbols[i].symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1719 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1720 return core_symbols;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1721 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1722 // return if the background was not a uniform generated background
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1723 Alphabet.prototype.has_bg = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1724 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1725 return !this.genbg;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1726 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1727 // get the background frequency for the index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1728 Alphabet.prototype.get_bg_freq = function(alph_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1729 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1730 var freq, i, symbols;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1731 if (alph_index >= 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1732 if (alph_index < this.ncore) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1733 return this.background[alph_index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1734 } else if (alph_index < this.symbols.length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1735 freq = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1736 symbols = this.symbols[alph_index].equals;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1737 for (i = 0; i < symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1738 freq += this.background[this.encode2core[symbols.charAt(i)]];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1739 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1740 return freq;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1741 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1742 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1743 throw new Error("The alphabet index is out of range.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1744 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1745 // get the colour of the index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1746 Alphabet.prototype.get_colour = function(alph_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1747 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1748 if (alph_index < 0 || alph_index >= this.symbols.length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1749 throw new Error("BAD_ALPHABET_INDEX");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1750 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1751 if (typeof this.symbols[alph_index].colour != "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1752 return "black";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1753 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1754 return "#" + this.symbols[alph_index].colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1755 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1756 // get the rgb components of the colour at the index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1757 Alphabet.prototype.get_rgb = function(alph_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1758 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1759 if (alph_index < 0 || alph_index >= this.symbols.length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1760 throw new Error("BAD_ALPHABET_INDEX");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1761 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1762 if (typeof this.symbols[alph_index].colour != "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1763 return {"red": 0, "green": 0, "blue": 0};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1764 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1765 var colour = this.symbols[alph_index].colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1766 var red = parseInt(colour.substr(0, 2), 16) / 255;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1767 var green = parseInt(colour.substr(2, 2), 16) / 255;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1768 var blue = parseInt(colour.substr(4, 2), 16) / 255;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1769 return {"red": red, "green": green, "blue": blue};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1770 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1771 // convert a symbol into the index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1772 Alphabet.prototype.get_index = function(letter) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1773 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1774 var alph_index;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1775 alph_index = this.encode[letter];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1776 if (typeof alph_index === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1777 return -1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1778 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1779 return alph_index;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1780 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1781 // convert a symbol into the list of core indexes that it equals
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1782 Alphabet.prototype.get_indexes = function(letter) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1783 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1784 var alph_index, comprise_str, i, comprise_list;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1785 alph_index = this.encode[letter];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1786 if (typeof alph_index === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1787 throw new Error("Unknown letter");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1788 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1789 comprise_str = this.symbols[alph_index].equals;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1790 comprise_list = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1791 if (typeof comprise_str == "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1792 for (i = 0; i < comprise_str.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1793 comprise_list.push(this.encode2core[comprise_str.charAt(i)]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1794 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1795 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1796 comprise_list.push(alph_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1797 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1798 return comprise_list;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1799 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1800 // check if a symbol is the primary way of representing the symbol in the alphabet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1801 Alphabet.prototype.is_prime_symbol = function(letter) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1802 var alph_index;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1803 alph_index = this.encode[letter];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1804 if (alph_index == null) return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1805 if (this.is_case_insensitive()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1806 return (this.symbols[alph_index].symbol.toUpperCase() == letter.toUpperCase());
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1807 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1808 return (this.symbols[alph_index].symbol == letter);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1809 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1810 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1811 // compare 2 alphabets
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1812 Alphabet.prototype.equals = function(other) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1813 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1814 var i, sym1, sym2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1815 // first check that it's actually an alphabet object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1816 if (!(typeof other === "object" && other != null && other instanceof Alphabet)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1817 return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1818 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1819 // second shortcircuit if it's the same object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1820 if (this === other) return true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1821 // compare
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1822 if (this.name !== other.name) return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1823 if (this.ncore !== other.ncore) return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1824 if (this.symbols.length !== other.symbols.length) return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1825 for (i = 0; i < this.symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1826 sym1 = this.symbols[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1827 sym2 = other.symbols[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1828 if (sym1.symbol !== sym2.symbol) return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1829 if (sym1.aliases !== sym2.aliases) return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1830 if (sym1.name !== sym2.name) return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1831 if (typeof sym1.colour !== typeof sym2.colour ||
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1832 (typeof sym1.colour === "string" && typeof sym2.colour === "string" &&
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1833 parseInt(sym1.colour, 16) != parseInt(sym2.colour, 16))) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1834 return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1835 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1836 if (sym1.complement !== sym2.complement) return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1837 if (sym1.equals !== sym2.equals) return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1838 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1839 return true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1840 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1841 Alphabet.prototype.check_core_subset = function(super_alph) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1842 var complement_same = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1843 var seen_set = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1844 var sub_i, sub_symbol, super_i, super_symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1845 for (sub_i = 0; sub_i < this.ncore; sub_i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1846 sub_symbol = this.symbols[sub_i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1847 super_i = super_alph.encode[sub_symbol.symbol];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1848 if (super_i == null) return 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1849 super_symbol = super_alph.symbols[super_i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1850 if (seen_set[super_i]) return 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1851 seen_set[super_i] = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1852 // check complement
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1853 if (sub_symbol.complement != null && super_symbol.complement != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1854 if (super_alph.encode[sub_symbol.complement] != super_alph.encode[super_symbol.complement]) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1855 complement_same = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1856 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1857 } else if (sub_symbol.complement != null || super_symbol.complement != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1858 complement_same = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1859 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1860 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1861 return (complement_same ? 1 : -1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1862 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1863 // convert a sequence to its reverse complement
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1864 Alphabet.prototype.invcomp_seq = function(seq) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1865 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1866 var syms, i, e_sym, comp_e_sym;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1867 if (!this.has_complement()) throw new Error("Alphabet must be complementable");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1868 syms = seq.split("");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1869 for (i = 0; i < syms.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1870 e_sym = this.encode[syms[i]];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1871 if (typeof e_sym === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1872 e_sym = this.ncore; // wildcard
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1873 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1874 comp_e_sym = this.complement[e_sym];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1875 if (typeof comp_e_sym === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1876 comp_e_sym = e_sym; // not complementable
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1877 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1878 syms[i] = this.symbols[comp_e_sym].symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1879 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1880 return syms.reverse().join("");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1881 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1882 // convert the alphabet to the text version
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1883 Alphabet.prototype.as_text = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1884 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1885 function name_as_text(name) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1886 var i, c, out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1887 out = "\"";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1888 for (i = 0; i < name.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1889 c = name.charAt(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1890 if (c == "\"") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1891 out += "\\\"";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1892 } else if (c == "/") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1893 out += "\\/";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1894 } else if (c == "\\") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1895 out += "\\\\";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1896 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1897 out += c;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1898 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1899 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1900 out += "\"";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1901 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1902 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1903 function symbol_as_text(sym) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1904 var out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1905 out = sym.symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1906 if (typeof sym.name === "string" && sym.name != sym.symbol) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1907 out += " " + name_as_text(sym.name);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1908 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1909 if (typeof sym.colour === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1910 out += " " + sym.colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1911 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1912 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1913 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1914 var out, i, j, c, sym;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1915 out = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1916 // output core symbols with 2 way complements
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1917 for (i = 0; i < this.ncore; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1918 c = this.complement[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1919 if (typeof c === "number" && i < c && this.complement[c] === i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1920 out += symbol_as_text(this.symbols[i]) + " ~ " + symbol_as_text(this.symbols[c]) + "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1921 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1922 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1923 // output core symbols with no complement
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1924 for (i = 0; i < this.ncore; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1925 if (typeof this.complement[i] === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1926 out += symbol_as_text(this.symbols[i]) + "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1927 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1928 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1929 // output ambiguous symbols that have comprising characters
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1930 for (i = this.ncore; i < this.symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1931 if (this.symbols[i].equals.length == 0) break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1932 out += symbol_as_text(this.symbols[i]) + " = " + this.symbols[i].equals + "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1933 if (typeof this.symbols[i].aliases === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1934 for (j = 0; j < this.symbols[i].aliases.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1935 if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1936 out += this.symbols[i].aliases.charAt(j) + " = " + this.symbols[i].equals + "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1937 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1938 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1939 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1940 // output aliases of core symbols
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1941 for (i = 0; i < this.ncore; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1942 if (typeof this.symbols[i].aliases === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1943 for (j = 0; j < this.symbols[i].aliases.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1944 if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1945 out += this.symbols[i].aliases.charAt(j) + " = " + this.symbols[i].symbol + "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1946 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1947 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1948 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1949 // output gap symbols
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1950 i = this.symbols.length - 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1951 if (this.symbols[i].equals.length == 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1952 out += symbol_as_text(this.symbols[i]) + " =\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1953 if (typeof this.symbols[i].aliases === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1954 for (j = 0; j < this.symbols[i].aliases.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1955 if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1956 out += this.symbols[i].aliases.charAt(j) + " =\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1957 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1958 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1959 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1960 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1961 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1962 // output the alphabet as it appears in minimal MEME format
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1963 Alphabet.prototype.as_meme = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1964 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1965 function name_as_text(name) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1966 var i, c, out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1967 out = "\"";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1968 for (i = 0; i < name.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1969 c = name.charAt(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1970 if (c == "\"") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1971 out += "\\\"";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1972 } else if (c == "/") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1973 out += "\\/";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1974 } else if (c == "\\") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1975 out += "\\\\";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1976 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1977 out += c;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1978 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1979 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1980 out += "\"";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1981 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1982 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1983 if (this.equals(AlphStd.DNA)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1984 return "ALPHABET= ACGT\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1985 } else if (this.equals(AlphStd.PROTEIN)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1986 return "ALPHABET= ACDEFGHIKLMNPQRSTVWY\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1987 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1988 return "ALPHABET" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1989 (this.name != null ? " " + name_as_text(this.name) : "") +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1990 (this.like != null ? " " + this.like + "-LIKE" : "") + "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1991 this.as_text() + "END ALPHABET\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1992 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1993 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1994
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1995 // Returns a table showing all the letters in the alphabet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1996 Alphabet.prototype.as_table = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1997 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1998 var i, j, row, th, td, aliases, equals, sym;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
1999 var table = document.createElement("table");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2000 // create the core symbol header
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2001 row = table.insertRow(table.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2002 th = document.createElement("th");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2003 th.appendChild(document.createTextNode("Symbol(s)"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2004 row.appendChild(th);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2005 th = document.createElement("th");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2006 th.appendChild(document.createTextNode("Name"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2007 row.appendChild(th);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2008 th = document.createElement("th");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2009 if (this.has_complement()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2010 th.appendChild(document.createTextNode("Complement"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2011 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2012 row.appendChild(th);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2013 // list the core symbols
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2014 for (i = 0; i < this.ncore; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2015 row = table.insertRow(table.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2016 td = document.createElement("td");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2017 if (this.symbols[i].colour != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2018 td.style.color = '#' + this.symbols[i].colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2019 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2020 td.appendChild(document.createTextNode(this.symbols[i].symbol));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2021 aliases = this.get_aliases(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2022 if (aliases.length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2023 td.appendChild(document.createTextNode(' ' + aliases.split('').join(' ')));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2024 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2025 row.appendChild(td);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2026 td = document.createElement("td");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2027 if (this.symbols[i].name != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2028 td.appendChild(document.createTextNode(this.symbols[i].name));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2029 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2030 row.appendChild(td);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2031 td = document.createElement("td");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2032 if (this.symbols[i].complement != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2033 td.style.color = this.get_colour(this.get_index(this.symbols[i].complement));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2034 td.appendChild(document.createTextNode(this.symbols[i].complement));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2035 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2036 row.appendChild(td);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2037 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2038 // create the ambiguous symbol header
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2039 row = table.insertRow(table.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2040 th = document.createElement("th");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2041 th.appendChild(document.createTextNode("Symbol(s)"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2042 row.appendChild(th);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2043 th = document.createElement("th");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2044 th.appendChild(document.createTextNode("Name"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2045 row.appendChild(th);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2046 th = document.createElement("th");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2047 th.appendChild(document.createTextNode("Matches"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2048 row.appendChild(th);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2049 // list the ambiguous symbols
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2050 for (i = this.ncore; i < this.symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2051 row = table.insertRow(table.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2052 td = document.createElement("td");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2053 if (this.symbols[i].colour != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2054 td.style.color = '#' + this.symbols[i].colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2055 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2056 td.appendChild(document.createTextNode(this.symbols[i].symbol));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2057 aliases = this.get_aliases(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2058 if (aliases.length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2059 td.appendChild(document.createTextNode(' ' + aliases.split('').join(' ')));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2060 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2061 row.appendChild(td);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2062 td = document.createElement("td");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2063 if (this.symbols[i].name != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2064 td.appendChild(document.createTextNode(this.symbols[i].name));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2065 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2066 row.appendChild(td);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2067 td = document.createElement("td");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2068 equals = this.symbols[i].equals.split('');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2069 for (j = 0; j < equals.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2070 if (j != 0) td.appendChild(document.createTextNode(' '));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2071 sym = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2072 sym.style.color = this.get_colour(this.get_index(equals[j]));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2073 sym.appendChild(document.createTextNode(equals[j]));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2074 td.appendChild(sym);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2075 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2076 row.appendChild(td);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2077 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2078 return table;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2079 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2080
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2081 // returns a dictionary of the colours for EPS
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2082 Alphabet.prototype._as_eps_dict = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2083 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2084 var i, sym, rgb;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2085 var out = "/fullColourDict <<\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2086 for (i = 0; i < this.ncore; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2087 sym = this.get_symbol(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2088 sym = sym.replace(/\\/g, "\\\\");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2089 sym = sym.replace(/\(/g, "\\(");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2090 sym = sym.replace(/\)/g, "\\)");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2091 rgb = this.get_rgb(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2092 out += " (" + sym + ") [" + rgb.red.toFixed(4) + " " + rgb.green.toFixed(4) + " " + rgb.blue.toFixed(4) + "]\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2093 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2094 out += ">> def\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2095 out += "/mutedColourDict <<\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2096 for (i = 0; i < this.ncore; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2097 sym = this.get_symbol(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2098 sym = sym.replace(/\\/g, "\\\\");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2099 sym = sym.replace(/\(/g, "\\(");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2100 sym = sym.replace(/\)/g, "\\)");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2101 rgb = Alphabet.lighten_colour(this.get_rgb(i));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2102 out += " (" + sym + ") [" + rgb.red.toFixed(4) + " " + rgb.green.toFixed(4) + " " + rgb.blue.toFixed(4) + "]\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2103 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2104 out += ">> def\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2105 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2106 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2107
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2108 // return the alphabet name or a list of primary symbols
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2109 Alphabet.prototype.toString = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2110 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2111 if (this.name != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2112 return this.name;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2113 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2114 return this.get_symbols();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2115 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2116 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2117
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2118 //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2119 // Helper functions
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2120 //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2121
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2122 // Convert a colour specified in RGB colourspace values into LAB colourspace
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2123 Alphabet.rgb2lab = function(rgb) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2124 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2125 var xyzHelper, labHelper;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2126 // XYZ helper
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2127 xyzHelper = function(value) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2128 if (value > 0.0445) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2129 value = (value + 0.055) / 1.055;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2130 value = Math.pow(value, 2.4);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2131 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2132 value /= 12.92;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2133 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2134 value *= 100;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2135 return value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2136 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2137 // lab helper
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2138 labHelper = function(value) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2139 if (value > 0.008856) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2140 value = Math.pow(value, 1.0 / 3.0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2141 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2142 value = (7.787 * value) + (16.0 / 116.0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2143 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2144 return value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2145 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2146 // convert into XYZ colourspace
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2147 var c1, c2, c3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2148 if (typeof rgb == "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2149 c1 = xyzHelper(((rgb >> 16) & 0xFF) / 255.0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2150 c2 = xyzHelper(((rgb >> 8) & 0xFF) / 255.0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2151 c3 = xyzHelper((rgb & 0xFF) / 255.0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2152 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2153 c1 = xyzHelper(rgb.red);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2154 c2 = xyzHelper(rgb.green);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2155 c3 = xyzHelper(rgb.blue);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2156 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2157 var x = (c1 * 0.4124) + (c2 * 0.3576) + (c3 * 0.1805);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2158 var y = (c1 * 0.2126) + (c2 * 0.7152) + (c3 * 0.0722);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2159 var z = (c1 * 0.0193) + (c2 * 0.1192) + (c3 * 0.9505);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2160 // convert into Lab colourspace
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2161 c1 = labHelper(x / 95.047);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2162 c2 = labHelper(y / 100.0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2163 c3 = labHelper(z / 108.883);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2164 var l = (116.0 * c2) - 16;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2165 var a = 500.0 * (c1 - c2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2166 var b = 200.0 * (c2 - c3);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2167 return {"l": l, "a": a, "b": b};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2168 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2169
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2170 // Convert a colour specified in HSV colourspace into RGB colourspace
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2171 Alphabet.hsv2rgb = function(hue, sat, value, output_object) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2172 // achromatic (grey)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2173 var r = value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2174 var g = value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2175 var b = value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2176 if (sat != 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2177 var h = hue / 60.0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2178 var i = Math.floor(h);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2179 var f = h - i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2180 var p = value * (1.0 - sat);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2181 var q = value * (1.0 - (sat * f));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2182 var t = value * (1.0 - (sat * (1.0 - f)));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2183 if (i == 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2184 r = value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2185 g = t;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2186 b = p;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2187 } else if (i == 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2188 r = q;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2189 g = value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2190 b = p;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2191 } else if (i == 2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2192 r = p;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2193 g = value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2194 b = t;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2195 } else if (i == 3) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2196 r = p;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2197 g = q;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2198 b = value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2199 } else if (i == 4) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2200 r = t;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2201 g = p;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2202 b = value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2203 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2204 r = value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2205 g = p;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2206 b = q;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2207 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2208 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2209 if (output_object) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2210 return {"red": r, "green": g, "blue": b};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2211 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2212 return (Math.floor(r * 255) << 15) | (Math.floor(g * 255) << 8) | (Math.floor(b * 255));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2213 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2214 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2215
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2216 // Calculate a distance score between two colours in LAB colourspace
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2217 Alphabet.lab_dist = function(lab1, lab2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2218 var c1 = Math.sqrt((lab1.l * lab1.l) + (lab1.a * lab1.a));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2219 var c2 = Math.sqrt((lab2.l * lab2.l) + (lab2.a * lab2.a));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2220 var dc = c1 - c2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2221 var dl = lab1.l - lab2.l;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2222 var da = lab1.a - lab2.a;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2223 var db = lab1.b - lab2.b;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2224 // we don't want NaN due to rounding errors so fudge things a bit...
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2225 var dh = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2226 var dh_squared = (da * da) + (db * db) - (dc * dc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2227 if (dh_squared > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2228 dh = Math.sqrt(dh_squared);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2229 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2230 var first = dl;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2231 var second = dc / (1.0 + (0.045 * c1));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2232 var third = dh / (1.0 + (0.015 * c1));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2233 return Math.sqrt((first * first) + (second * second) + (third * third));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2234 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2235
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2236 // convert an RGB value into a HSL value
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2237 Alphabet.rgb2hsl = function(rgb) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2238 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2239 var min, max, delta, h, s, l, r, g, b;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2240 if (typeof rgb == "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2241 r = ((rgb >> 16) & 0xFF) / 255.0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2242 g = ((rgb >> 8) & 0xFF) / 255.0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2243 b = (rgb & 0xFF) / 255.0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2244 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2245 r = rgb.red;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2246 g = rgb.green;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2247 b = rgb.blue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2248 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2249 min = Math.min(r, g, b);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2250 max = Math.max(r, g, b);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2251 delta = max - min;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2252 l = min + (delta / 2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2253 if (max == min) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2254 h = 0; // achromatic (grayscale)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2255 s = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2256 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2257 if (l > 0.5) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2258 s = delta / (2 - max - min);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2259 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2260 s = delta / (max + min);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2261 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2262 if (max == r) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2263 h = (g - b) / delta;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2264 if (g < b) h += 6;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2265 } else if (max == g) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2266 h = ((b - r) / delta) + 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2267 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2268 h = ((r - g) / delta) + 4;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2269 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2270 h /= 6;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2271 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2272 return {"h": h, "s": s, "l": l};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2273 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2274
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2275 // convert a HSL value into an RGB value
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2276 Alphabet.hsl2rgb = function(hsl, output_object) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2277 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2278 function _hue(p, q, t) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2279 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2280 if (t < 0) t += 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2281 else if (t > 1) t -= 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2282 if (t < (1.0 / 6.0)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2283 return p + ((q - p) * 6.0 * t);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2284 } else if (t < 0.5) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2285 return q;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2286 } else if (t < (2.0 / 3.0)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2287 return p + ((q - p) * ((2.0 / 3.0) - t) * 6.0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2288 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2289 return p;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2290 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2291 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2292 var r, g, b, p, q;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2293 if (hsl.s == 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2294 // achromatic (grayscale)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2295 r = hsl.l;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2296 g = hsl.l;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2297 b = hsl.l;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2298 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2299 if (hsl.l < 0.5) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2300 q = hsl.l * (1 + hsl.s);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2301 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2302 q = hsl.l + hsl.s - (hsl.l * hsl.s);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2303 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2304 p = (2 * hsl.l) - q;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2305 r = _hue(p, q, hsl.h + (1.0 / 3.0));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2306 g = _hue(p, q, hsl.h);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2307 b = _hue(p, q, hsl.h - (1.0 / 3.0));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2308 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2309 if (output_object) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2310 return {"red": r, "green": g, "blue": b};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2311 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2312 return (Math.floor(r * 255) << 15) | (Math.floor(g * 255) << 8) | (Math.floor(b * 255));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2313 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2314 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2315
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2316 Alphabet.lighten_colour = function(rgb) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2317 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2318 var hsl = Alphabet.rgb2hsl(rgb);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2319 hsl.l += (1.0 - hsl.l) * 2 / 3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2320 return Alphabet.hsl2rgb(hsl, typeof rgb != "number");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2321 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2322
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2323 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2324 // end Alphabet object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2325 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2326
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2327 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2328 // start StandardAlphabet object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2329 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2330
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2331 // an extension of the alphabet object to support some additional fields
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2332 // only present in standard alphabets.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2333 var StandardAlphabet = function(enum_code, enum_name, alphabet_data) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2334 Alphabet.apply(this, [alphabet_data]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2335 this.enum_code = enum_code;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2336 this.enum_name = enum_name;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2337 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2338 StandardAlphabet.prototype = Alphabet.prototype;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2339 StandardAlphabet.prototype.constructor = StandardAlphabet;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2340
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2341 // A unique code for this standard alphabet.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2342 // This code will be a power of 2 to enable creation of bitsets for
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2343 // a selection of standard alphabets.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2344 StandardAlphabet.prototype.get_code = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2345 return this.enum_code;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2346 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2347
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2348 // A unique name for this standard alphabet.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2349 // this name will be all upper case and the same as the property that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2350 // refers to this alphabet in the AlphStd collection.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2351 StandardAlphabet.prototype.get_enum = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2352 return this.enum_name;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2353 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2354
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2355 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2356 // end StandardAlphabet object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2357 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2358
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2359 // A collection of standard alphabets.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2360 var AlphStd = {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2361 RNA: new StandardAlphabet(1, "RNA", {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2362 "name": "RNA",
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2363 "like": "RNA",
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2364 "ncore": 4,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2365 "symbols": [
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2366 {"symbol": "A", "name": "Adenine", "colour": "CC0000"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2367 {"symbol": "C", "name": "Cytosine", "colour": "0000CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2368 {"symbol": "G", "name": "Guanine", "colour": "FFB300"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2369 {"symbol": "U", "name": "Uracil", "colour": "008000",
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2370 "aliases": "T"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2371 {"symbol": "N", "name": "Any base", "equals": "ACGU", "aliases": "X."},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2372 {"symbol": "V", "name": "Not U", "equals": "ACG"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2373 {"symbol": "H", "name": "Not G", "equals": "ACU"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2374 {"symbol": "D", "name": "Not C", "equals": "AGU"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2375 {"symbol": "B", "name": "Not A", "equals": "CGU"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2376 {"symbol": "M", "name": "Amino", "equals": "AC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2377 {"symbol": "R", "name": "Purine", "equals": "AG"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2378 {"symbol": "W", "name": "Weak", "equals": "AU"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2379 {"symbol": "S", "name": "Strong", "equals": "CG"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2380 {"symbol": "Y", "name": "Pyrimidine", "equals": "CU"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2381 {"symbol": "K", "name": "Keto", "equals": "GU"}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2382 ]
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2383 }),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2384 DNA: new StandardAlphabet(2, "DNA", {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2385 "name": "DNA",
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2386 "like": "DNA",
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2387 "ncore": 4,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2388 "symbols": [
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2389 {"symbol": "A", "name": "Adenine", "colour": "CC0000", "complement": "T"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2390 {"symbol": "C", "name": "Cytosine", "colour": "0000CC", "complement": "G"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2391 {"symbol": "G", "name": "Guanine", "colour": "FFB300", "complement": "C"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2392 {"symbol": "T", "name": "Thymine", "colour": "008000", "complement": "A",
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2393 "aliases": "U"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2394 {"symbol": "N", "name": "Any base", "equals": "ACGT", "aliases": "X."},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2395 {"symbol": "V", "name": "Not T", "equals": "ACG"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2396 {"symbol": "H", "name": "Not G", "equals": "ACT"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2397 {"symbol": "D", "name": "Not C", "equals": "AGT"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2398 {"symbol": "B", "name": "Not A", "equals": "CGT"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2399 {"symbol": "M", "name": "Amino", "equals": "AC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2400 {"symbol": "R", "name": "Purine", "equals": "AG"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2401 {"symbol": "W", "name": "Weak", "equals": "AT"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2402 {"symbol": "S", "name": "Strong", "equals": "CG"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2403 {"symbol": "Y", "name": "Pyrimidine", "equals": "CT"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2404 {"symbol": "K", "name": "Keto", "equals": "GT"}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2405 ]
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2406 }),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2407 PROTEIN: new StandardAlphabet(4, "PROTEIN", {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2408 "name": "Protein",
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2409 "like": "PROTEIN",
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2410 "ncore": 20,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2411 "symbols": [
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2412 {"symbol": "A", "name": "Alanine", "colour": "0000CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2413 {"symbol": "C", "name": "Cysteine", "colour": "0000CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2414 {"symbol": "D", "name": "Aspartic acid", "colour": "FF00FF"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2415 {"symbol": "E", "name": "Glutamic acid", "colour": "FF00FF"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2416 {"symbol": "F", "name": "Phenylalanine", "colour": "0000CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2417 {"symbol": "G", "name": "Glycine", "colour": "FFB300"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2418 {"symbol": "H", "name": "Histidine", "colour": "FFCCCC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2419 {"symbol": "I", "name": "Isoleucine", "colour": "0000CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2420 {"symbol": "K", "name": "Lysine", "colour": "CC0000"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2421 {"symbol": "L", "name": "Leucine", "colour": "0000CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2422 {"symbol": "M", "name": "Methionine", "colour": "0000CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2423 {"symbol": "N", "name": "Asparagine", "colour": "008000"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2424 {"symbol": "P", "name": "Proline", "colour": "FFFF00"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2425 {"symbol": "Q", "name": "Glutamine", "colour": "008000"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2426 {"symbol": "R", "name": "Arginine", "colour": "CC0000"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2427 {"symbol": "S", "name": "Serine", "colour": "008000"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2428 {"symbol": "T", "name": "Threonine", "colour": "008000"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2429 {"symbol": "V", "name": "Valine", "colour": "0000CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2430 {"symbol": "W", "name": "Tryptophan", "colour": "0000CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2431 {"symbol": "Y", "name": "Tyrosine", "colour": "33E6CC"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2432 {"symbol": "X", "name": "Any amino acid", "equals": "ACDEFGHIKLMNPQRSTVWY", "aliases": "*."},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2433 {"symbol": "B", "name": "Asparagine or Aspartic acid", "equals": "DN"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2434 {"symbol": "Z", "name": "Glutamine or Glutamic acid", "equals": "EQ"},
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2435 {"symbol": "J", "name": "Leucine or Isoleucine", "equals": "IL"}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2436 ]
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2437 })
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2438 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2439
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2440 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2441 // start Symbol object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2442 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2443 var Symbol = function(alph_index, scale, alphabet) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2444 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2445 //variable prototype
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2446 this.symbol = alphabet.get_symbol(alph_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2447 this.scale = scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2448 this.colour = alphabet.get_colour(alph_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2449 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2450
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2451 Symbol.prototype.get_symbol = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2452 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2453 return this.symbol;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2454 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2455
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2456 Symbol.prototype.get_scale = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2457 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2458 return this.scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2459 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2460
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2461 Symbol.prototype.get_colour = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2462 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2463 return this.colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2464 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2465
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2466 Symbol.prototype.toString = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2467 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2468 return this.symbol + " " + (Math.round(this.scale*1000)/10) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2469 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2470
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2471 function compare_symbol(sym1, sym2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2472 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2473 if (sym1.get_scale() < sym2.get_scale()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2474 return -1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2475 } else if (sym1.get_scale() > sym2.get_scale()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2476 return 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2477 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2478 return 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2479 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2480 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2481 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2482 // end Symbol object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2483 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2484
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2485 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2486 // start Pspm object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2487 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2488 var Pspm = function(matrix, name, ltrim, rtrim, nsites, evalue, pssm, alt, pgm) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2489 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2490 var row, col, data, row_sum, delta, evalue_re;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2491 if (typeof name !== "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2492 name = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2493 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2494 this.name = name;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2495 //construct
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2496 if (matrix instanceof Pspm) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2497 // copy constructor
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2498 this.alph_length = matrix.alph_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2499 this.motif_length = matrix.motif_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2500 this.name = matrix.name;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2501 this.alt = matrix.alt;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2502 this.nsites = matrix.nsites;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2503 this.evalue = matrix.evalue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2504 this.ltrim = matrix.ltrim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2505 this.rtrim = matrix.rtrim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2506 this.pspm = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2507 this.pgm = matrix.pgm;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2508 for (row = 0; row < matrix.motif_length; row++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2509 this.pspm[row] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2510 for (col = 0; col < matrix.alph_length; col++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2511 this.pspm[row][col] = matrix.pspm[row][col];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2512 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2513 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2514 if (matrix.pssm != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2515 this.pssm = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2516 for (row = 0; row < matrix.motif_length; row++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2517 this.pspm[row] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2518 for (col = 0; col < matrix.alph_length; col++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2519 this.pssm[row][col] = matrix.pssm[row][col];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2520 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2521 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2522 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2523 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2524 // check parameters
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2525 if (ltrim == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2526 ltrim = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2527 } else if (typeof ltrim !== "number" || ltrim % 1 !== 0 || ltrim < 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2528 throw new Error("ltrim must be a non-negative integer, got: " + ltrim);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2529 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2530 if (rtrim == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2531 rtrim = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2532 } else if (typeof rtrim !== "number" || rtrim % 1 !== 0 || rtrim < 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2533 throw new Error("rtrim must be a non-negative integer, got: " + rtrim);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2534 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2535 if (nsites != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2536 if (typeof nsites !== "number" || nsites < 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2537 throw new Error("nsites must be a positive number, got: " + nsites);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2538 } else if (nsites == 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2539 nsites = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2540 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2541 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2542 if (evalue != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2543 if (typeof evalue === "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2544 if (evalue < 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2545 throw new Error("evalue must be a non-negative number, got: " + evalue);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2546 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2547 } else if (typeof evalue === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2548 evalue_re = /^((?:[+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)|inf)$/;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2549 if (!evalue_re.test(evalue)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2550 throw new Error("evalue must be a non-negative number, got: " + evalue);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2551 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2552 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2553 throw new Error("evalue must be a non-negative number, got: " + evalue);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2554 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2555 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2556 // set properties
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2557 this.name = name;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2558 this.alt = alt;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2559 this.nsites = nsites;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2560 this.evalue = evalue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2561 this.ltrim = ltrim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2562 this.rtrim = rtrim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2563 this.pgm = pgm;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2564 if (typeof matrix === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2565 // string constructor
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2566 data = parse_pspm_string(matrix);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2567 this.alph_length = data["alph_length"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2568 this.motif_length = data["motif_length"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2569 this.pspm = data["pspm"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2570 if (this.evalue == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2571 if (data["evalue"] != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2572 this.evalue = data["evalue"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2573 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2574 this.evalue = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2575 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2576 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2577 if (this.nsites == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2578 if (typeof data["nsites"] === "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2579 this.nsites = data["nsites"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2580 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2581 this.nsites = 20;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2582 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2583 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2584 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2585 // assume pspm is a nested array
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2586 this.motif_length = matrix.length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2587 this.alph_length = (matrix.length > 0 ? matrix[0].length : 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2588 if (this.nsites == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2589 this.nsites = 20;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2590 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2591 if (this.evalue == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2592 this.evalue = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2593 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2594 this.pspm = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2595 // copy pspm and check
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2596 for (row = 0; row < this.motif_length; row++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2597 if (this.alph_length != matrix[row].length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2598 throw new Error("COLUMN_MISMATCH");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2599 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2600 this.pspm[row] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2601 row_sum = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2602 for (col = 0; col < this.alph_length; col++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2603 this.pspm[row][col] = matrix[row][col];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2604 row_sum += this.pspm[row][col];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2605 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2606 delta = 0.1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2607 if (isNaN(row_sum) || (row_sum > 1 && (row_sum - 1) > delta) ||
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2608 (row_sum < 1 && (1 - row_sum) > delta)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2609 throw new Error("INVALID_SUM");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2610 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2611 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2612 // copy pssm
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2613 if (pssm != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2614 this.pssm = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2615 for (row = 0; row < this.motif_length; row++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2616 this.pssm[row] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2617 for (col = 0; col < this.alph_length; col++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2618 this.pssm[row][col] = pssm[row][col];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2619 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2620 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2621 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2622 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2623 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2624 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2625
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2626 Pspm.prototype.copy = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2627 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2628 return new Pspm(this);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2629 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2630
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2631 Pspm.prototype.reverse = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2632 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2633 var x, y, temp, temp_trim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2634 //reverse
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2635 x = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2636 y = this.motif_length-1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2637 while (x < y) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2638 temp = this.pspm[x];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2639 this.pspm[x] = this.pspm[y];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2640 this.pspm[y] = temp;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2641 x++;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2642 y--;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2643 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2644 // reverse pssm (if defined)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2645 if (typeof this.pssm !== "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2646 //reverse
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2647 x = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2648 y = this.motif_length-1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2649 while (x < y) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2650 temp = this.pssm[x];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2651 this.pspm[x] = this.pssm[y];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2652 this.pssm[y] = temp;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2653 x++;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2654 y--;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2655 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2656 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2657 //swap triming
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2658 temp_trim = this.ltrim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2659 this.ltrim = this.rtrim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2660 this.rtrim = temp_trim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2661 return this; //allow function chaining...
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2662 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2663
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2664 Pspm.prototype.reverse_complement = function(alphabet) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2665 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2666 var x, y, temp, i, row, c, temp_trim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2667 if (this.alph_length != alphabet.get_size_core()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2668 throw new Error("The alphabet size does not match the size of the pspm.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2669 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2670 if (!alphabet.has_complement()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2671 throw new Error("The specified alphabet can not be complemented.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2672 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2673 // reverse motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2674 this.reverse();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2675 //complement
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2676 for (x = 0; x < this.motif_length; x++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2677 row = this.pspm[x];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2678 for (i = 0; i < row.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2679 c = alphabet.get_complement(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2680 if (c < i) continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2681 temp = row[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2682 row[i] = row[c];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2683 row[c] = temp;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2684 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2685 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2686 // complement pssm (if defined)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2687 if (typeof this.pssm !== "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2688 //complement
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2689 for (x = 0; x < this.motif_length; x++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2690 row = this.pssm[x];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2691 for (i = 0; i < row.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2692 c = alphabet.get_complement(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2693 if (c < i) continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2694 temp = row[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2695 row[i] = row[c];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2696 row[c] = temp;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2697 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2698 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2699 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2700 return this; //allow function chaining...
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2701 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2702
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2703 Pspm.prototype.get_stack = function(position, alphabet, ssc) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2704 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2705 var row, stack_ic, alphabet_ic, stack, i, sym;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2706 if (this.alph_length != alphabet.get_size_core()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2707 throw new Error("The alphabet size does not match the size of the pspm.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2708 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2709 row = this.pspm[position];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2710 stack_ic = this.get_stack_ic(position, alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2711 if (ssc) stack_ic -= this.get_error(alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2712 alphabet_ic = alphabet.get_ic();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2713 stack = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2714 for (i = 0; i < this.alph_length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2715 sym = new Symbol(i, row[i]*stack_ic/alphabet_ic, alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2716 if (sym.get_scale() <= 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2717 continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2718 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2719 stack.push(sym);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2720 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2721 stack.sort(compare_symbol);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2722 return stack;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2723 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2724
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2725 Pspm.prototype.get_stack_ic = function(position, alphabet) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2726 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2727 var row, H, i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2728 if (this.alph_length != alphabet.get_size_core()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2729 throw new Error("The alphabet size does not match the size fo the pspm.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2730 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2731 row = this.pspm[position];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2732 H = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2733 for (i = 0; i < this.alph_length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2734 if (row[i] === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2735 continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2736 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2737 H -= (row[i] * (Math.log(row[i]) / Math.LN2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2738 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2739 return alphabet.get_ic() - H;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2740 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2741
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2742 Pspm.prototype.get_error = function(alphabet) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2743 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2744 if (this.nsites === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2745 return 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2746 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2747 return (alphabet.get_size_core()-1) / (2 * Math.LN2 * this.nsites);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2748 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2749
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2750 Pspm.prototype.get_motif_length = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2751 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2752 return this.motif_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2753 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2754
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2755 Pspm.prototype.get_alph_length = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2756 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2757 return this.alph_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2758 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2759
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2760 Pspm.prototype.get_left_trim = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2761 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2762 return this.ltrim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2763 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2764
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2765 Pspm.prototype.get_right_trim = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2766 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2767 return this.rtrim;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2768 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2769
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2770 Pspm.prototype.as_best_match = function(alphabet) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2771 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2772 var match, odds, best_odds, best_index;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2773 var i, j;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2774 match = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2775 for (i = 0; i < this.motif_length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2776 best_index = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2777 best_odds = this.pspm[i][0] / alphabet.get_bg_freq(0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2778 for (j = 1; j < this.alph_length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2779 odds = this.pspm[i][j] / alphabet.get_bg_freq(j);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2780 if (odds > best_odds) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2781 best_odds = odds;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2782 best_index = j;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2783 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2784 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2785 match += alphabet.get_symbol(best_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2786 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2787 return match;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2788 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2789
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2790 Pspm.prototype.as_count_matrix = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2791 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2792 var count, count_text, text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2793 var i, j;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2794 text = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2795 for (i = 0; i < this.motif_length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2796 if (i !== 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2797 text += "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2798 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2799 for (j = 0; j < this.alph_length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2800 if (j !== 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2801 text += " ";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2802 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2803 count = Math.round(this.nsites * this.pspm[i][j]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2804 count_text = "" + count;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2805 // pad up to length of 4
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2806 if (count_text.length < 4) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2807 text += (new Array(5 - count_text.length)).join(" ") + count_text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2808 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2809 text += count_text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2810 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2811 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2812 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2813 return text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2814 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2815
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2816 Pspm.prototype.as_probability_matrix = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2817 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2818 var text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2819 var i, j;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2820 text = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2821 for (i = 0; i < this.motif_length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2822 if (i !== 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2823 text += "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2824 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2825 for (j = 0; j < this.alph_length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2826 if (j !== 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2827 text += " ";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2828 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2829 text += this.pspm[i][j].toFixed(6);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2830 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2831 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2832 return text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2833 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2834
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2835 Pspm.prototype.as_score_matrix = function(alphabet, pseudo) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2836 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2837 var me, score, out, row, col, score_text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2838 me = this;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2839 if (typeof this.pssm === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2840 if (!(typeof alphabet === "object" && alphabet != null && alphabet instanceof Alphabet)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2841 throw new Error("The alphabet is required to generate the pssm.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2842 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2843 if (typeof pseudo === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2844 pseudo = 0.01;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2845 } else if (typeof pseudo !== "number" || pseudo < 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2846 throw new Error("Expected positive number for pseudocount");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2847 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2848 score = function(row, col) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2849 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2850 var p, bg, p2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2851 p = me.pspm[row][col];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2852 bg = alphabet.get_bg_freq(col);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2853 p2 = (p * me.nsites + bg * pseudo) / (me.nsites + pseudo);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2854 return (p2 > 0 ? Math.round((Math.log(p2 / bg) / Math.LN2) * 100) : -10000);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2855 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2856 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2857 score = function(row, col) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2858 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2859 return me.pssm[row][col];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2860 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2861 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2862 out = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2863 for (row = 0; row < this.motif_length; row++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2864 for (col = 0; col < this.alph_length; col++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2865 if (col !== 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2866 out += " ";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2867 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2868 score_text = "" + score(row, col);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2869 // pad out to 6 characters
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2870 if (score_text.length < 6) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2871 out += (new Array(7 - score_text.length)).join(" ") + score_text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2872 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2873 out += score_text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2874 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2875 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2876 out += "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2877 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2878 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2879 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2880
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2881 Pspm.prototype.as_pspm = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2882 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2883 return "letter-probability matrix: alength= " + this.alph_length +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2884 " w= " + this.motif_length + " nsites= " + this.nsites +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2885 (this.pgm === "STREME" ? " P= " : " E= ") +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2886 (typeof this.evalue === "number" ?
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2887 this.evalue.toExponential() : this.evalue) + "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2888 this.as_probability_matrix();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2889 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2890
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2891 Pspm.prototype.as_pssm = function(alphabet, pseudo) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2892 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2893 return "log-odds matrix: alength= " + this.alph_length +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2894 " w= " + this.motif_length +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2895 " E= " + (typeof this.evalue == "number" ?
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2896 this.evalue.toExponential() : this.evalue) + "\n" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2897 this.as_score_matrix(alphabet, pseudo);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2898 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2899
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2900 Pspm.prototype.as_meme = function(options) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2901 var with_header, with_pspm, with_pssm, version, alphabet, bg_source, pseudocount, strands;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2902 var out, alen, i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2903 // get the options
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2904 if (typeof options !== "object" || options === null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2905 options = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2906 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2907 with_header = (typeof options["with_header"] === "boolean" ? options["with_header"] : false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2908 with_pspm = (typeof options["with_pspm"] === "boolean" ? options["with_pspm"] : false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2909 with_pssm = (typeof options["with_pssm"] === "boolean" ? options["with_pssm"] : false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2910 if (!with_pspm && !with_pssm) with_pspm = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2911 if (with_header) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2912 if (typeof options["version"] === "string" && /^\d+(?:\.\d+){0,2}$/.test(options["version"])) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2913 version = options["version"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2914 } else if (typeof options["version"] === "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2915 version = options["version"].toFixed(0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2916 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2917 version = "4";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2918 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2919 if (typeof options["strands"] === "number" && options["strands"] === 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2920 strands = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2921 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2922 strands = 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2923 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2924 if (typeof options["bg_source"] === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2925 bg_source = options["bg_source"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2926 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2927 bg_source = "unknown source";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2928 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2929 if (typeof options["alphabet"] === "object" && options["alphabet"] != null
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2930 && options["alphabet"] instanceof Alphabet) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2931 alphabet = options["alphabet"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2932 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2933 throw new Error("The alphabet is required to generate the header.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2934 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2935 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2936 // now create the output
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2937 out = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2938 if (with_header) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2939 out = "MEME version " + version + "\n\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2940 out += alphabet.as_meme() + "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2941 if (alphabet.has_complement()) { // assume DNA has both strands unless otherwise specified
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2942 out += "strands: " + (strands === 1 ? "+" : "+ -") + "\n\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2943 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2944 out += "Background letter frequencies (from " + bg_source + "):\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2945 alen = alphabet.get_size_core();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2946 for (i = 0; i < alen; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2947 if (i !== 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2948 if (i % 9 === 0) { // maximum of nine entries per line
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2949 out += "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2950 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2951 out += " ";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2952 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2953 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2954 out += alphabet.get_symbol(i) + " " + alphabet.get_bg_freq(i).toFixed(3);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2955 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2956 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2957 out += "\n\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2958 out += "MOTIF " + this.name + (this.alt == null ? "" : " " + this.alt);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2959 if (with_pssm) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2960 out += "\n\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2961 out += this.as_pssm(options["alphabet"], options["pseudocount"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2962 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2963 if (with_pspm) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2964 out += "\n\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2965 out += this.as_pspm();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2966 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2967 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2968 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2969
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2970 Pspm.prototype.toString = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2971 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2972 var str, i, row;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2973 str = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2974 for (i = 0; i < this.pspm.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2975 row = this.pspm[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2976 str += row.join("\t") + "\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2977 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2978 return str;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2979 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2980
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2981 function parse_pspm_properties(str) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2982 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2983 var parts, i, eqpos, before, after, properties, prop, num, num_re;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2984 num_re = /^((?:[+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)|inf)$/;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2985 parts = trim(str).split(/\s+/);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2986 // split up words containing =
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2987 for (i = 0; i < parts.length;) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2988 eqpos = parts[i].indexOf("=");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2989 if (eqpos != -1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2990 before = parts[i].substr(0, eqpos);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2991 after = parts[i].substr(eqpos+1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2992 if (before.length > 0 && after.length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2993 parts.splice(i, 1, before, "=", after);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2994 i += 3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2995 } else if (before.length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2996 parts.splice(i, 1, before, "=");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2997 i += 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2998 } else if (after.length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
2999 parts.splice(i, 1, "=", after);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3000 i += 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3001 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3002 parts.splice(i, 1, "=");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3003 i++;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3004 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3005 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3006 i++;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3007 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3008 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3009 properties = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3010 for (i = 0; i < parts.length; i += 3) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3011 if (parts.length - i < 3) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3012 throw new Error("Expected PSPM property was incomplete. "+
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3013 "Remaing parts are: " + parts.slice(i).join(" "));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3014 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3015 if (parts[i+1] !== "=") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3016 throw new Error("Expected '=' in PSPM property between key and " +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3017 "value but got " + parts[i+1]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3018 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3019 prop = parts[i].toLowerCase();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3020 num = parts[i+2];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3021 if (!num_re.test(num)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3022 throw new Error("Expected numeric value for PSPM property '" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3023 prop + "' but got '" + num + "'");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3024 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3025 properties[prop] = num;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3026 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3027 return properties;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3028 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3029
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3030 function parse_pspm_string(pspm_string) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3031 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3032 var header_re, lines, first_line, line_num, col_num, alph_length,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3033 motif_length, nsites, evalue, pspm, i, line, match, props, parts,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3034 j, prob;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3035 header_re = /^letter-probability\s+matrix:(.*)$/i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3036 lines = pspm_string.split(/\n/);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3037 first_line = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3038 line_num = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3039 col_num = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3040 alph_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3041 motif_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3042 nsites;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3043 evalue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3044 pspm = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3045 for (i = 0; i < lines.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3046 line = trim(lines[i]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3047 if (line.length === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3048 continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3049 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3050 // check the first line for a header though allow matrices without it
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3051 if (first_line) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3052 first_line = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3053 match = header_re.exec(line);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3054 if (match !== null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3055 props = parse_pspm_properties(match[1]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3056 if (props.hasOwnProperty("alength")) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3057 alph_length = parseFloat(props["alength"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3058 if (alph_length != 4 && alph_length != 20) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3059 throw new Error("PSPM property alength should be 4 or 20" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3060 " but got " + alph_length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3061 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3062 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3063 if (props.hasOwnProperty("w")) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3064 motif_length = parseFloat(props["w"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3065 if (motif_length % 1 !== 0 || motif_length < 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3066 throw new Error("PSPM property w should be an integer larger " +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3067 "than zero but got " + motif_length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3068 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3069 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3070 if (props.hasOwnProperty("nsites")) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3071 nsites = parseFloat(props["nsites"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3072 if (nsites <= 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3073 throw new Error("PSPM property nsites should be larger than " +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3074 "zero but got " + nsites);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3075 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3076 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3077 if (props.hasOwnProperty("e")) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3078 evalue = props["e"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3079 if (evalue < 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3080 throw new Error("PSPM property evalue should be " +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3081 "non-negative but got " + evalue);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3082 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3083 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3084 continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3085 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3086 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3087 pspm[line_num] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3088 col_num = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3089 parts = line.split(/\s+/);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3090 for (j = 0; j < parts.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3091 prob = parseFloat(parts[j]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3092 if (prob != parts[j] || prob < 0 || prob > 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3093 throw new Error("Expected probability but got '" + parts[j] + "'");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3094 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3095 pspm[line_num][col_num] = prob;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3096 col_num++;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3097 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3098 line_num++;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3099 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3100 if (typeof motif_length === "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3101 if (pspm.length != motif_length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3102 throw new Error("Expected PSPM to have a motif length of " +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3103 motif_length + " but it was actually " + pspm.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3104 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3105 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3106 motif_length = pspm.length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3107 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3108 if (typeof alph_length !== "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3109 alph_length = pspm[0].length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3110 if (alph_length != 4 && alph_length != 20) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3111 throw new Error("Expected length of first row in the PSPM to be " +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3112 "either 4 or 20 but got " + alph_length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3113 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3114 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3115 for (i = 0; i < pspm.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3116 if (pspm[i].length != alph_length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3117 throw new Error("Expected PSPM row " + i + " to have a length of " +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3118 alph_length + " but the length was " + pspm[i].length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3119 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3120 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3121 return {"pspm": pspm, "motif_length": motif_length,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3122 "alph_length": alph_length, "nsites": nsites, "evalue": evalue};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3123 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3124 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3125 // end Pspm object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3126 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3127
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3128 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3129 // start Logo object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3130 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3131
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3132 var Logo = function(alphabet, options) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3133 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3134 this.alphabet = alphabet;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3135 this.fine_text = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3136 this.x_axis = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3137 this.y_axis = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3138 this.xlate_nsyms = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3139 this.xlate_start = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3140 this.xlate_end = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3141 this.pspm_list = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3142 this.pspm_column = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3143 this.rows = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3144 this.columns = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3145 if (typeof options === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3146 // the old method signature had fine_text here so we support that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3147 this.fine_text = options;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3148 } else if (typeof options === "object" && options != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3149 this.fine_text = (typeof options.fine_text === "string" ? options.fine_text : "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3150 this.x_axis = (typeof options.x_axis === "boolean" ? (options.x_axis ? 1 : 0) : 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3151 if (options.x_axis_hidden != null && options.x_axis_hidden) this.x_axis = -1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3152 this.y_axis = (typeof options.y_axis === "boolean" ? options.y_axis : true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3153 this.xlate_nsyms = (typeof options.xlate_nsyms === "number" ? options.xlate_nsyms : this.xlate_nsyms);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3154 this.xlate_start = (typeof options.xlate_start === "number" ? options.xlate_start : this.xlate_start);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3155 this.xlate_end = (typeof options.xlate_end === "number" ? options.xlate_end : this.xlate_end);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3156 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3157 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3158
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3159 Logo.prototype.add_pspm = function(pspm, column) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3160 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3161 var col;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3162 if (typeof column === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3163 column = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3164 } else if (column < 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3165 throw new Error("Column index out of bounds.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3166 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3167 this.pspm_list[this.rows] = pspm;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3168 this.pspm_column[this.rows] = column;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3169 this.rows++;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3170 col = column + pspm.get_motif_length();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3171 if (col > this.columns) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3172 this.columns = col;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3173 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3174 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3175
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3176 Logo.prototype.get_columns = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3177 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3178 return this.columns;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3179 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3180
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3181 Logo.prototype.get_xlate_nsyms = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3182 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3183 return this.xlate_nsyms;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3184 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3185
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3186 Logo.prototype.get_xlate_start = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3187 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3188 return (this.xlate_start != null ? this.xlate_start : 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3189 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3190
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3191 Logo.prototype.get_xlate_end = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3192 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3193 return (this.xlate_end != null ? this.xlate_end : this.columns * this.xlate_nsyms);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3194 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3195
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3196 Logo.prototype.get_xlate_columns = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3197 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3198 return this.get_xlate_end() - this.get_xlate_start();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3199 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3200
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3201 Logo.prototype.get_rows = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3202 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3203 return this.rows;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3204 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3205
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3206 Logo.prototype.get_pspm = function(row_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3207 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3208 if (row_index < 0 || row_index >= this.rows) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3209 throw new Error("INDEX_OUT_OF_BOUNDS");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3210 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3211 return this.pspm_list[row_index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3212 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3213
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3214 Logo.prototype.get_offset = function(row_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3215 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3216 if (row_index < 0 || row_index >= this.rows) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3217 throw new Error("INDEX_OUT_OF_BOUNDS");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3218 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3219 return this.pspm_column[row_index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3220 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3221
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3222 Logo.prototype._as_eps_data = function(ssc, errbars) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3223 var i, j, pos, stack_pos, pspm, stack, sym, out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3224 out = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3225 for (i = 0; i < this.rows; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3226 out += "\nStartLine\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3227 // Indent
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3228 for (j = 0; j < this.pspm_column[i]; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3229 out += "() startstack\nendstack\n\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3230 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3231 pspm = this.pspm_list[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3232 if (pspm.get_left_trim() > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3233 out += "MuteColour\nDrawTrimEdge\n" + pspm.get_left_trim() + " DrawTrimBg\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3234 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3235 for (pos = 0; pos < pspm.get_motif_length(); pos++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3236 if (pos != 0 && pos == pspm.get_left_trim()) { // enable full colour
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3237 out += "DrawTrimEdge\nRestoreColour\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3238 } else if (pos == (pspm.get_motif_length() - pspm.get_right_trim())) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3239 out += "MuteColour\n" + pspm.get_right_trim() + " DrawTrimBg\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3240 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3241 out += "(" + (pos + 1) + ") startstack\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3242 stack = pspm.get_stack(pos, this.alphabet, ssc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3243 for (stack_pos = 0; stack_pos < stack.length; stack_pos++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3244 sym = stack[stack_pos];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3245 out += " " + (sym.get_scale() * this.alphabet.get_ic()) + " (" + sym.get_symbol() + ") numchar\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3246 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3247 if (errbars) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3248 out += " " + pspm.get_error(this.alphabet) + " Ibeam\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3249 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3250 out += "endstack\n\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3251 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3252 if (pspm.get_right_trim() > 0 || pspm.get_left_trim() == pspm.get_motif_length()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3253 out += "RestoreColour\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3254 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3255 out += "EndLine\n";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3256 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3257 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3258 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3259
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3260 Logo.prototype.as_eps = function(options) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3261 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3262 if (this.xlate_nsyms != 1) throw new Error("Unsupported setting xlate_nsyms for EPS");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3263 if (this.xlate_start != null) throw new Error("Unsupported setting xlate_start for EPS");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3264 if (this.xlate_end != null) throw new Error("Unsupported setting xlate_end for EPS");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3265
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3266 var LOGOHEIGHT = 7.5; // default height of line in cm
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3267 var cm2pts, height, width, now, ssc, errbars;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3268 if (typeof options === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3269 options = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3270 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3271 cm2pts = 72 / 2.54;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3272 if (typeof options.logo_height == "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3273 height = options.logo_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3274 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3275 height = LOGOHEIGHT * this.rows;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3276 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3277 if (typeof options.logo_width == "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3278 width = options.logo_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3279 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3280 width = this.columns + 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3281 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3282 now = new Date();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3283 ssc = (typeof options.ssc == "boolean" ? options.ssc : false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3284 errbars = (typeof options.show_error_bar == "boolean" ? options.show_error_bar : ssc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3285 var values = {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3286 "LOGOHEIGHT": height,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3287 "LOGOWIDTH": width,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3288 "BOUNDINGHEIGHT": Math.round(height * cm2pts),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3289 "BOUNDINGWIDTH": Math.round(width * cm2pts),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3290 "LOGOLINEHEIGHT": (height / this.rows),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3291 "CHARSPERLINE": this.columns,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3292 "BARBITS": this.alphabet.get_ic(),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3293 "LOGOTYPE": (this.alphabet.has_complement() ? "NA" : "AA"),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3294 "CREATIONDATE": now.getDate() + "." + (now.getMonth() + 1) + "." + now.getFullYear() + " " + now.getHours() + ":" + now.getMinutes() + ":" + now.getSeconds(),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3295 "ERRORBARFRACTION": (typeof options.error_bar_fraction == "number" ? options.error_bar_fraction : 1.0),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3296 "TICBITS": (typeof options.ticbits == "number" ? options.ticbits : 1.0),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3297 "TITLE": (typeof options.title == "string" ? options.title : ""),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3298 "FINEPRINT": (typeof options.fineprint == "string" ? options.fineprint : this.fine_text),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3299 "XAXISLABEL": (typeof options.xaxislabel == "string" ? options.xaxislabel : ""),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3300 "YAXISLABEL": (typeof options.yaxislabel == "string" ? options.yaxislabel : "bits"),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3301 "SSC": ssc,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3302 "YAXIS": (typeof options.show_y_axis == "boolean" ? options.show_y_axis : this.y_axis),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3303 "SHOWENDS": (typeof options.show_ends == "boolean" ? options.show_ends : false),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3304 "ERRBAR": errbars,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3305 "OUTLINE": (typeof options.show_outline == "boolean" ? options.show_outline : false),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3306 "NUMBERING": (typeof options.show_numbering == "boolean" ? options.show_numbering : this.x_axis != 0),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3307 "SHOWINGBOX": (typeof options.show_box == "boolean" ? options.show_box : false),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3308 "CREATOR": (typeof options.creator == "string" ? options.creator : "motif_logo.js"),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3309 "FONTSIZE": (typeof options.label_font_size == "number" ? options.label_font_size : 12),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3310 "TITLEFONTSIZE": (typeof options.title_font_size == "number" ? options.title_font_size : 12),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3311 "SMALLFONTSIZE": (typeof options.small_font_size == "number" ? options.small_font_size : 6),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3312 "TOPMARGIN" : (typeof options.top_margin == "number" ? options.top_margin : 0.9),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3313 "BOTTOMMARGIN": (typeof options.bottom_margin == "number" ? options.bottom_margin : 0.9),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3314 "COLORDICT": this.alphabet._as_eps_dict(),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3315 "DATA": this._as_eps_data(ssc, errbars)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3316 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3317 // now this requires that the script containing the template has been imported!
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3318 return motif_logo_template(values);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3319 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3320
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3321 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3322 // end Logo object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3323 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3324
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3325 // calculate the exact size (in pixels) of an object drawn on the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3326 // canvas assuming that the background of the canvas is transparent.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3327 function canvas_bounds(ctx, cwidth, cheight) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3328 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3329 var data, r, c, top_line, bottom_line, left_line, right_line,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3330 txt_width, txt_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3331
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3332 // extract the image data
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3333 data = ctx.getImageData(0, 0, cwidth, cheight).data;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3334
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3335 // set initial values
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3336 top_line = -1; bottom_line = -1; left_line = -1; right_line = -1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3337 txt_width = 0; txt_height = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3338
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3339 // Find the top-most line with a non-transparent pixel
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3340 for (r = 0; r < cheight; r++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3341 for (c = 0; c < cwidth; c++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3342 if (data[r * cwidth * 4 + c * 4 + 3]) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3343 top_line = r;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3344 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3345 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3346 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3347 if (top_line != -1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3348 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3349 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3350 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3351
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3352 // Only bother looking if we found at least one set pixel...
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3353 if (top_line != -1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3354
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3355 //find the last line with a non-transparent pixel
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3356 for (r = cheight-1; r >= top_line; r--) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3357 for(c = 0; c < cwidth; c++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3358 if(data[r * cwidth * 4 + c * 4 + 3]) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3359 bottom_line = r;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3360 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3361 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3362 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3363 if (bottom_line != -1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3364 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3365 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3366 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3367 // calculate height
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3368 txt_height = bottom_line - top_line + 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3369
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3370 // Find the left-most line with a non-transparent pixel
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3371 for (c = 0; c < cwidth; c++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3372 for (r = top_line; r <= bottom_line; r++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3373 if (data[r * cwidth * 4 + c * 4 + 3]) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3374 left_line = c;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3375 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3376 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3377 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3378 if (left_line != -1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3379 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3380 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3381 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3382
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3383 //find the right most line with a non-transparent pixel
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3384 for (c = cwidth-1; c >= left_line; c--) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3385 for(r = top_line; r <= bottom_line; r++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3386 if(data[r * cwidth * 4 + c * 4 + 3]) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3387 right_line = c;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3388 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3389 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3390 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3391 if (right_line != -1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3392 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3393 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3394 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3395 txt_width = right_line - left_line + 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3396 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3397
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3398 //return the bounds
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3399 return {bound_top: top_line, bound_bottom: bottom_line,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3400 bound_left: left_line, bound_right: right_line, width: txt_width,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3401 height: txt_height};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3402 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3403
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3404 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3405 // start RasterizedAlphabet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3406 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3407
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3408 // Rasterize Alphabet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3409 // 1) Measure width of text at default font for all symbols in alphabet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3410 // 2) sort in width ascending
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3411 // 3) Drop the top and bottom 10% (designed to ignore outliers like 'W' and 'I')
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3412 // 4) Calculate the average as the maximum scaling factor (designed to stop I becoming a rectangular blob).
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3413 // 5) Assume scale of zero would result in width of zero, interpolate scale required to make perfect width font
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3414 // 6) Draw text onto temp canvas at calculated scale
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3415 // 7) Find bounds of drawn text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3416 // 8) Paint on to another canvas at the desired height (but only scaling width to fit if larger).
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3417 var RasterizedAlphabet = function(alphabet, logo_scale, font, width) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3418 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3419 var default_size, safety_pad, canvas, ctx, middle, baseline, widths, sizes,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3420 i, sym, size, tenpercent, avg_width, scale,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3421 target_width, target_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3422 //variable prototypes
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3423 this.alphabet = alphabet;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3424 this.scale = logo_scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3425 this.sym_cache = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3426 this.stack_num_cache = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3427 this.scale_num_cache = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3428 // size of canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3429 default_size = 60; // size of measuring canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3430 safety_pad = 20; // pixels to pad around so we don't miss the edges
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3431 // create a canvas to do our measuring
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3432 canvas = document.createElement("canvas");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3433 if (!canvas.getContext) throw new Error("No canvas support");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3434 canvas.width = default_size + 2 * safety_pad;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3435 canvas.height = default_size + 2 * safety_pad;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3436 middle = Math.round(canvas.width / 2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3437 baseline = Math.round(canvas.height - safety_pad);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3438 ctx = canvas.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3439 if (!supports_text(ctx)) throw new Error("Canvas does not support text");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3440 ctx.font = font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3441 ctx.textAlign = "center";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3442 ctx.translate(middle, baseline);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3443 // list of widths
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3444 widths = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3445 sizes = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3446 //now measure each letter in the alphabet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3447 for (i = 0; i < alphabet.get_size_core(); ++i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3448 // reset the canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3449 ctx.clearRect(0, 0, canvas.width, canvas.height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3450 ctx.fillStyle = alphabet.get_colour(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3451 // draw the test text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3452 ctx.fillText(alphabet.get_symbol(i), 0, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3453 //measure
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3454 size = canvas_bounds(ctx, canvas.width, canvas.height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3455 if (size.width === 0) throw new Error("Invisible symbol!");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3456 widths.push(size.width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3457 sizes[i] = size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3458 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3459 //sort the widths
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3460 widths.sort(function(a,b) {return a - b;});
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3461 //drop 10% of the items off each end
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3462 tenpercent = Math.floor(widths.length / 10);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3463 for (i = 0; i < tenpercent; ++i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3464 widths.pop();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3465 widths.shift();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3466 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3467 //calculate average width
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3468 avg_width = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3469 for (i = 0; i < widths.length; ++i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3470 avg_width += widths[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3471 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3472 avg_width /= widths.length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3473 // calculate the target width
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3474 target_width = width * this.scale * 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3475 // calculate scales
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3476 for (i = 0; i < alphabet.get_size_core(); ++i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3477 sym = alphabet.get_symbol(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3478 size = sizes[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3479 // calculate scale
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3480 scale = target_width / Math.max(avg_width, size.width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3481 // estimate scaled height
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3482 target_height = size.height * scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3483 // create an appropriately sized canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3484 canvas = document.createElement("canvas");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3485 canvas.width = target_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3486 canvas.height = target_height + safety_pad * 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3487 // calculate the middle
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3488 middle = Math.round(canvas.width / 2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3489 // calculate the baseline
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3490 baseline = Math.round(canvas.height - safety_pad);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3491 // get the context and prepare to draw the rasterized text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3492 ctx = canvas.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3493 ctx.font = font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3494 ctx.fillStyle = alphabet.get_colour(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3495 ctx.textAlign = "center";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3496 ctx.translate(middle, baseline);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3497 ctx.save();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3498 ctx.scale(scale, scale);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3499 // draw the text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3500 ctx.fillText(sym, 0, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3501 ctx.restore();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3502 this.sym_cache[sym] = {"image": canvas, "size": canvas_bounds(ctx, canvas.width, canvas.height)};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3503 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3504 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3505
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3506 RasterizedAlphabet.prototype.get_alphabet = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3507 return this.alphabet;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3508 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3509
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3510 RasterizedAlphabet.prototype.get_scale = function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3511 return this.scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3512 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3513
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3514 RasterizedAlphabet.prototype.draw_stack_sym = function(ctx, letter, dx, dy, dWidth, dHeight) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3515 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3516 var entry, image, size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3517 entry = this.sym_cache[letter];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3518 image = entry.image;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3519 size = entry.size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3520 ctx.drawImage(image, 0, size.bound_top -1, image.width, size.height+1, dx, dy, dWidth, dHeight);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3521 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3522
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3523 RasterizedAlphabet.prototype.draw_stack_num = function(ctx, font, stack_width, index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3524 var image, image_ctx, text_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3525 if (index >= this.stack_num_cache.length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3526 image = document.createElement("canvas");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3527 // measure the text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3528 image_ctx = image.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3529 image_ctx.save();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3530 image_ctx.font = font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3531 text_length = image_ctx.measureText("" + (index + 1)).width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3532 image_ctx.restore();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3533 // resize the canvas to fit
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3534 image.width = Math.ceil(stack_width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3535 image.height = Math.ceil(text_length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3536 // draw the text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3537 image_ctx = image.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3538 image_ctx.translate(Math.round(stack_width / 2), 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3539 image_ctx.font = font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3540 image_ctx.textBaseline = "middle";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3541 image_ctx.textAlign = "right";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3542 image_ctx.rotate(-(Math.PI / 2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3543 image_ctx.fillText("" + (index + 1), 0, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3544 this.stack_num_cache[index] = image;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3545 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3546 image = this.stack_num_cache[index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3547 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3548 ctx.drawImage(image, 0, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3549 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3550
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3551 RasterizedAlphabet.prototype.draw_scale_num = function(ctx, font, num) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3552 var image, image_ctx, text_size, m_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3553 if (num >= this.scale_num_cache.length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3554 image = document.createElement("canvas");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3555 // measure the text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3556 image_ctx = image.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3557 image_ctx.font = font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3558 text_size = image_ctx.measureText("" + num);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3559 if (text_size.actualBoundingBoxAscent && text_size.actualBoundingBoxDesent) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3560 // resize the canvas to fit
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3561 image.width = Math.ceil(text_size.width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3562 image.height = Math.ceil(text_size.actualBoundingBoxAscent + text_size.actualBoundingBoxDesent);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3563 // draw the text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3564 image_ctx = image.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3565 image_ctx.font = font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3566 image_ctx.textAlign = "right";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3567 image_ctx.fillText("" + num, image.width, text_size.actualBoundingBoxAscent);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3568 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3569 // measure width of 'm' to approximate height, we double it later anyway
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3570 m_length = image_ctx.measureText("m").width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3571 // resize the canvas to fit
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3572 image.width = Math.ceil(text_size.width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3573 image.height = Math.ceil(2 * m_length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3574 // draw the text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3575 image_ctx = image.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3576 image_ctx.font = font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3577 image_ctx.textAlign = "right";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3578 image_ctx.textBaseline = "middle";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3579 image_ctx.fillText("" + num, image.width, m_length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3580 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3581 this.scale_num_cache[num] = image;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3582 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3583 image = this.scale_num_cache[num];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3584 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3585 ctx.drawImage(image, -image.width, -Math.round(image.height / 2))
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3586 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3587
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3588 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3589 // end RasterizedAlphabet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3590 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3591
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3592 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3593 // start LogoMetrics object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3594 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3595
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3596 var LogoMetrics = function(ctx, logo_columns, logo_rows, has_names, has_finetext, x_axis, y_axis) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3597 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3598 var i, row_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3599 //variable prototypes
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3600 this.pad_top = (has_names ? 5 : 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3601 this.pad_left = (y_axis ? 10 : 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3602 this.pad_right = (has_finetext ? 15 : 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3603 this.pad_bottom = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3604 this.pad_middle = 20;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3605 this.name_height = 14;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3606 this.name_font = "bold " + this.name_height + "px Times, sans-serif";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3607 this.name_spacer = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3608 this.y_axis = y_axis;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3609 this.y_label = "bits";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3610 this.y_label_height = 12;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3611 this.y_label_font = "bold " + this.y_label_height + "px Helvetica, sans-serif";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3612 this.y_label_spacer = 3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3613 this.y_num_height = 12;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3614 this.y_num_width = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3615 this.y_num_font = "bold " + this.y_num_height + "px Helvetica, sans-serif";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3616 this.y_tic_width = 5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3617 this.stack_pad_left = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3618 this.stack_font = "bold 25px Helvetica, sans-serif";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3619 this.stack_height = 90;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3620 this.stack_width = 26;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3621 this.stacks_pad_right = 5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3622 this.x_axis = x_axis;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3623 this.x_num_above = 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3624 this.x_num_height = 12;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3625 this.x_num_width = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3626 this.x_num_font = "bold " + this.x_num_height + "px Helvetica, sans-serif";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3627 this.fine_txt_height = 6;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3628 this.fine_txt_above = 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3629 this.fine_txt_font = "normal " + this.fine_txt_height + "px Helvetica, sans-serif";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3630 this.letter_metrics = new Array();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3631 this.summed_width = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3632 this.summed_height = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3633 //calculate the width of the y axis numbers
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3634 ctx.font = this.y_num_font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3635 for (i = 0; i <= 2; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3636 this.y_num_width = Math.max(this.y_num_width, ctx.measureText("" + i).width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3637 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3638 //calculate the width of the x axis numbers (but they are rotated so it becomes height)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3639 if (x_axis == 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3640 ctx.font = this.x_num_font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3641 for (i = 1; i <= logo_columns; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3642 this.x_num_width = Math.max(this.x_num_width, ctx.measureText("" + i).width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3643 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3644 } else if (x_axis == 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3645 this.x_num_height = 4;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3646 this.x_num_width = 4;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3647 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3648 this.x_num_height = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3649 this.x_num_width = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3650 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3651
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3652 //calculate how much vertical space we want to draw this
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3653 //first we add the padding at the top and bottom since that's always there
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3654 this.summed_height += this.pad_top + this.pad_bottom;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3655 //all except the last row have the same amount of space allocated to them
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3656 if (logo_rows > 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3657 row_height = this.stack_height + this.pad_middle;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3658 if (has_names) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3659 row_height += this.name_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3660 //the label is allowed to overlap into the spacer
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3661 row_height += Math.max(this.y_num_height/2, this.name_spacer);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3662 //the label is allowed to overlap the space used by the other label
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3663 row_height += Math.max(this.y_num_height/2, this.x_num_height + this.x_num_above);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3664 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3665 row_height += this.y_num_height/2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3666 //the label is allowed to overlap the space used by the other label
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3667 row_height += Math.max(this.y_num_height/2, this.x_num_height + this.x_num_above);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3668 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3669 this.summed_height += row_height * (logo_rows - 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3670 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3671 //the last row has the name and fine text below it but no padding
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3672 this.summed_height += this.stack_height + (this.y_axis ? this.y_num_height/2 : 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3673
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3674 var fine_txt_total = (has_finetext ? this.fine_txt_height + this.fine_txt_above : 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3675 if (has_names) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3676 this.summed_height += fine_txt_total + this.name_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3677 this.summed_height += Math.max((this.y_axis ? this.y_num_height/2 : 0),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3678 this.x_num_height + this.x_num_above + this.name_spacer);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3679 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3680 this.summed_height += Math.max((this.y_axis ? this.y_num_height/2 : 0),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3681 this.x_num_height + this.x_num_above + fine_txt_total);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3682 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3683
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3684 //calculate how much horizontal space we want to draw this
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3685 //first add the padding at the left and right since that's always there
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3686 this.summed_width += this.pad_left + this.pad_right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3687 if (this.y_axis) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3688 //add on the space for the y-axis label
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3689 this.summed_width += this.y_label_height + this.y_label_spacer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3690 //add on the space for the y-axis
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3691 this.summed_width += this.y_num_width + this.y_tic_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3692 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3693 //add on the space for the stacks
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3694 this.summed_width += (this.stack_pad_left + this.stack_width) * logo_columns;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3695 //add on the padding after the stacks (an offset from the fine text)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3696 this.summed_width += this.stacks_pad_right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3697
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3698 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3699
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3700 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3701 // end LogoMetrics object
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3702 //======================================================================
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3703
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3704 //found this trick at http://talideon.com/weblog/2005/02/detecting-broken-images-js.cfm
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3705 function image_ok(img) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3706 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3707 // During the onload event, IE correctly identifies any images that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3708 // weren't downloaded as not complete. Others should too. Gecko-based
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3709 // browsers act like NS4 in that they report this incorrectly.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3710 if (!img.complete) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3711 return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3712 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3713 // However, they do have two very useful properties: naturalWidth and
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3714 // naturalHeight. These give the true size of the image. If it failed
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3715 // to load, either of these should be zero.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3716 if (typeof img.naturalWidth !== "undefined" && img.naturalWidth === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3717 return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3718 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3719 // No other way of checking: assume it's ok.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3720 return true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3721 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3722
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3723 function supports_text(ctx) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3724 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3725 if (!ctx.fillText) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3726 return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3727 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3728 if (!ctx.measureText) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3729 return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3730 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3731 return true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3732 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3733
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3734 //draws the scale, returns the width
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3735 function draw_scale(ctx, metrics, alphabet_ic, raster) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3736 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3737 var tic_height, i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3738 tic_height = metrics.stack_height / alphabet_ic;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3739 ctx.save();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3740 ctx.translate(metrics.y_label_height, metrics.y_num_height/2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3741 //draw the axis label
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3742 ctx.save();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3743 ctx.font = metrics.y_label_font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3744 ctx.translate(0, metrics.stack_height/2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3745 ctx.rotate(-(Math.PI / 2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3746 ctx.textAlign = "center";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3747 ctx.fillText("bits", 0, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3748 ctx.restore();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3749
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3750 ctx.translate(metrics.y_label_spacer + metrics.y_num_width, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3751
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3752 //draw the axis tics
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3753 ctx.save();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3754 ctx.translate(0, metrics.stack_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3755 for (i = 0; i <= alphabet_ic; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3756 //draw the number
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3757 ctx.save();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3758 ctx.translate(-1, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3759 raster.draw_scale_num(ctx, metrics.y_num_font, i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3760 ctx.restore();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3761 //draw the tic
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3762 ctx.fillRect(0, -1, metrics.y_tic_width, 2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3763 //prepare for next tic
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3764 ctx.translate(0, -tic_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3765 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3766 ctx.restore();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3767
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3768 ctx.fillRect(metrics.y_tic_width - 2, 0, 2, metrics.stack_height)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3769
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3770 ctx.restore();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3771 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3772
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3773 function draw_stack_num(ctx, metrics, row_index, raster) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3774 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3775 ctx.save();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3776 ctx.translate(0, Math.round(metrics.stack_height + metrics.x_num_above));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3777 if (metrics.x_axis == 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3778 raster.draw_stack_num(ctx, metrics.x_num_font, metrics.stack_width, row_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3779 } else if (metrics.x_axis == 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3780 // draw dots instead of the numbers (good for small logos)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3781 ctx.beginPath();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3782 var radius = Math.round(metrics.x_num_height / 2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3783 ctx.arc(Math.round(metrics.stack_width / 2), radius, radius, 0, 2 * Math.PI, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3784 ctx.fill();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3785 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3786 ctx.restore();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3787 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3788
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3789 function draw_stack(ctx, metrics, symbols, raster) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3790 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3791 var preferred_pad, sym_min, i, sym, sym_height, pad;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3792 preferred_pad = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3793 sym_min = 5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3794
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3795 ctx.save();//1
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3796 ctx.translate(0, metrics.stack_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3797 for (i = 0; i < symbols.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3798 sym = symbols[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3799 sym_height = metrics.stack_height * sym.get_scale();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3800
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3801 pad = preferred_pad;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3802 if (sym_height - pad < sym_min) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3803 pad = Math.min(pad, Math.max(0, sym_height - sym_min));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3804 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3805 sym_height -= pad;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3806
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3807 //translate to the correct position
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3808 ctx.translate(0, -(pad/2 + sym_height));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3809
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3810 //draw
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3811 raster.draw_stack_sym(ctx, sym.get_symbol(), 0, 0, metrics.stack_width, sym_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3812 //translate past the padding
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3813 ctx.translate(0, -(pad/2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3814 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3815 ctx.restore();//1
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3816 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3817
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3818 function draw_dashed_line(ctx, pattern, start, x1, y1, x2, y2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3819 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3820 var x, y, len, i, dx, dy, tlen, theta, mulx, muly, lx, ly;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3821 dx = x2 - x1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3822 dy = y2 - y1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3823 tlen = Math.pow(dx*dx + dy*dy, 0.5);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3824 theta = Math.atan2(dy,dx);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3825 mulx = Math.cos(theta);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3826 muly = Math.sin(theta);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3827 lx = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3828 ly = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3829 for (i = 0; i < pattern; ++i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3830 lx.push(pattern[i] * mulx);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3831 ly.push(pattern[i] * muly);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3832 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3833 i = start;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3834 x = x1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3835 y = y1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3836 len = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3837 ctx.beginPath();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3838 while (len + pattern[i] < tlen) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3839 ctx.moveTo(x, y);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3840 x += lx[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3841 y += ly[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3842 ctx.lineTo(x, y);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3843 len += pattern[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3844 i = (i + 1) % pattern.length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3845 x += lx[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3846 y += ly[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3847 len += pattern[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3848 i = (i + 1) % pattern.length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3849 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3850 if (len < tlen) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3851 ctx.moveTo(x, y);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3852 x += mulx * (tlen - len);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3853 y += muly * (tlen - len);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3854 ctx.lineTo(x, y);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3855 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3856 ctx.stroke();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3857 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3858
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3859 function draw_trim_background(ctx, metrics, left_start, left_end, left_divider, right_start, right_end, right_divider) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3860 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3861 var left_size = left_end - left_start;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3862 var right_size = right_end - right_start;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3863 var line_x;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3864
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3865 ctx.save();//s8
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3866 ctx.fillStyle = "rgb(240, 240, 240)";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3867 if (left_size > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3868 ctx.fillRect(left_start * metrics.stack_width, 0, left_size * metrics.stack_width, metrics.stack_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3869 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3870 if (right_size > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3871 ctx.fillRect(right_start * metrics.stack_width, 0, right_size * metrics.stack_width, metrics.stack_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3872 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3873 ctx.fillStyle = "rgb(51, 51, 51)";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3874 if (left_size > 0 && left_divider) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3875 line_x = (left_end * metrics.stack_width) - 0.5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3876 draw_dashed_line(ctx, [3], 0, line_x, 0, line_x, metrics.stack_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3877 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3878 if (right_size > 0 && right_divider) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3879 line_x = (right_start * metrics.stack_width) + 0.5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3880 draw_dashed_line(ctx, [3], 0, line_x, 0, line_x, metrics.stack_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3881 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3882 ctx.restore();//s8
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3883 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3884
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3885 function size_logo_on_canvas(logo, canvas, show_names, scale) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3886 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3887 var draw_name, draw_finetext, metrics;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3888 draw_name = (typeof show_names === "boolean" ? show_names : (logo.get_rows() > 1));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3889 draw_finetext = (logo.fine_text.length > 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3890 if (canvas.width !== 0 && canvas.height !== 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3891 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3892 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3893 metrics = new LogoMetrics(canvas.getContext('2d'),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3894 logo.get_xlate_columns(), logo.get_rows(), draw_name, draw_finetext, logo.x_axis, logo.y_axis);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3895 if (typeof scale == "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3896 //resize the canvas to fit the scaled logo
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3897 canvas.width = metrics.summed_width * scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3898 canvas.height = metrics.summed_height * scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3899 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3900 if (canvas.width === 0 && canvas.height === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3901 canvas.width = metrics.summed_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3902 canvas.height = metrics.summed_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3903 } else if (canvas.width === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3904 canvas.width = metrics.summed_width * (canvas.height / metrics.summed_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3905 } else if (canvas.height === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3906 canvas.height = metrics.summed_height * (canvas.width / metrics.summed_width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3907 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3908 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3909 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3910
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3911 function draw_logo_on_canvas(logo, canvas, show_names, scale) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3912 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3913 var i, draw_name, draw_finetext, ctx, metrics, raster, pspm_i, pspm,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3914 offset, col_index, motif_position, ssc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3915 ssc = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3916 draw_name = (typeof show_names === "boolean" ? show_names : (logo.get_rows() > 1));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3917 draw_finetext = (logo.fine_text.length > 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3918 ctx = canvas.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3919 //assume that the user wants the canvas scaled equally so calculate what the best width for this image should be
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3920 metrics = new LogoMetrics(ctx, logo.get_xlate_columns(), logo.get_rows(), draw_name, draw_finetext, logo.x_axis, logo.y_axis);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3921 if (typeof scale == "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3922 //resize the canvas to fit the scaled logo
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3923 canvas.width = metrics.summed_width * scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3924 canvas.height = metrics.summed_height * scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3925 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3926 if (canvas.width === 0 && canvas.height === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3927 scale = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3928 canvas.width = metrics.summed_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3929 canvas.height = metrics.summed_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3930 } else if (canvas.width === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3931 scale = canvas.height / metrics.summed_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3932 canvas.width = metrics.summed_width * scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3933 } else if (canvas.height === 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3934 scale = canvas.width / metrics.summed_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3935 canvas.height = metrics.summed_height * scale;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3936 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3937 scale = Math.min(canvas.width / metrics.summed_width, canvas.height / metrics.summed_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3938 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3939 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3940 // cache the raster based on the assumption that we will be drawing a lot
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3941 // of logos the same size and alphabet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3942 if (typeof draw_logo_on_canvas.raster_cache === "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3943 draw_logo_on_canvas.raster_cache = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3944 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3945 for (i = 0; i < draw_logo_on_canvas.raster_cache.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3946 raster = draw_logo_on_canvas.raster_cache[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3947 if (raster.get_alphabet().equals(logo.alphabet) &&
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3948 Math.abs(raster.get_scale() - scale) < 0.1) break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3949 raster = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3950 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3951 if (raster == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3952 raster = new RasterizedAlphabet(logo.alphabet, scale, metrics.stack_font, metrics.stack_width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3953 draw_logo_on_canvas.raster_cache.push(raster);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3954 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3955 ctx = canvas.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3956 ctx.save();//s1
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3957 ctx.scale(scale, scale);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3958 ctx.save();//s2
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3959 ctx.save();//s7
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3960 //create margin
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3961 ctx.translate(Math.round(metrics.pad_left), Math.round(metrics.pad_top));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3962 for (pspm_i = 0; pspm_i < logo.get_rows(); ++pspm_i) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3963 pspm = logo.get_pspm(pspm_i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3964 offset = logo.get_offset(pspm_i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3965 //optionally draw name if this isn't the last row or is the only row
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3966 if (draw_name && (logo.get_rows() == 1 || pspm_i != (logo.get_rows()-1))) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3967 ctx.save();//s4
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3968 ctx.translate(Math.round(metrics.summed_width/2), Math.round(metrics.name_height));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3969 ctx.font = metrics.name_font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3970 ctx.textAlign = "center";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3971 ctx.fillText(pspm.name, 0, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3972 ctx.restore();//s4
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3973 ctx.translate(0, Math.round(metrics.name_height +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3974 Math.min(0, metrics.name_spacer - metrics.y_num_height/2)));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3975 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3976 //draw scale
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3977 if (logo.y_axis) draw_scale(ctx, metrics, logo.alphabet.get_ic(), raster);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3978 ctx.save();//s5
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3979 //translate across past the scale
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3980 if (logo.y_axis) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3981 ctx.translate(Math.round(metrics.y_label_height + metrics.y_label_spacer +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3982 metrics.y_num_width + metrics.y_tic_width), Math.round(metrics.y_num_height / 2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3983 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3984 //draw the trimming background
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3985 if (pspm.get_left_trim() > 0 || pspm.get_right_trim() > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3986 var left_start = offset * logo.get_xlate_nsyms();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3987 var left_end = (offset + pspm.get_left_trim()) * logo.get_xlate_nsyms();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3988 var left_divider = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3989 if (left_end < logo.get_xlate_start() || left_start > logo.get_xlate_end()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3990 // no overlap
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3991 left_start = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3992 left_end = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3993 left_divider = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3994 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3995 if (left_start < logo.get_xlate_start()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3996 left_start = logo.get_xlate_start();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3997 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3998 if (left_end > logo.get_xlate_end()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
3999 left_end = logo.get_xlate_end();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4000 left_divider = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4001 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4002 left_start -= logo.get_xlate_start();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4003 left_end -= logo.get_xlate_start();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4004 if (left_end < left_start) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4005 left_start = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4006 left_end = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4007 left_divider = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4008 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4009 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4010 var right_end = (offset + pspm.get_motif_length()) * logo.get_xlate_nsyms();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4011 //var right_start = right_end - (pspm.get_left_trim() * logo.get_xlate_nsyms());
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4012 var right_start = right_end - (pspm.get_right_trim() * logo.get_xlate_nsyms());
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4013 var right_divider = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4014 if (right_end < logo.get_xlate_start() || right_start > logo.get_xlate_end()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4015 // no overlap
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4016 right_start = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4017 right_end = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4018 right_divider = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4019 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4020 if (right_start < logo.get_xlate_start()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4021 right_start = logo.get_xlate_start();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4022 right_divider = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4023 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4024 if (right_end > logo.get_xlate_end()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4025 right_end = logo.get_xlate_end();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4026 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4027 right_start -= logo.get_xlate_start();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4028 right_end -= logo.get_xlate_start();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4029 if (right_end < right_start) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4030 right_start = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4031 right_end = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4032 right_divider = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4033 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4034 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4035 draw_trim_background(ctx, metrics, left_start, left_end, left_divider, right_start, right_end, right_divider);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4036 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4037 //draw letters
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4038 var xlate_col;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4039 for (xlate_col = logo.get_xlate_start(); xlate_col < logo.get_xlate_end(); xlate_col++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4040 ctx.translate(metrics.stack_pad_left,0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4041 col_index = Math.floor(xlate_col / logo.get_xlate_nsyms());
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4042 if (xlate_col % logo.get_xlate_nsyms() == 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4043 if (col_index >= offset && col_index < (offset + pspm.get_motif_length())) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4044 motif_position = col_index - offset;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4045 draw_stack_num(ctx, metrics, motif_position, raster);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4046 draw_stack(ctx, metrics, pspm.get_stack(motif_position, logo.alphabet, ssc), raster);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4047 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4048 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4049 if (col_index >= offset && col_index < (offset + pspm.get_motif_length())) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4050 ctx.save();// s5.1
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4051 ctx.translate(0, Math.round(metrics.stack_height));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4052 // TODO draw a dot or dash or something to indicate continuity of the motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4053 ctx.restore(); //s5.1
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4054 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4055 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4056 ctx.translate(Math.round(metrics.stack_width), 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4057 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4058 ctx.restore();//s5
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4059 ////optionally draw name if this is the last row but isn't the only row
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4060 if (draw_name && (logo.get_rows() != 1 && pspm_i == (logo.get_rows()-1))) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4061 //translate vertically past the stack and axis's
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4062 ctx.translate(0, metrics.y_num_height/2 + metrics.stack_height +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4063 Math.max(metrics.y_num_height/2, metrics.x_num_above + metrics.x_num_width + metrics.name_spacer));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4064
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4065 ctx.save();//s6
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4066 ctx.translate(metrics.summed_width/2, metrics.name_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4067 ctx.font = metrics.name_font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4068 ctx.textAlign = "center";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4069 ctx.fillText(pspm.name, 0, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4070 ctx.restore();//s6
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4071 ctx.translate(0, metrics.name_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4072 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4073 //translate vertically past the stack and axis's
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4074 ctx.translate(0, metrics.y_num_height/2 + metrics.stack_height +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4075 Math.max(metrics.y_num_height/2, metrics.x_num_above + metrics.x_num_width));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4076 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4077 //if not the last row then add middle padding
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4078 if (pspm_i != (logo.get_rows() -1)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4079 ctx.translate(0, metrics.pad_middle);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4080 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4081 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4082 ctx.restore();//s7
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4083 if (logo.fine_text.length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4084 ctx.translate(metrics.summed_width - metrics.pad_right, metrics.summed_height - metrics.pad_bottom);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4085 ctx.font = metrics.fine_txt_font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4086 ctx.textAlign = "right";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4087 ctx.fillText(logo.fine_text, 0,0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4088 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4089 ctx.restore();//s2
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4090 ctx.restore();//s1
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4091 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4092
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4093 function create_canvas(c_width, c_height, c_id, c_title, c_display) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4094 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4095 var canvas = document.createElement("canvas");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4096 //check for canvas support before attempting anything
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4097 if (!canvas.getContext) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4098 return null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4099 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4100 var ctx = canvas.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4101 //check for html5 text drawing support
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4102 if (!supports_text(ctx)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4103 return null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4104 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4105 //size the canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4106 canvas.width = c_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4107 canvas.height = c_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4108 canvas.id = c_id;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4109 canvas.title = c_title;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4110 canvas.style.display = c_display;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4111 return canvas;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4112 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4113
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4114 function logo_1(alphabet, fine_text, pspm) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4115 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4116 var logo = new Logo(alphabet, fine_text);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4117 logo.add_pspm(pspm);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4118 return logo;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4119 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4120
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4121 function logo_2(alphabet, fine_text, target, query, query_offset) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4122 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4123 var logo = new Logo(alphabet, fine_text);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4124 if (query_offset < 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4125 logo.add_pspm(target, -query_offset);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4126 logo.add_pspm(query);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4127 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4128 logo.add_pspm(target);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4129 logo.add_pspm(query, query_offset);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4130 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4131 return logo;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4132 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4133
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4134 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4135 * Specifies an alternate source for an image.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4136 * If the image with the image_id specified has
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4137 * not loaded then a generated logo will be used
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4138 * to replace it.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4139 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4140 * Note that the image must either have dimensions
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4141 * or a scale must be set.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4142 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4143 function alternate_logo(logo, image_id, scale) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4144 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4145 var image = document.getElementById(image_id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4146 if (!image) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4147 alert("Can't find specified image id (" + image_id + ")");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4148 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4149 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4150 //if the image has loaded then there is no reason to use the canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4151 if (image_ok(image)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4152 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4153 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4154 //the image has failed to load so replace it with a canvas if we can.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4155 var canvas = create_canvas(image.width, image.height, image_id, image.title, image.style.display);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4156 if (canvas === null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4157 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4158 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4159 //draw the logo on the canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4160 draw_logo_on_canvas(logo, canvas, null, scale);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4161 //replace the image with the canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4162 image.parentNode.replaceChild(canvas, image);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4163 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4164
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4165 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4166 * Specifies that the element with the specified id
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4167 * should be replaced with a generated logo.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4168 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4169 function replace_logo(logo, replace_id, scale, title_txt, display_style) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4170 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4171 var element = document.getElementById(replace_id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4172 if (!replace_id) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4173 alert("Can't find specified id (" + replace_id + ")");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4174 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4175 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4176 //found the element!
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4177 var canvas = create_canvas(50, 120, replace_id, title_txt, display_style);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4178 if (canvas === null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4179 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4180 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4181 //draw the logo on the canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4182 draw_logo_on_canvas(logo, canvas, null, scale);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4183 //replace the element with the canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4184 element.parentNode.replaceChild(canvas, element);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4185 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4186
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4187 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4188 * Fast string trimming implementation found at
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4189 * http://blog.stevenlevithan.com/archives/faster-trim-javascript
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4190 *
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4191 * Note that regex is good at removing leading space but
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4192 * bad at removing trailing space as it has to first go through
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4193 * the whole string.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4194 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4195 function trim (str) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4196 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4197 var ws, i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4198 str = str.replace(/^\s\s*/, '');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4199 ws = /\s/; i = str.length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4200 while (ws.test(str.charAt(--i)));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4201 return str.slice(0, i + 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4202 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4203
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4204 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4205 // Delay drawing a logo
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4206 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4207 var DelayLogoTask = function(logo, canvas) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4208 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4209 canvas.width = canvas.width; // clear canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4210 this.logo = logo;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4211 this.canvas = canvas;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4212 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4213
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4214 DelayLogoTask.prototype.run = function () {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4215 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4216 this.canvas.width = this.canvas.width; // clear canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4217 draw_logo_on_canvas(this.logo, this.canvas, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4218 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4219
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4220 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4221 * Make a canvas with the motif logo drawn on it.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4222 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4223 function make_logo(alphabet, pspm, height, rc, offset, className) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4224 if (rc) pspm = pspm.copy().reverse_complement(alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4225 var logo = new Logo(alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4226 logo.add_pspm(pspm, offset);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4227 var canvas = document.createElement('canvas');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4228 var sizeit = (height < 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4229 canvas.height = (sizeit ? -height : height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4230 canvas.width = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4231 canvas.className = className;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4232 if (sizeit) size_logo_on_canvas(logo, canvas, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4233 add_draw_task(canvas, new DelayLogoTask(logo, canvas));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4234 return canvas;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4235 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4236 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4237 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4238
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4239 // PRIVATE GLOBAL (uhoh)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4240 var _block_colour_lookup = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4241
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4242 function block_colour(index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4243 function hsl2rgb(hue, saturation, lightness) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4244 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4245 function _hue(p, q, t) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4246 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4247 if (t < 0) t += 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4248 else if (t > 1) t -= 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4249 if (t < (1.0 / 6.0)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4250 return p + ((q - p) * 6.0 * t);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4251 } else if (t < 0.5) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4252 return q;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4253 } else if (t < (2.0 / 3.0)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4254 return p + ((q - p) * ((2.0 / 3.0) - t) * 6.0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4255 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4256 return p;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4257 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4258 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4259 function _pad_hex(value) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4260 var hex = Math.round(value * 255).toString(16);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4261 if (hex.length < 2) hex = "0" + hex;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4262 return hex;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4263 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4264 var r, g, b, p, q;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4265 if (saturation == 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4266 // achromatic (grayscale)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4267 r = lightness;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4268 g = lightness;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4269 b = lightness;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4270 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4271 if (lightness < 0.5) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4272 q = lightness * (1 + saturation);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4273 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4274 q = lightness + saturation - (lightness * saturation);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4275 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4276 p = (2 * lightness) - q;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4277 r = _hue(p, q, hue + (1.0 / 3.0));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4278 g = _hue(p, q, hue);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4279 b = _hue(p, q, hue - (1.0 / 3.0));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4280 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4281 return "#" + _pad_hex(r) + _pad_hex(g) + _pad_hex(b);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4282 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4283 if (typeof index !== "number" || index % 1 !== 0 || index < 0) return "#000000";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4284 // check for override
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4285 if (_block_colour_lookup[index] == null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4286 var start = 0; //red
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4287 var sat = 100;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4288 var light = 50;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4289 var divisions = 1 << Math.ceil(Math.log(index + 1) / Math.LN2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4290 hue = start + (360 / divisions) * ((index - (divisions >> 1)) * 2 + 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4291 // colour input fields only support values in the form #RRGGBB
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4292 _block_colour_lookup[index] = hsl2rgb(hue / 360, sat / 100, light / 100);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4293 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4294 return _block_colour_lookup[index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4295 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4296
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4297 function set_block_colour(index, new_colour) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4298 _block_colour_lookup[index] = new_colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4299 var blocks = document.querySelectorAll("div.block_motif[data-colour-index=\"" + index + "\"]");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4300 var i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4301 for (i = 0; i < blocks.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4302 blocks[i].style.backgroundColor = new_colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4303 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4304 var swatches = document.querySelectorAll("div.legend_swatch[data-colour-index=\"" + index + "\"]");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4305 var picker;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4306 for (i = 0; i < swatches.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4307 swatches[i].style.backgroundColor = new_colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4308 picker = swatches[i].querySelector("input[type=\"color\"]");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4309 if (picker != null) picker.value = new_colour;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4310 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4311 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4312
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4313 function make_block_legend_entry(motif_name, motif_colour_index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4314 if (typeof make_block_legend_entry.has_colour_picker !== "boolean") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4315 // test if colour picker is supported, based off Modernizer
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4316 // see http://stackoverflow.com/a/7787648/66387
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4317 make_block_legend_entry.has_colour_picker = (function() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4318 var doc_ele = document.documentElement;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4319 // We first check to see if the type we give it sticks..
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4320 var input_ele = document.createElement('input');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4321 input_ele.setAttribute('type', 'color');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4322 var value_ok = input_ele.type !== 'text';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4323 if (value_ok) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4324 // If the type does, we feed it a textual value, which shouldn't be valid.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4325 // If the value doesn't stick, we know there's input sanitization which infers a custom UI
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4326 var smile = ':)';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4327 input_ele.value = smile;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4328 input_ele.style.cssText = 'position:absolute;visibility:hidden;';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4329 // chuck into DOM and force reflow for Opera bug in 11.00
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4330 // github.com/Modernizr/Modernizr/issues#issue/159
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4331 doc_ele.appendChild(input_ele);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4332 doc_ele.offsetWidth;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4333 value_ok = input_ele.value != smile;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4334 doc_ele.removeChild(input_ele);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4335 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4336 return value_ok;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4337 })();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4338 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4339 var entry = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4340 entry.className = "legend_entry";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4341 var swatch;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4342 swatch = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4343 swatch.className = "legend_swatch";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4344 swatch.setAttribute("data-colour-index", motif_colour_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4345 swatch.style.backgroundColor = block_colour(motif_colour_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4346 if (make_block_legend_entry.has_colour_picker) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4347 var picker = document.createElement("input");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4348 picker.type = "color";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4349 picker.value = block_colour(motif_colour_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4350 picker.addEventListener("change", function(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4351 set_block_colour(motif_colour_index, picker.value);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4352 }, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4353 swatch.addEventListener("click", function(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4354 picker.click();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4355 }, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4356 swatch.appendChild(picker);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4357 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4358 entry.appendChild(swatch);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4359 var name = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4360 name.className = "legend_text";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4361 name.appendChild(document.createTextNode(motif_name));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4362 entry.appendChild(name);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4363 return entry;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4364 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4365
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4366 function make_block_ruler(max_len) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4367 var container = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4368 container.className = "block_container";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4369 var step;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4370 if (max_len < 50) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4371 step = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4372 } else if (max_len < 100) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4373 step = 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4374 } else if (max_len < 200) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4375 step = 4;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4376 } else if (max_len < 500) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4377 step = 10;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4378 } else if (max_len < 1000) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4379 step = 20;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4380 } else if (max_len < 2000) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4381 step = 40;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4382 } else if (max_len < 5000) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4383 step = 100;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4384 } else if (max_len < 10000) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4385 step = 200;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4386 } else if (max_len < 20000) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4387 step = 400;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4388 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4389 step = Math.floor(max_len / 20000) * 400;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4390 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4391 var peroid;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4392 if (max_len < 10) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4393 peroid = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4394 } else if (max_len < 20) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4395 peroid = 2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4396 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4397 peroid = 5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4398 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4399 var i, cycle, offset, tic, label;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4400 for (i = 0, cycle = 0; i < max_len; i += step, cycle = (cycle + 1) % peroid) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4401 offset = "" + ((i / max_len) * 100) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4402 tic = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4403 tic.style.left = offset;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4404 tic.className = (cycle == 0 ? "tic_major" : "tic_minor");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4405 container.appendChild(tic);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4406 if (cycle == 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4407 label = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4408 label.className = "tic_label";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4409 label.style.left = offset;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4410 label.appendChild(document.createTextNode(i));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4411 container.appendChild(label);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4412 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4413 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4414 return container;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4415 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4416
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4417 function _calculate_block_needle_drag_pos(e, data) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4418 var mouse;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4419 e = e || window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4420 if (e.pageX || ev.pageY) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4421 mouse = {"x": e.pageX, "y": e.pageY};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4422 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4423 mouse = {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4424 x:e.clientX + document.body.scrollLeft - document.body.clientLeft,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4425 y:e.clientY + document.body.scrollTop - document.body.clientTop
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4426 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4427 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4428 var cont = data.container;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4429 var dragable_length = cont.clientWidth -
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4430 (cont.style.paddingLeft ? cont.style.paddingLeft : 0) -
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4431 (cont.style.paddingRight ? cont.style.paddingRight : 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4432 //I believe that the offset parent is the body
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4433 //otherwise I would need to make this recursive
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4434 //maybe clientLeft would work, but the explanation of
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4435 //it is hard to understand and it apparently doesn't work
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4436 //in firefox 2.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4437 var diff = mouse.x - cont.offsetLeft;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4438 if (diff < 0) diff = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4439 if (diff > dragable_length) diff = dragable_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4440 var pos = Math.round(diff / dragable_length * data.max);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4441 if (pos > data.len) pos = data.len;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4442 return pos;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4443 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4444
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4445 function _update_block_needle_drag(e, data, done) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4446 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4447 var pos = _calculate_block_needle_drag_pos(e, data);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4448 // read the needle positions
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4449 var left = parseInt(data.llabel.textContent, 10) - data.off - 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4450 var right = parseInt(data.rlabel.textContent, 10) - data.off;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4451 // validate needle positions
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4452 if (left >= data.len) left = data.len - 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4453 if (left < 0) left = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4454 if (right > data.len) right = data.len;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4455 if (right <= left) right = left + 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4456 // calculate the new needle positions
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4457 if (data.moveboth) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4458 var size = right - left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4459 if (data.isleft) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4460 if ((pos + size) > data.len) pos = data.len - size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4461 left = pos;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4462 right = pos + size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4463 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4464 if ((pos - size) < 0) pos = size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4465 left = pos - size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4466 right = pos;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4467 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4468 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4469 if (data.isleft) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4470 if (pos >= right) pos = right - 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4471 left = pos;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4472 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4473 if (pos <= left) pos = left + 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4474 right = pos;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4475 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4476 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4477 // update the needle positions
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4478 data.lneedle.style.left = "" + (left / data.max * 100) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4479 data.llabel.textContent = "" + (left + data.off + 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4480 data.rneedle.style.left = "" + (right / data.max * 100) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4481 data.rlabel.textContent = "" + (right + data.off);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4482 data.handler(left, right, done);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4483 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4484
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4485 function _make_block_needle_drag_start_handler(isleft, data) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4486 return function (e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4487 data.isleft = isleft;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4488 data.moveboth = !(e.shiftKey);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4489 document.addEventListener("mousemove", data.drag_during, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4490 document.addEventListener("mouseup", data.drag_end, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4491 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4492 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4493
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4494 function _make_block_needle_drag_end_handler(data) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4495 return function (e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4496 document.removeEventListener("mousemove", data.drag_during, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4497 document.removeEventListener("mouseup", data.drag_end, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4498 _update_block_needle_drag(e, data, true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4499 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4500 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4501
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4502 function _make_block_needle_drag_during_handler(data) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4503 return function (e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4504 _update_block_needle_drag(e, data, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4505 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4506 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4507
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4508 // private function used by make_block_container
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4509 function _make_block_needle(isleft, value, data) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4510 var vbar = document.createElement('div');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4511 vbar.className = "block_needle " + (isleft ? "left" : "right");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4512 vbar.style.left = "" + (value / data.max * 100)+ "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4513 var label = document.createElement('div');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4514 label.className = "block_handle " + (isleft ? "left" : "right");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4515 // The needles sit between the sequence positions, so the left one sits at the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4516 // start and the right at the end. This is why 1 is added to the displayed
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4517 // value for a left handle as the user doesn't need to know about this detail
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4518 label.textContent = "" + (isleft ? value + data.off + 1 : value + data.off);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4519 label.unselectable = "on"; // so IE and Opera don't select the text, others are done in css
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4520 label.title = "Drag to move the displayed range. Hold shift and drag to change " + (isleft ? "lower" : "upper") + " bound of the range.";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4521 vbar.appendChild(label);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4522 if (isleft) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4523 data.lneedle = vbar;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4524 data.llabel = label;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4525 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4526 data.rneedle = vbar;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4527 data.rlabel = label;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4528 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4529 label.addEventListener("mousedown", _make_block_needle_drag_start_handler(isleft, data), false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4530 return vbar;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4531 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4532
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4533 function make_block_container(is_stranded, has_both_strands, max_len, show_len, offset, range_handler) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4534 offset = (offset != null ? offset : 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4535 // make the container for the block diagram
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4536 var container = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4537 container.className = "block_container";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4538 container.setAttribute("data-max", max_len);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4539 container.setAttribute("data-off", offset);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4540 if (is_stranded) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4541 var plus = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4542 plus.appendChild(document.createTextNode("+"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4543 plus.className = "block_plus_sym";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4544 container.appendChild(plus);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4545 if (has_both_strands) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4546 var minus = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4547 minus.appendChild(document.createTextNode("-"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4548 minus.className = "block_minus_sym";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4549 container.appendChild(minus);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4550 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4551 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4552 var rule = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4553 rule.className = "block_rule";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4554 rule.style.width = ((show_len / max_len) * 100) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4555 container.appendChild(rule);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4556 if (range_handler != null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4557 var range_data = {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4558 "max": max_len,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4559 "len": show_len,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4560 "off": offset,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4561 "handler": range_handler,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4562 "container": container,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4563 "lneedle": null, "llabel": null,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4564 "rneedle": null, "rlabel": null,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4565 "isleft": false, "moveboth" : false
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4566 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4567 range_data.drag_during = _make_block_needle_drag_during_handler(range_data);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4568 range_data.drag_end = _make_block_needle_drag_end_handler(range_data);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4569 container.appendChild(_make_block_needle(false, 1, range_data)); // add right first so z-index works
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4570 container.appendChild(_make_block_needle(true, 0, range_data));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4571 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4572 return container;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4573 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4574
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4575 function make_block_label(container, max_len, pos, length, message) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4576 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4577 var label = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4578 label.className = "block_label";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4579 label.style.left = (((pos + (length / 2)) / max_len) * 100) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4580 label.appendChild(document.createTextNode(message));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4581 container.appendChild(label);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4582 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4583
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4584 function make_block(container, max_len,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4585 site_pos, site_len, site_pvalue, site_rc, site_colour_index, site_secondary) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4586 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4587 var block_height, block, block_region1, block_region2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4588 var max_block_height = 12;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4589 var max_pvalue = 1e-10;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4590 // calculate the height of the block
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4591 block_height = (site_pvalue < max_pvalue ? max_block_height :
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4592 (Math.log(site_pvalue) / Math.log(max_pvalue)) * max_block_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4593 if (block_height < 1) block_height = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4594 // create a block to represent the motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4595 block = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4596 block.className = "block_motif" + (site_secondary ? " scanned_site" : "") + (site_rc ? " bottom" : " top");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4597 block.style.left = ((site_pos / max_len) * 100) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4598 block.style.top = (!site_rc ? max_block_height - block_height :
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4599 max_block_height + 1) + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4600 block.style.width = ((site_len / max_len) * 100) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4601 block.style.height = block_height + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4602 block.style.backgroundColor = block_colour(site_colour_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4603 block.setAttribute("data-colour-index", site_colour_index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4604 // add to container
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4605 container.appendChild(block);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4606 var activator = function (e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4607 toggle_class(block, "active", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4608 var new_e = new e.constructor(e.type, e);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4609 block.dispatchEvent(new_e);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4610 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4611 var deactivator = function (e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4612 toggle_class(block, "active", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4613 var new_e = new e.constructor(e.type, e);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4614 block.dispatchEvent(new_e);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4615 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4616 // create a larger region to detect mouseover for the block
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4617 block_region1 = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4618 block_region1.className = "block_region top" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4619 (site_secondary ? " scanned_site" : "") + (site_rc ? "" : " main");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4620 block_region1.style.left = block.style.left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4621 block_region1.style.width = block.style.width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4622 block_region1.addEventListener('mouseover', activator, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4623 block_region1.addEventListener('mouseout', deactivator, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4624 container.appendChild(block_region1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4625 block_region2 = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4626 block_region2.className = "block_region bottom" +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4627 (site_secondary ? " scanned_site" : "") + (site_rc ? " main" : "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4628 block_region2.style.left = block.style.left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4629 block_region2.style.width = block.style.width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4630 block_region2.addEventListener('mouseover', activator, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4631 block_region2.addEventListener('mouseout', deactivator, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4632 container.appendChild(block_region2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4633 return block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4634 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4635
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4636 function set_block_needle_positions(containingNode, start, end) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4637 var container, lneedle, llabel, rneedle, rlabel, max, off, left, right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4638 container = (/\bblock_container\b/.test(containingNode.className) ? containingNode : containingNode.querySelector(".block_container"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4639 max = parseInt(container.getAttribute("data-max"), 10);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4640 off = parseInt(container.getAttribute("data-off"), 10);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4641 left = start - off;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4642 right = end - off;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4643 lneedle = containingNode.querySelector(".block_needle.left");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4644 llabel = lneedle.querySelector(".block_handle.left");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4645 rneedle = containingNode.querySelector(".block_needle.right");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4646 rlabel = rneedle.querySelector(".block_handle.right");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4647 // update the needle positions
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4648 lneedle.style.left = "" + (left / max * 100) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4649 llabel.textContent = "" + (left + off + 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4650 rneedle.style.left = "" + (right / max * 100) + "%";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4651 rlabel.textContent = "" + (right + off);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4652 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4653
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4654 function get_block_needle_positions(containingNode) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4655 var container, llabel, rlabel, max, off, left, right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4656 container = (/\bblock_container\b/.test(containingNode.className) ? containingNode : containingNode.querySelector(".block_container"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4657 max = parseInt(container.getAttribute("data-max"), 10);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4658 off = parseInt(container.getAttribute("data-off"), 10);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4659 llabel = containingNode.querySelector(".block_needle.left > .block_handle.left");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4660 rlabel = containingNode.querySelector(".block_needle.right > .block_handle.right");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4661 left = parseInt(llabel.textContent, 10) - off - 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4662 right = parseInt(rlabel.textContent, 10) - off;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4663 return {"start": left + off, "end": right + off};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4664 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4665 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4666 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4667 function make_alpha_bg_table(alph, freqs) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4668 function colour_symbol(index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4669 var span = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4670 span.appendChild(document.createTextNode(alph.get_symbol(index)));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4671 span.style.color = alph.get_colour(index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4672 span.className = "alpha_symbol";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4673 return span;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4674 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4675 var table, thead, tbody, row, th, span, i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4676 // create table
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4677 table = document.createElement("table");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4678 table.className = "alpha_bg_table";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4679 // create header
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4680 thead = document.createElement("thead");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4681 table.appendChild(thead);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4682 row = thead.insertRow(thead.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4683 if (alph.has_complement()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4684 add_text_header_cell(row, "Name", "pop_alph_name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4685 if (freqs != null) add_text_header_cell(row, "Freq.", "pop_alph_freq");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4686 if (alph.has_bg()) add_text_header_cell(row, "Bg.", "pop_alph_bg");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4687 add_text_header_cell(row, "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4688 add_text_header_cell(row, "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4689 add_text_header_cell(row, "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4690 if (alph.has_bg()) add_text_header_cell(row, "Bg.", "pop_alph_bg");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4691 if (freqs != null) add_text_header_cell(row, "Freq.", "pop_alph_freq");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4692 add_text_header_cell(row, "Name", "pop_alph_name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4693 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4694 add_text_header_cell(row, "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4695 add_text_header_cell(row, "Name", "pop_alph_name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4696 if (freqs != null) add_text_header_cell(row, "Freq.", "pop_alph_freq");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4697 if (alph.has_bg()) add_text_header_cell(row, "Bg.", "pop_alph_bg");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4698 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4699 // add alphabet entries
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4700 tbody = document.createElement("tbody");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4701 table.appendChild(tbody);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4702 if (alph.has_complement()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4703 for (i = 0; i < alph.get_size_core(); i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4704 var c = alph.get_complement(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4705 if (i > c) continue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4706 row = tbody.insertRow(tbody.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4707 add_text_cell(row, alph.get_name(i));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4708 if (freqs != null) add_text_cell(row, "" + freqs[i]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4709 if (alph.has_bg()) add_text_cell(row, "" + alph.get_bg_freq(i));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4710 add_cell(row, colour_symbol(i));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4711 add_text_cell(row, "~");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4712 add_cell(row, colour_symbol(c));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4713 if (alph.has_bg()) add_text_cell(row, "" + alph.get_bg_freq(c));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4714 if (freqs != null) add_text_cell(row, "" + freqs[c]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4715 add_text_cell(row, alph.get_name(c));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4716 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4717 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4718 for (i = 0; i < alph.get_size_core(); i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4719 row = tbody.insertRow(tbody.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4720 add_cell(row, colour_symbol(i));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4721 add_text_cell(row, alph.get_name(i));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4722 if (freqs != null) add_text_cell(row, "" + freqs[i]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4723 if (alph.has_bg()) add_text_cell(row, "" + alph.get_bg_freq(i));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4724 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4725 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4726 return table;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4727 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4728
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4729 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4730 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4731 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4732 // simple-shared-doc.js
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4733 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4734
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4735 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4736 // Function to redirect to appropriate doc file.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4737 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4738 function get_doc_text(pgm, doc_type, extra, extra2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4739 switch (pgm) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4740 case 'shared':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4741 return(get_shared_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4742 case 'ame':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4743 return(get_ame_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4744 case 'centrimo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4745 return(get_centrimo_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4746 case 'discovery':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4747 return(get_discovery_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4748 case 'fimo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4749 return(get_fimo_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4750 case 'gomo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4751 return(get_gomo_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4752 case 'mcast':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4753 return(get_mcast_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4754 case 'meme-chip':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4755 return(get_meme_chip_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4756 case 'momo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4757 return(get_momo_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4758 case 'sea':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4759 return(get_sea_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4760 case 'spamo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4761 return(get_spamo_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4762 case 'streme':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4763 return(get_streme_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4764 case 'tgene':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4765 return(get_tgene_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4766 case 'tomtom':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4767 return(get_tomtom_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4768 case 'xstreme':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4769 return(get_xstreme_doc_text(doc_type, extra, extra2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4770 default:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4771 return("<b>Unknown program type: <font color=red>" + pgm + "</font></b>");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4772 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4773 } // get_doc_text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4774
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4775 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4776 // Function to replace the innerHTML of element "id" with the HTML indicated by "doc_type".
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4777 // Easier to read and update than the more flexible approach in shared-doc.js.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4778 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4779 function print_doc(id, pgm, doc_type, extra) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4780 document.getElementById(id).insertAdjacentHTML('beforeend', get_doc_text(pgm, doc_type, extra));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4781 } // print_doc
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4782
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4783 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4784 // Function to replace the innerHTML of element "id" with an HTML paragraph
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4785 // containing the text for 'pgm' and 'doc_type'.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4786 // This function can be used in help pop-ups.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4787 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4788 function print_doc_para(id, pgm, doc_type, extra, extra2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4789 html = "<p>" + get_doc_text(pgm, doc_type, extra, extra2) + "</p>";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4790 document.getElementById(id).insertAdjacentHTML('beforeend', html);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4791 } // print_doc_para
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4792
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4793 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4794 // Function to return the Shared HTML text of a given type.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4795 // This function can be used directly to document the output format (xx-output-format.html)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4796 // and indirectly via print_doc_para for help pop-ups in the actual output HTML,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4797 // to prevent duplication of documentation.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4798 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4799 function get_shared_doc_text(doc_type, extra, extra2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4800 if (extra == undefined) {extra = ""};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4801 if (extra2 == undefined) {extra2 = ""};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4802 switch (doc_type) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4803 case 'fasta-coordinates-name':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4804 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4805 The sequence IDs in the FASTA header lines are used as the source of sequence names.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4806 The sequence ID is the string following the initial '>' up to the first white space character.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4807 If the sequence ID is in an accepted <a href="` + site_url + `/doc/fasta-coordinates-format.html">FASTA Coordinates Format</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4808 (e.g., UCSC or Galaxy format), and you did NOT specify the <code>` + extra + `-no-pgc</code> option,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4809 then the coordinates are removed from the sequence ID to create the sequence name.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4810 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4811 case 'fasta-coordinates-brief':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4812 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4813 The sequence IDs in the FASTA header lines are used as the source of sequence names.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4814 The sequence ID is the string following the initial '>' up to the first white space character.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4815 If the sequence ID is in an accepted <a href="` + site_url + `/doc/fasta-coordinates-format.html">FASTA Coordinates Format</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4816 (e.g., UCSC or Galaxy format), and you did NOT specify the <code>` + extra + `-no-pgc</code> option,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4817 then the coordinates are removed from the sequence ID to create the sequence name,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4818 and the starting coordinate given in the sequence ID will be used as the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4819 coordinate of the first position of the sequence.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4820 Otherwise, the coordinate of the first position of the sequence is taken as 1 and the entire
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4821 sequence ID is used as the sequence name.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4822 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4823 case 'fasta-coordinates':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4824 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4825 For sequence coordinates embedded in FASTA sequence headers to be parsed
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4826 correctly by MEME Suite programs, the sequence ID in the FASTA header should have one of the two
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4827 following formats:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4828
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4829 <h4>UCSC Format</h4>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4830 <div style='margin: 5px 0'>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4831 &gt;<span class='pdat'>sequence name</span>:<span class='pdat'
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4832 >starting position</span>-<span class='pdat'>ending position</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4833 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4834 where
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4835 <ul style='margin-top: 0; margin-bottom: 5px'>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4836 <li><span class='pdat'>sequence name</span> is the name of the genomic sequence,</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4837 <li><span class='pdat'>starting position</span> is the genomic position of the first base and</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4838 <li><span class='pdat'>ending position</span> is the genomic position of the final base.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4839 </ul>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4840 <b>Example:</b> <span class="pdata">chr1:156887119-156887619</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4841
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4842 <h4>Galaxy Format</h4>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4843 <div style='margin: 5px 0'>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4844 &gt;<span class='pdat'>assembly name</span>_<span class='pdat'
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4845 >sequence name</span>_<span class='pdat'
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4846 >starting position</span>_<span class='pdat'
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4847 >ending position</span>_<span class='pdat'
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4848 >strand</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4849 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4850 where
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4851 <ul style='margin-top: 0; margin-bottom: 5px'>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4852 <li><span class='pdat'>assembly name</span> is the name of the genomic assembly,</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4853 <li><span class='pdat'>sequence name</span> is the name of the genomic sequence,</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4854 <li><span class='pdat'>starting position</span> is the genomic position of the first base and</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4855 <li><span class='pdat'>ending position</span> is the genomic position of the final base.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4856 </ul>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4857 <b>Example:</b> <span class="pdata">>mm9_chr18_75759530_7575972_-</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4858
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4859 <p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4860 For both formats, the following rules also apply:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4861 <ul>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4862 <li>The the coordinates are 1-start, fully-closed. This means
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4863 that the first base of the chromosome is position "1", and the bases at the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4864 first and last positions of the given range are included.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4865 <li>The <span class='pdat'>sequence name</span> may not contain any white space.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4866 <li>The <span class='pdat'>assembly name</span> is not optional.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4867 <li>The <span class='pdat'>strand</span> is ignored.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4868 <li>When no valid genomic coordinates are found in a FASTA sequence header, the starting
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4869 position of the sequence is taken to be position 1.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4870 </ul>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4871 </p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4872 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4873 case 'motif-db':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4874 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4875 The name of ` + extra2 + ` a file of motifs ("motif database file") that contains ` + extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4876 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4877 case 'motif-id':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4878 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4879 The name of the ` + extra + ` motif, which is unique ` + extra2 + ` in the motif database file.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4880 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4881 case 'motif-alt-id':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4882 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4883 An alternate name for the ` + extra + ` motif that may be provided ` + extra2 + ` in the motif database file.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4884 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4885 case 'motif-width':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4886 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4887 The width of the motif. No gaps are allowed in motifs supplied to ` + extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4888 as it only works for motifs of a fixed width.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4889 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4890 case 'motif-cons':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4891 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4892 A consensus sequence computed from the ` + extra + ` motif (as described <a href="#consensus_doc">below</a>).
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4893 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4894 case 'motif-match-score':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4895 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4896 ` + extra2 + ` The motif match score of a position in a sequence is
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4897 computed by summing the appropriate entry from each column of the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4898 position-dependent scoring matrix that represents the motif. ` + extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4899 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4900 case 'motif-match-p-value':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4901 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4902 The <i>p</i>-value of a motif match is the probability of a single random
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4903 subsequence of the length of the motif <a href="javascript:help_refine('pop_motif_match_score')">scoring</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4904 at least as well as the observed match.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4905 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4906 case 'bh-q-value':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4907 if (extra2 == "") extra2 = "match";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4908 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4909 The q-value is the minimum False Discovery Rate (FDR) required to consider this
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4910 ` + extra2 + ` significant.</br>` +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4911 get_shared_doc_text('bh-q-value-method', extra, extra2) + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4912 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4913 case 'bh-q-value-method':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4914 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4915 <br>` + extra + ` estimates q-values from all the ` + extra2 + ` <i>p</i>-values
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4916 using the method proposed by Benjamini & Hochberg (<i>Journal of the Royal Statistical Society B</i>, 57:289-300, 1995).
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4917 See also Storey JD, Tibshirani R. Statistical significance for
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4918 genome-wide studies, <i>Proc. Natl. Acad. Sci. USA</i> (2003) <b>100</b>:9440&ndash;9445.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4919 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4920 case 'sdb-name':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4921 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4922 The name of the (FASTA) sequence database file.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4923 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4924 case 'sdb-psp':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4925 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4926 The name of the position specific priors (PSP) file.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4927 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4928 case 'sdb-dist':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4929 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4930 The name of the binned distribution of priors file.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4931 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4932 case 'sdb-count':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4933 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4934 The number of sequences in the database.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4935 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4936 case 'sdb-letters':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4937 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4938 The number of letters in the sequence database.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4939 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4940 case 'lastmod':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4941 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4942 The date of the last modification to the ` + extra + ` database.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4943 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4944 case 'sequence-id':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4945 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4946 The identifier of the sequence (from the FASTA sequence header line)` + extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4947 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4948 case 'sequence-desc':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4949 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4950 The description appearing after the identifier of the sequence in the FASTA header line.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4951 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4952 case 'alph-name':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4953 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4954 The name of the alphabet symbol.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4955 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4956 case 'alph-bg':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4957 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4958 The frequency of the alphabet symbol as defined by the background model.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4959 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4960 case 'match-start':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4961 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4962 The start position of the ` + extra + `.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4963 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4964 case 'match-stop':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4965 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4966 The end position of the ` + extra + `.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4967 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4968 case 'match-start-seq':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4969 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4970 The start position of the ` + extra + `; 1-based sequence coordinates.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4971 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4972 case 'match-stop-seq':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4973 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4974 The end position of the ` + extra + `; 1-based sequence coordinates.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4975 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4976 case 'match-start-genomic':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4977 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4978 The start position of the ` + extra + `; genomic coordinates.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4979 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4980 case 'match-stop-genomic':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4981 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4982 The end position of the ` + extra + `; genomic coordinates.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4983 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4984 case 'motif-consensus':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4985 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4986 <p id="consensus_doc">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4987 A <b>consensus sequence</b> is constructed from each column in a
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4988 motif's frequency matrix using the <b>"50% rule"</b>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4989 as follows:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4990 </p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4991 <ol>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4992 <li>The letter frequencies in the column are sorted in decreasing order.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4993 <li>Letters with frequency less 50% of the maximum are discarded.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4994 <li>The letter used in this position in the consensus sequence is determined
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4995 by the first rule below that applies:</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4996 <ul>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4997 <li>If there is only one letter left, or if the remaining letters exactly match
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4998 an ambiguous symbol in the alphabet, the <b>letter</b> or <b>ambiguous symbol</b>,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
4999 respectively, is used.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5000 <li>Otherwise, if the remaining set contains at least 50% of the core
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5001 symbols in the alphabet, the alphabet's <b>wildcard</b>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5002 (e.g., "N" for DNA or RNA, and "X" for protein) is used.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5003 <li>Otherwise, the letter with the <b>maximum frequency</b> is used.</li>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5004 </ul>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5005 </ol>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5006 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5007 default:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5008 return("Error--Unrecognized shared doc_type: " + doc_type);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5009 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5010 } // get_shared_doc_text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5011 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5012 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5013 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5014 // discovery_doc.js
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5015 // Documentation common to motif discovery tools.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5016 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5017
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5018 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5019 // Function to return the HTML text of a given type.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5020 // This function can be used directly to document the output format (xx-output-format.html)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5021 // and indirectly via print_doc_para for help pop-ups in the actual output HTML,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5022 // to prevent duplication of documentation.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5023 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5024 function get_discovery_doc_text(doc_type, extra, extra2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5025 if (extra == undefined) {extra = ""};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5026 if (extra2 == undefined) {extra2 = ""};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5027
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5028 switch (doc_type) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5029 case 'motif_logo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5030 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5031 The sequence logo of the motif.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5032 The rules for construction logos are given in
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5033 the <i>Description</i> section of the documentation for the MEME Suite utility
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5034 <a href="` + extra + `/doc/ceqlogo.html#description">ceqlogo</a>.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5035 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5036 case 'motif_rc_logo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5037 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5038 The sequence logo of the reverse complement motif.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5039 The rules for construction logos are given in
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5040 the <i>Description</i> section of the documentation for the MEME Suite utility
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5041 <a href="` + extra + `/doc/ceqlogo.html#description">ceqlogo</a>.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5042 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5043 case 'more':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5044 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5045 Click on the blue symbol below to reveal detailed information about the motif.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5046 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5047 case 'submit_dl':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5048 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5049 Click on the blue symbol below to reveal options allowing you
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5050 to submit this motif to another MEME Suite motif analysis program, to download this
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5051 motif in various text formats, or to download a sequence "logo" of
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5052 this motif PNG or EPS format.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5053 <h5>Supported Programs</h5>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5054 <dl>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5055 <dt>Tomtom</dt>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5056 <dd>Tomtom is a tool for searching for similar known motifs.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5057 [<a href="` + extra + `/doc/tomtom.html?man_type=web">manual</a>]</dd>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5058 <dt>MAST</dt>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5059 <dd>MAST is a tool for searching biological sequence databases for
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5060 sequences that contain one or more of a group of known motifs.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5061 [<a href="` + extra + `/doc/mast.html?man_type=web">manual</a>]</dd>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5062 <dt>FIMO</dt>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5063 <dd>FIMO is a tool for searching biological sequence databases for
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5064 sequences that contain one or more known motifs.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5065 [<a href="` + extra + `/doc/fimo.html?man_type=web">manual</a>]</dd>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5066 <dt>GOMo</dt>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5067 <dd>GOMo is a tool for identifying possible roles (Gene Ontology
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5068 terms) for DNA binding motifs.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5069 [<a href="` + extra + `/doc/gomo.html?man_type=web">manual</a>]</dd>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5070 <dt>SpaMo</dt>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5071 <dd>SpaMo is a tool for inferring possible transcription factor
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5072 complexes by finding motifs with enriched spacings.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5073 [<a href="` + extra + `/doc/spamo.html?man_type=web">manual</a>]</dd>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5074 </dl>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5075 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5076 case 'site_distr':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5077 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5078 This plot shows the positional distribution of the best match to the motif in the ` +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5079 extra + ` sequences.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5080 Only matches with scores at least the ` +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5081 extra2 + ` score threshold are considered.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5082 The plot is smoothed with a triangular function whose width is 5% of the maximum ` +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5083 extra + ` sequence length.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5084 The position of the dotted vertical line indicates whether the sequences were
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5085 aligned on their left ends, centers, or right ends, respectively.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5086 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5087 case 'site_hist':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5088 return(`
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5089 This histogram shows the distribution of the <b>number</b> of matches to the motif in the ` +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5090 extra + ` sequences with at least one match.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5091 Only matches with scores at least the ` +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5092 extra2 + ` score threshold are considered.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5093 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5094 default:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5095 return("Error--Unrecognized discovery doc_type: " + doc_type);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5096 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5097 } // get_discovery_doc_text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5098 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5099 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5100 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5101 // submit_or_download_motif.js
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5102 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5103
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5104 function make_submit_or_download_motif_form(id, site_url, program) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5105 var html = `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5106 <div class="popup_wrapper">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5107 <div class="popup" style="display:none; top: -150px;" id="download">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5108 <div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5109 <div style="float:right; ">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5110 <div id="outpop_close" class="close" tabindex="0">x</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5111 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5112 <h2 class="mainh" style="margin:0; padding:0;">Submit or Download</h2>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5113 <div style="clear:both"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5114 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5115 <div style="height:100px">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5116 <div style="float:right; width: 30px;">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5117 <div id="outpop_prev" class="navarrow" tabindex="0">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5118 <span class="inactive">&#8679;</span><span class="active">&#11014;</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5119 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5120 <div id="outpop_num" class="navnum"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5121 <div id="outpop_next" class="navarrow" tabindex="0">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5122 <span class="inactive">&#8681;</span><span class="active">&#11015;</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5123 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5124 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5125 <div id="logo_box" style="height: 100px; margin-right: 40px;">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5126 <canvas id="outpop_logo" height="100" width="250"></canvas>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5127 <canvas id="outpop_logo_rc" height="100" width="250"></canvas>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5128 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5129 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5130 <!-- tabs start -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5131 <div class="tabArea top">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5132 <span id="outpop_tab_1" class="tab">Submit Motif</span><span
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5133 id="outpop_tab_2" class="tab middle">Download Motif</span><span
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5134 id="outpop_tab_3" class="tab middle">Download Logo</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5135 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5136 <div class="tabMain top">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5137 <!-- Submit to another program -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5138 <div id="outpop_pnl_1">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5139 <h4 class="compact">Submit to program</h4>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5140 <table id="programs" class="programs">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5141 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5142 <td><input type="radio" name="program" value="tomtom" id="submit_tomtom"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5143 <td><label for="submit_tomtom">Tomtom</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5144 <td><label for="submit_tomtom">Find similar motifs in
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5145 published libraries or a library you supply.</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5146 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5147 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5148 <td><input type="radio" name="program" value="fimo" id="submit_fimo"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5149 <td><label for="submit_fimo">FIMO</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5150 <td><label for="submit_fimo">Find motif occurrences in
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5151 sequence data.</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5152 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5153 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5154 <td><input type="radio" name="program" value="mast" id="submit_mast"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5155 <td><label for="submit_mast">MAST</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5156 <td><label for="submit_mast">Rank sequences by affinity to
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5157 groups of motifs.</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5158 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5159 <tr class="dna_only">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5160 <td><input type="radio" name="program" value="gomo" id="submit_gomo"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5161 <td><label for="submit_gomo">GOMo</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5162 <td><label for="submit_gomo">Identify possible roles (Gene
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5163 Ontology terms) for motifs.</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5164 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5165 <tr class="dna_only">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5166 <td><input type="radio" name="program" value="spamo" id="submit_spamo"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5167 <td><label for="submit_spamo">SpaMo</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5168 <td><label for="submit_spamo">Find other motifs that are
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5169 enriched at specific close spacings which might imply the existence of a complex.</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5170 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5171 </table>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5172 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5173 <!-- download text format -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5174 <div id="outpop_pnl_2">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5175 <div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5176 <label for="text_format">Format:</label>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5177 <select id="text_format">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5178 <option value="0">Count Matrix</option>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5179 <option value="1">Probability Matrix</option>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5180 <option value="2">Minimal MEME</option> ` +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5181 (program == "MEME" ? `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5182 <option value="3">FASTA</option>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5183 <option value="4">Raw</option> ` : ``) + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5184 </select>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5185 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5186 <textarea id="outpop_text" name="content"
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5187 style="width:99%; white-space: pre; word-wrap: normal; overflow-x: scroll;"
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5188 rows="8" readonly="readonly" wrap="off"></textarea>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5189 <a id="outpop_text_dl" download="meme.txt" href=""></a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5190 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5191 <!-- download logo format -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5192 <div id="outpop_pnl_3">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5193 <form id="logo_form" method="post" action="">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5194 <input type="hidden" name="program" value=" ` + program + `"/>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5195 <input type="hidden" id="logo_motifs" name="motifs" value=""/>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5196 <input type="hidden" id="logo_id1" name="id1" value=""/>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5197 <table>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5198 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5199 <td><label for="logo_format">Format:</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5200 <td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5201 <select id="logo_format" name="png">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5202 <option value="1">PNG (for web)</option>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5203 <option value="0">EPS (for publication)</option>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5204 </select>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5205 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5206 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5207 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5208 <td><label for="logo_rc">Orientation:</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5209 <td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5210 <select id="logo_rc" name="rc1">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5211 <option value="0">Normal</option>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5212 <option value="1" id="logo_rc_option">Reverse Complement</option>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5213 </select>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5214 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5215 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5216 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5217 <td><label for="logo_ssc">Small Sample Correction:</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5218 <td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5219 <input type="hidden" id="logo_err" name="errbars" value="0"/>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5220 <select id="logo_ssc" name="ssc">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5221 <option value="0">Off</option>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5222 <option value="1">On</option>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5223 </select>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5224 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5225 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5226 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5227 <td><label for="logo_width">Width:</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5228 <td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5229 <input type="text" id="logo_width" size="4" placeholder="default" name="width"/>&nbsp;cm
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5230 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5231 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5232 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5233 <td><label for="logo_height">Height:</label></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5234 <td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5235 <input type="text" id="logo_height" size="4" placeholder="default" name="height"/>&nbsp;cm
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5236 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5237 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5238 </table>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5239 </form>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5240 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5241 <!-- Buttons -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5242 <div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5243 <div style="float:left;">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5244 <input type="button" id="outpop_do" value="Submit" />
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5245 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5246 <div style="float:right;">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5247 <input id="outpop_cancel" type="button" value="Cancel" />
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5248 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5249 <div style="clear:both;"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5250 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5251 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5252 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5253 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5254 `;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5255 document.getElementById(id).insertAdjacentHTML('beforeend', html);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5256 $("logo_form").action = site_url + "/utilities/generate_logo";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5257 } // make_submit_or_download_motif_form
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5258
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5259 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5260 // Functions to update the submit_or_download_motif form.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5261 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5262
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5263 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5264 // Initialise and display the download popup.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5265 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5266 function action_show_outpop(e, ordinal) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5267 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5268 function init() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5269 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5270 var close_btn, next_btn, prev_btn, cancel_btn, do_btn;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5271 var tab1, tab2, tab3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5272 var pnl1, pnl2, pnl3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5273 var format_list;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5274 var tbl_submit, inputs, i, default_prog;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5275 close_btn = $("outpop_close");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5276 close_btn.addEventListener("click", action_hide_outpop, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5277 close_btn.addEventListener("keydown", action_hide_outpop, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5278 next_btn = $("outpop_next");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5279 next_btn.addEventListener("click", action_outpop_next, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5280 next_btn.addEventListener("keydown", action_outpop_next, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5281 prev_btn = $("outpop_prev");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5282 prev_btn.addEventListener("click", action_outpop_prev, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5283 prev_btn.addEventListener("keydown", action_outpop_prev, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5284 cancel_btn = $("outpop_cancel");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5285 cancel_btn.addEventListener("click", action_hide_outpop, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5286 do_btn = $("outpop_do");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5287 do_btn.addEventListener("click", action_outpop_submit, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5288 tab1 = $("outpop_tab_1");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5289 tab1.tabIndex = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5290 tab1.addEventListener("click", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5291 tab1.addEventListener("keydown", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5292 tab2 = $("outpop_tab_2");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5293 tab2.tabIndex = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5294 tab2.addEventListener("click", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5295 tab2.addEventListener("keydown", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5296 tab3 = $("outpop_tab_3");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5297 tab3.tabIndex = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5298 tab3.addEventListener("click", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5299 tab3.addEventListener("keydown", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5300 pnl1 = $("outpop_pnl_1");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5301 pnl2 = $("outpop_pnl_2");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5302 pnl3 = $("outpop_pnl_3");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5303 toggle_class(tab1, "activeTab", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5304 toggle_class(tab2, "activeTab", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5305 toggle_class(tab3, "activeTab", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5306 pnl1.style.display = "block";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5307 pnl2.style.display = "none";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5308 pnl3.style.display = "none";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5309 format_list = $("text_format");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5310 format_list.addEventListener("change", action_outpop_format, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5311 // setup program selection
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5312 tbl_submit = $("programs");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5313 // when not dna, hide the inputs for programs that require dna motifs
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5314 toggle_class(tbl_submit, "alphabet_dna", current_alphabet.has_complement());//TODO alphabet_dna is a bad name for a field when allowing custom alphabets
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5315 // add a click listener for the radio buttons
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5316 inputs = tbl_submit.querySelectorAll("input[type='radio']");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5317 for (i = 0; i < inputs.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5318 inputs[i].addEventListener("click", action_outpop_program, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5319 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5320 // ensure that a default program option is selected for DNA and Protein
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5321 default_prog = document.getElementById(current_alphabet.has_complement() ? "submit_tomtom" : "submit_fimo"); //TODO Tomtom might require a more strict definition of DNA
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5322 default_prog.checked = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5323 action_outpop_program.call(default_prog);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5324 // disable reverse-complement when not DNA
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5325 $("logo_rc_option").disabled = !current_alphabet.has_complement();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5326 // set errorbars on when ssc is on
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5327 $("logo_ssc").addEventListener("change", action_outpop_ssc, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5328 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5329 // store the focused element
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5330 action_hide_outpop.last_active = document.activeElement;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5331 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5332 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5333 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5334 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5335 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5336 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5337 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5338 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5339 // hide the help popup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5340 help_popup();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5341 // on first load initilize the popup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5342 if (!action_show_outpop.ready) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5343 init();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5344 action_show_outpop.ready = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5345 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5346 update_outpop_motif(ordinal - 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5347 // display the download popup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5348 $("grey_out_page").style.display = "block";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5349 $("download").style.display = "block";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5350 $("outpop_close").focus();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5351 } // action_show_output
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5352
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5353 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5354 // Hide the submit or download popup.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5355 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5356 function action_hide_outpop(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5357 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5358 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5359 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5360 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5361 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5362 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5363 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5364 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5365 $("download").style.display = "none";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5366 $("grey_out_page").style.display = "none";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5367 if (typeof action_hide_outpop.last_active !== "undefined") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5368 action_hide_outpop.last_active.focus();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5369 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5370 } // action_hide_outpop
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5371
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5372 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5373 * Show the next motif in the download popup.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5374 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5375 function action_outpop_next(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5376 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5377 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5378 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5379 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5380 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5381 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5382 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5383 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5384 update_outpop_motif(current_motif + 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5385 } // action_outpop_next
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5386
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5387 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5388 * Show the previous motif in the download popup.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5389 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5390 function action_outpop_prev(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5391 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5392 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5393 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5394 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5395 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5396 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5397 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5398 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5399 update_outpop_motif(current_motif - 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5400 } // action_outpop_prev
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5401
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5402 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5403 * Highlight the selected row in the program list.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5404 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5405 function action_outpop_program() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5406 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5407 var table, tr, rows, i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5408 tr = find_parent_tag(this, "TR");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5409 table = find_parent_tag(tr, "TABLE");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5410 rows = table.querySelectorAll("tr");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5411 for (i = 0; i < rows.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5412 toggle_class(rows[i], "selected", rows[i] === tr);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5413 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5414 } // action_outpop_program
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5415
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5416 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5417 * Submit the motif to the selected program.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5418 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5419 function action_outpop_submit(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5420 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5421 var form, input, program, motifs;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5422 // find out which program is selected
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5423 var radios, i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5424 radios = document.getElementsByName("program");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5425 program = "fimo"; // default to fimo, since it works with all alphabet types
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5426 for (i = 0; i < radios.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5427 if (radios[i].checked) program = radios[i].value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5428 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5429
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5430 motifs = motif_minimal_meme(data.motifs[current_motif]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5431 form = document.createElement("form");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5432 form.setAttribute("method", "post");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5433 form.setAttribute("action", site_url + "/tools/" + program);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5434
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5435 input = document.createElement("input");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5436 input.setAttribute("type", "hidden");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5437 input.setAttribute("name", "motifs_embed");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5438 input.setAttribute("value", motifs);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5439 form.appendChild(input);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5440
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5441 var current_file = location.pathname.substring(location.pathname.lastIndexOf('/')+1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5442 input = document.createElement("input");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5443 input.setAttribute("type", "hidden");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5444 input.setAttribute("name", "motifs_name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5445 input.setAttribute("value", "motif number " + (current_motif+1) + " from " + current_file);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5446 form.appendChild(input);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5447
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5448 document.body.appendChild(form);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5449 form.submit();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5450 document.body.removeChild(form);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5451 } // action_outpop_submit(e)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5452
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5453 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5454 * Enable error bars when small sample correction is enabled.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5455 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5456 function action_outpop_ssc() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5457 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5458 $("logo_err").value = $("logo_ssc").value;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5459 } // action_outpop_ssc
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5460
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5461 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5462 // Update the motif logos and format download text in the popup.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5463 // This is called whenever the current motif changes.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5464 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5465 function update_outpop_motif(index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5466 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5467 var motifs, motif, pspm, logo, canvas, num;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5468 motifs = data["motifs"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5469 if (index < 0 || index >= motifs.length) {return;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5470 current_motif = index;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5471 motif = motifs[index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5472 pspm = new Pspm(motif["pwm"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5473 logo = new Logo(current_alphabet, "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5474 logo.add_pspm(pspm, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5475 canvas = $("outpop_logo");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5476 canvas.width = canvas.width; // clear canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5477 draw_logo_on_canvas(logo, canvas, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5478 canvas = $("outpop_logo_rc");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5479 canvas.width = canvas.width; // clear rc canvas
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5480 if (data.options.strands === "both" || data.options.revcomp) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5481 pspm.reverse_complement(current_alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5482 logo = new Logo(current_alphabet, "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5483 logo.add_pspm(pspm, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5484 draw_logo_on_canvas(logo, canvas, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5485 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5486 num = $("outpop_num");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5487 num.innerHTML = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5488 num.appendChild(document.createTextNode("" + (index + 1)));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5489 update_outpop_format(index);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5490 } // action_outpop_motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5491
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5492 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5493 // Create the download menu.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5494 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5495 function update_outpop_format(index) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5496 var motif = data.motifs[index];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5497 var fn = [motif_count_matrix, motif_prob_matrix, motif_minimal_meme, motif_fasta, motif_raw];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5498 var suffix = ["_counts.txt", "_freqs.txt", ".meme", "_fasta.txt", "_raw.txt"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5499 var format = parseInt($("text_format").value);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5500 var text = fn[format](motif);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5501 prepare_download(text, "text/plain", motif.id + suffix[format], $("outpop_text_dl"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5502 $("outpop_text").value = text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5503 } // update_outpop_format
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5504
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5505 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5506 * Update the text in the download format popup.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5507 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5508 function action_outpop_format() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5509 update_outpop_format(current_motif);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5510 } // action_outpop_format
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5511
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5512 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5513 * Download the format text.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5514 * Wire the link containing the data URI text to a download button so it looks
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5515 * the same as the server submit stuff.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5516 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5517 function action_outpop_download_motif(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5518 $("outpop_text_dl").click();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5519 } // action_outpop_download_motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5520
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5521 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5522 * Download the motif logo.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5523 * The EPS format can be calculated locally in Javascript
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5524 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5525 function action_outpop_download_logo(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5526 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5527 var motif = data.motifs[current_motif];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5528 if ($("logo_format").value === "0") { // EPS
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5529 var pspm, logo, eps;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5530 var logo_rc, logo_ssc, logo_width, logo_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5531 logo_rc = ($("logo_rc").value === "1");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5532 logo_ssc = ($("logo_ssc").value === "1");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5533 logo_width = parseFloat($("logo_width").value);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5534 if (isNaN(logo_width) || !isFinite(logo_width) || logo_width <= 0) logo_width = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5535 logo_height = parseFloat($("logo_height").value);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5536 if (isNaN(logo_height) || !isFinite(logo_height) || logo_height <= 0) logo_height = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5537 // create a PSPM from the motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5538 pspm = motif_pspm(motif);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5539 if (logo_rc) pspm.reverse_complement(current_alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5540 logo = new Logo(current_alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5541 logo.add_pspm(pspm, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5542 eps = logo.as_eps({"ssc": logo_ssc, "logo_width": logo_width, "logo_height": logo_height});
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5543 prepare_download(eps, "application/postscript", motif.id + (logo_rc ? "_rc" : "") + ".eps");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5544 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5545 $("logo_motifs").value = motif_minimal_meme(motif);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5546 $("logo_id1").value = motif.id;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5547 $("logo_form").submit();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5548 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5549 } // action_outpop_download_logo
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5550
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5551 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5552 * Change the selected tab in the download popup.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5553 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5554 function action_outpop_tab(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5555 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5556 var tab1, tab2, tab3, pnl1, pnl2, pnl3, do_btn;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5557 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5558 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5559 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5560 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5561 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5562 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5563 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5564 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5565 tab1 = $("outpop_tab_1");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5566 tab2 = $("outpop_tab_2");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5567 tab3 = $("outpop_tab_3");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5568 pnl1 = $("outpop_pnl_1");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5569 pnl2 = $("outpop_pnl_2");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5570 pnl3 = $("outpop_pnl_3");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5571 do_btn = $("outpop_do");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5572
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5573 toggle_class(tab1, "activeTab", (this === tab1));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5574 toggle_class(tab2, "activeTab", (this === tab2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5575 toggle_class(tab3, "activeTab", (this === tab3));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5576 pnl1.style.display = ((this === tab1) ? "block" : "none");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5577 pnl2.style.display = ((this === tab2) ? "block" : "none");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5578 pnl3.style.display = ((this === tab3) ? "block" : "none");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5579 do_btn.value = ((this === tab1) ? "Submit" : "Download");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5580 do_btn.removeEventListener("click", action_outpop_submit, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5581 do_btn.removeEventListener("click", action_outpop_download_logo, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5582 do_btn.removeEventListener("click", action_outpop_download_motif, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5583 if (this === tab1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5584 do_btn.addEventListener("click", action_outpop_submit, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5585 } else if (this === tab2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5586 do_btn.addEventListener("click", action_outpop_download_motif, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5587 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5588 do_btn.addEventListener("click", action_outpop_download_logo, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5589 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5590 } // action_outpop_tab
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5591
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5592 function motif_fasta(motif) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5593 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5594 var sites, site, seq, sequences, sequence, i, num, counter, out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5595 counter = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5596 sequences = data["sequence_db"]["sequences"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5597 sites = motif["sites"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5598 out = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5599 for (i = 0; i < sites.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5600 site = sites[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5601 seq = site["seq"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5602 sequence = sequences[seq];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5603 counter[seq] = (num = counter[seq]) ? (++num) : (num = 1); // inc counter
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5604 if (i !== 0) {out += "\n";}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5605 out += ">" + sequence["name"] + "_site_" + num + " offset= " + site["pos"] +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5606 (site["rc"] ? " RC\n" : "\n");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5607 out += site["match"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5608 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5609 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5610 } // motif_fasta
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5611
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5612 function motif_raw(motif) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5613 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5614 var sites, i, out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5615 sites = motif["sites"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5616 out = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5617 for (i = 0; i < sites.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5618 if (i !== 0) {out += "\n";}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5619 out += sites[i]["match"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5620 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5621 return out;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5622 } // motif_raw
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5623
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5624 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5625 * Create a pspm for the given motif data
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5626 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5627 function motif_pspm(motif) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5628 var pwm = motif.pwm;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5629 var name = motif.id;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5630 var ltrim = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5631 var rtrim = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5632 var nsites = motif.nsites;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5633 var sig = (current_program === "STREME" ? motif.test_pvalue : motif.evalue);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5634 return new Pspm(pwm, name, ltrim, rtrim, nsites, sig, null, motif.alt, current_program);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5635 } // motif_pspm
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5636
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5637 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5638 * Create a count matrix from the given motif data
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5639 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5640 function motif_count_matrix(motif) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5641 return motif_pspm(motif).as_count_matrix();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5642 } // motif_count_matrix
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5643
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5644 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5645 * Create a probablity matrix from the given motif data
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5646 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5647 function motif_prob_matrix(motif) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5648 return motif_pspm(motif).as_probability_matrix();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5649 } // motif_prob_matrix
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5650
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5651 function motif_minimal_meme(motif) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5652 var strands;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5653 if (current_program === "STREME") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5654 strands = (data.options.strands === "both" ? 2 : 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5655 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5656 strands = (data.options.revcomp ? 2 : 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5657 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5658 return motif_pspm(motif).as_meme({
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5659 "with_header": true,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5660 "with_pspm": true,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5661 "with_pssm": (current_program === "MEME" ? true : false),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5662 "version": data["version"],
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5663 "alphabet": current_alphabet,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5664 "strands": strands
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5665 });
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5666 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5667 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5668 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5669 var current_program = "MEME";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5670 var current_alphabet = new Alphabet(data.alphabet, data.background.freqs);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5671 var current_motif = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5672 //var new_icon_src = "data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABwAAAAQCAMAAAAyEe/dAAAACVBMVEX//wAAAAD////s2cV/AAAAdUlEQVQYlXVRBxLAIAhL+P+jC2HZhXcBZEWEldDsZcLIcAhHWWnK8SDcWQhMFUHdAQ1CqQ5+CWPmlHojl+nCJNRtzu4qRc3IUzmTVpXYK0nox0z0PI1stgchdK7lEv7ekhvalw8WW547Gyzedt/2/gLx8WXjXF/1AYFriNAWAAAAAElFTkSuQmCC";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5673
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5674 var DelayLogoTask = function(logo, canvas) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5675 this.logo = logo;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5676 this.canvas = canvas;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5677 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5678
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5679 DelayLogoTask.prototype.run = function () {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5680 draw_logo_on_canvas(this.logo, this.canvas, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5681 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5682
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5683 function clone_template(template) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5684 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5685 var node, help_btns, i, button;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5686 node = $(template).cloneNode(true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5687 toggle_class(node, "template", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5688 node.id = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5689 help_btns = node.querySelectorAll(".help");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5690 for (i = 0; i < help_btns.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5691 button = help_btns[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5692 if (button.hasAttribute("data-topic")) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5693 button.tabIndex = "0";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5694 button.addEventListener("click", __toggle_help, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5695 button.addEventListener("keydown", __toggle_help, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5696 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5697 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5698 return node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5699 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5700
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5701 function make_small_logo(alphabet, pspm, options) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5702 if (typeof options === "undefined") options = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5703 if (options.rc) pspm = pspm.copy().reverse_complement(alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5704 var logo = new Logo(alphabet, {x_axis: false, y_axis: false});
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5705 logo.add_pspm(pspm, (typeof options.offset === "number" ? options.offset : 0));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5706 var canvas = document.createElement('canvas');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5707 if (typeof options.className === "string") canvas.className = options.className;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5708 if (typeof options.width === "number" && options.width > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5709 canvas.height = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5710 canvas.width = options.width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5711 draw_logo_on_canvas(logo, canvas, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5712 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5713 draw_logo_on_canvas(logo, canvas, false, 1/3);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5714 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5715 return canvas;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5716 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5717
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5718 function make_large_logo(alphabet, pspm, rc, offset, className) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5719 if (rc) pspm = pspm.copy().reverse_complement(alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5720 var logo = new Logo(alphabet, "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5721 logo.add_pspm(pspm, offset);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5722 var canvas = document.createElement('canvas');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5723 canvas.height = 200;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5724 canvas.width = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5725 canvas.className = className;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5726 size_logo_on_canvas(logo, canvas, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5727 add_draw_task(canvas, new DelayLogoTask(logo, canvas));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5728 return canvas;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5729 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5730
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5731 function make_sym_btn(symbol, title, action) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5732 var box;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5733 box = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5734 box.tabIndex = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5735 box.className = "sym_btn";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5736 box.appendChild(document.createTextNode(symbol));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5737 box.title = title;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5738 box.addEventListener('click', action, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5739 box.addEventListener('keydown', action, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5740 return box;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5741 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5742
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5743 function make_seq(alphabet, seq) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5744 var i, j, letter, lbox, sbox;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5745 sbox = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5746 for (i = 0; i < seq.length; i = j) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5747 letter = seq.charAt(i);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5748 for (j = i+1; j < seq.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5749 if (seq.charAt(j) !== letter) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5750 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5751 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5752 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5753 lbox = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5754 lbox.style.color = alphabet.get_colour(alphabet.get_index(letter));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5755 lbox.appendChild(document.createTextNode(seq.substring(i, j)));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5756 sbox.appendChild(lbox);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5757 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5758 return sbox;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5759 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5760
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5761 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5762 // make_pv_text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5763 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5764 // Returns the string p-value, with the p italicised.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5765 ///
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5766 function make_pv_text() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5767 var pv_text = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5768 var pv_italic_text = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5769 pv_italic_text.appendChild(document.createTextNode("p"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5770 pv_italic_text.style.fontStyle = "italic";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5771 pv_text.appendChild(pv_italic_text);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5772 pv_text.appendChild(document.createTextNode("-value"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5773 return pv_text;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5774 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5775
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5776 function append_site_entries(tbody, motif, site_index, count) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5777 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5778 var i, end;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5779 var sites, site, sequences, sequence;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5780 var rbody;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5781 if (typeof count !== "number") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5782 count = 20;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5783 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5784 sequences = data["sequence_db"]["sequences"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5785 sites = motif["sites"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5786 end = Math.min(site_index + count, sites.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5787 for (i = site_index; i < end; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5788 site = sites[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5789 sequence = sequences[site["seq"]];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5790
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5791 rbody = tbody.insertRow(tbody.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5792 add_text_cell(rbody, "" + (site["seq"] + 1) + ".", "site_num");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5793 add_text_cell(rbody, sequence["name"], "site_name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5794 add_text_cell(rbody, site["rc"] ? "-" : "+", "site_strand");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5795 add_text_cell(rbody, site["pos"] + 1, "site_start");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5796 add_text_cell(rbody, site["pvalue"].toExponential(2), "site_pvalue");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5797 add_text_cell(rbody, site["lflank"], "site lflank");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5798 add_cell(rbody, make_seq(current_alphabet, site["match"]), "site match");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5799 add_text_cell(rbody, site["rflank"], "site rflank");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5800 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5801 return i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5802 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5803
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5804 function make_site_entries() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5805 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5806 var region;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5807 region = this;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5808 if (region.data_site_index >= region.data_motif["sites"].length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5809 // all sites created
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5810 region.removeEventListener('scroll', make_site_entries, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5811 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5812 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5813 // if there's still 100 pixels to scroll than don't do anything yet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5814 if (region.scrollHeight - (region.scrollTop + region.offsetHeight) > 100) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5815 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5816 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5817
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5818 region.data_site_index = append_site_entries(
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5819 find_child(region, "sites_tbl").tBodies[0],
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5820 region.data_motif, region.data_site_index, 20
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5821 );
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5822 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5823
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5824 function make_sites(motif) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5825 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5826 function add_site_header(row, title, nopad, help_topic, tag_class) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5827 var div, divcp, th;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5828 th = document.createElement("th");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5829 div = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5830 div.className = "sites_th_inner";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5831 if (typeof title !== "object") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5832 title = document.createTextNode("" + title);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5833 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5834 div.appendChild(title);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5835 if (help_topic) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5836 div.appendChild(document.createTextNode("\xA0"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5837 div.appendChild(help_button(help_topic));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5838 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5839 divcp = div.cloneNode(true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5840 divcp.className = "sites_th_hidden";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5841 th.appendChild(div);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5842 th.appendChild(divcp);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5843 if (nopad) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5844 th.className = "nopad";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5845 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5846 if (tag_class) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5847 th.className += " " + tag_class;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5848 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5849 row.appendChild(th);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5850 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5851 var outer_tbl, inner_tbl, tbl, thead, tbody, rhead;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5852
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5853 outer_tbl = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5854 outer_tbl.className = "sites_outer";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5855
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5856 inner_tbl = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5857 inner_tbl.className = "sites_inner";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5858 outer_tbl.appendChild(inner_tbl);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5859
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5860 tbl = document.createElement("table");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5861 tbl.className = "sites_tbl";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5862 inner_tbl.appendChild(tbl);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5863
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5864 thead = document.createElement("thead");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5865 tbl.appendChild(thead);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5866 tbody = document.createElement("tbody");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5867 tbl.appendChild(tbody);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5868
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5869 rhead = thead.insertRow(thead.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5870 add_site_header(rhead, "", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5871 add_site_header(rhead, "Name", false, "pop_seq_name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5872 add_site_header(rhead, "Strand", false, "pop_site_strand", "site_strand_title");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5873 add_site_header(rhead, "Start", false, "pop_site_start");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5874 add_site_header(rhead, make_pv_text(), false, "pop_site_pvalue");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5875 add_site_header(rhead, "", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5876 add_site_header(rhead, "Sites", true, "pop_site_match");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5877 add_site_header(rhead, "", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5878
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5879 inner_tbl.data_motif = motif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5880 inner_tbl.data_site_index = append_site_entries(tbody, motif, 0, 20);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5881 if (inner_tbl.data_site_index < motif["sites"].length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5882 inner_tbl.addEventListener('scroll', make_site_entries, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5883 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5884 return outer_tbl;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5885 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5886
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5887 function make_motif_table_entry(row, alphabet, ordinal, motif, colw) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5888 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5889 function ev_sig(evalue_str) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5890 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5891 var ev_re, match, sig, exp, num;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5892 ev_re = /^(.*)e(.*)$/;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5893 if (match = ev_re.exec(evalue_str)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5894 sig = parseFloat(match[1]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5895 exp = parseInt(match[2]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5896 if (exp >= 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5897 return false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5898 } else if (exp <= -3) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5899 return true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5900 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5901 return sig * Math.pow(10, exp) <= 0.05;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5902 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5903 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5904 return true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5905 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5906 function make_preview(alphabet, motif) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5907 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5908 var pspm, preview, preview_rc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5909 var box, btn_box, logo_box, btn_plus, btn_minus;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5910 if (motif["preview_logo"]) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5911 preview = motif["preview_logo"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5912 preview_rc = motif["preview_logo_rc"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5913 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5914 pspm = new Pspm(motif["pwm"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5915 preview = make_logo(alphabet, pspm, 50, false, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5916 motif["preview_logo"] = preview;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5917 if (alphabet.has_complement()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5918 preview_rc = make_logo(alphabet, pspm, 50, true, 0, "logo_rc");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5919 motif["preview_logo_rc"] = preview_rc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5920 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5921 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5922 if (preview_rc) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5923 btn_plus = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5924 btn_plus.appendChild(document.createTextNode("+"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5925 btn_plus.className = "preview_btn plus";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5926 btn_plus.tabIndex = "0";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5927 btn_plus.addEventListener("click", action_btn_rc, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5928 btn_plus.addEventListener("keydown", action_btn_rc, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5929 btn_minus = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5930 btn_minus.appendChild(document.createTextNode("-"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5931 btn_minus.className = "preview_btn minus";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5932 btn_minus.tabIndex = "0";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5933 btn_minus.addEventListener("click", action_btn_rc, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5934 btn_minus.addEventListener("keydown", action_btn_rc, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5935 btn_box = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5936 btn_box.className = "preview_btn_box";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5937 btn_box.appendChild(btn_plus);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5938 btn_box.appendChild(btn_minus);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5939 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5940 logo_box = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5941 logo_box.className = "preview_logo_box";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5942 logo_box.appendChild(preview);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5943 if (preview_rc) logo_box.appendChild(preview_rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5944 box = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5945 box.className = "preview_box";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5946 if (preview_rc) box.appendChild(btn_box);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5947 box.appendChild(logo_box);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5948 if (preview_rc) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5949 if (motif["rc"]) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5950 btn_minus.className += " active";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5951 logo_box.className += " show_rc_logo";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5952 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5953 btn_plus.className += " active";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5954 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5955 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5956 return box;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5957 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5958 var pspm, preview, preview_rc, c;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5959 row.data_motif = motif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5960 row.id = motif["alt"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5961 row.data_ordinal = ordinal;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5962 if (!ev_sig(motif["evalue"])) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5963 row.style.opacity = 0.4;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5964 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5965 add_text_cell(row, "" + ordinal + ".", "motif_ordinal");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5966 add_cell(row, make_preview(alphabet, motif), "motif_logo");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5967 add_text_cell(row, motif["evalue"], "motif_evalue");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5968 add_text_cell(row, motif["nsites"], "motif_nsites");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5969 add_text_cell(row, motif["len"], "motif_width");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5970 add_cell(row, make_sym_btn("\u21A7", "Show more information.",
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5971 action_show_more), "motif_more");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5972 add_cell(row, make_sym_btn("\u21E2", "Submit the motif to another MEME Suite program or download it.", function(e) { action_show_outpop(e, ordinal); }), "motif_submit");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5973 if (colw) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5974 for (c = 0; c < row.cells.length; c++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5975 row.cells[c].style.minWidth = colw[c] + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5976 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5977 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5978 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5979
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5980 function make_motifs_table(alphabet, start_ordinal, motifs, colw, stop_reason) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5981 var i, j;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5982 var tbl, thead, tbody, tfoot, row, preview;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5983 var motif, pspm;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5984
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5985 tbl = document.createElement("table");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5986
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5987 thead = document.createElement("thead");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5988 tbl.appendChild(thead);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5989 tbody = document.createElement("tbody");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5990 tbl.appendChild(tbody);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5991 tfoot = document.createElement("tfoot");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5992 tbl.appendChild(tfoot);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5993
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5994 row = thead.insertRow(thead.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5995 add_text_header_cell(row, "", "", "motif_ordinal");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5996 add_text_header_cell(row, "Logo", "pop_logo", "motif_logo");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5997 add_text_header_cell(row, "E-value", "pop_ev", "motif_evalue");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5998 add_text_header_cell(row, "Sites", "pop_sites", "motif_nsites");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
5999 add_text_header_cell(row, "Width", "pop_width", "motif_width");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6000 add_text_header_cell(row, "More", "pop_more", "motif_more");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6001 add_text_header_cell(row, "Submit/Download", "pop_submit_dl", "motif_submit");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6002
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6003 for (i = 0; i < motifs.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6004 row = tbody.insertRow(tbody.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6005 make_motif_table_entry(row, alphabet, start_ordinal + i, motifs[i], colw);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6006 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6007
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6008 row = tfoot.insertRow(tfoot.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6009 add_text_header_cell(row, stop_reason, "", "stop_reason", "", 6);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6010
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6011 return tbl;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6012 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6013
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6014 function make_expanded_motif(alphabet, ordinal, motif, less_x, submit_x) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6015 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6016 var box, pspm, logo_box, large_logo, large_logo_rc, tab_logo, tab_logo_rc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6017 var btn, offset, norc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6018
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6019 box = clone_template("tmpl_motif_expanded");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6020 box.data_motif = motif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6021 box.data_ordinal = ordinal;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6022
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6023 pspm = new Pspm(motif["pwm"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6024 if (typeof motif["rc"] !== "boolean") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6025 motif["rc"] = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6026 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6027 if (motif["large_logo"]) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6028 large_logo = motif["large_logo"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6029 large_logo_rc = motif["large_logo_rc"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6030 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6031 large_logo = make_large_logo(alphabet, pspm, false, 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6032 motif["large_logo"] = large_logo;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6033 if (alphabet.has_complement()) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6034 large_logo_rc = make_large_logo(alphabet, pspm, true, 0, "logo_rc");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6035 motif["large_logo_rc"] = large_logo_rc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6036 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6037 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6038 norc = (large_logo_rc == null);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6039 toggle_class(box, "norc", norc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6040
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6041 logo_box = find_child(box, "tvar_logo");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6042 logo_box.appendChild(large_logo);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6043 if (large_logo_rc) logo_box.appendChild(large_logo_rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6044 toggle_class(logo_box, "show_rc_logo", motif["rc"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6045
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6046 tab_logo = find_child(box, "tvar_tab");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6047 tab_logo_rc = find_child(box, "tvar_tab_rc");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6048
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6049 toggle_class(tab_logo, "activeTab", !motif["rc"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6050 toggle_class(tab_logo_rc, "activeTab", motif["rc"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6051
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6052 tab_logo.addEventListener('click', action_rc_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6053 tab_logo.addEventListener('keydown', action_rc_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6054 tab_logo_rc.addEventListener('click', action_rc_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6055 tab_logo_rc.addEventListener('keydown', action_rc_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6056
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6057 set_tvar(box, "tvar_ordinal", ordinal);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6058 set_tvar(box, "tvar_evalue", motif["evalue"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6059 set_tvar(box, "tvar_width", motif["len"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6060 set_tvar(box, "tvar_site_count", motif["nsites"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6061 set_tvar(box, "tvar_llr", motif["llr"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6062 set_tvar(box, "tvar_ic", motif["ic"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6063 set_tvar(box, "tvar_re", motif["re"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6064 set_tvar(box, "tvar_bt", motif["bt"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6065 if (data.sequence_db.primary_count > data.options.brief) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6066 if (data.options.brief == 1000) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6067 set_tvar(box, "tvar_sites", "Output of sites suppressed because there were more than 1000 (primary) sequences.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6068 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6069 set_tvar(box, "tvar_sites", "Output of sites suppressed by -brief option.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6070 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6071 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6072 set_tvar(box, "tvar_sites", make_sites(motif));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6073 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6074
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6075 offset = 32; // 1* 5px padding + 2 * 10px padding + 2 * 2px border + 3px ??
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6076
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6077 btn = find_child(box, "tvar_less");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6078 btn.style.left = (less_x - offset) + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6079 btn.addEventListener('click', action_show_less, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6080 btn.addEventListener('keydown', action_show_less, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6081 btn = find_child(box, "tvar_submit");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6082 btn.style.left = (submit_x - offset) + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6083 btn.addEventListener('click', action_show_outpop, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6084 btn.addEventListener('keydown', action_show_outpop, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6085 return box;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6086 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6087
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6088 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6089 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6090 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6091 function make_motifs() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6092 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6093 function pixel_value(str_in) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6094 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6095 var px_re, match;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6096 px_re = /^(\d+)px$/;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6097 if (match = px_re.exec(str_in)) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6098 return parseInt(match[1], 10);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6099 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6100 return 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6101 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6102 var container, tbl;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6103 var colw, r, row, c, cell, cell_style, pad_left, pad_right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6104
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6105 // make the motifs table
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6106 container = $("motifs");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6107 container.innerHTML = ""; // clear content
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6108
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6109 tbl = make_motifs_table(current_alphabet, 1, data["motifs"], colw, data["stop_reason"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6110 container.appendChild(tbl);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6111
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6112 // measure table column widths
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6113 colw = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6114 row = tbl.tBodies[0].rows[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6115 for (c = 0; c < row.cells.length; c++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6116 var padLeft, padRight;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6117 cell = row.cells[c];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6118 cell_style = window.getComputedStyle(cell, null);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6119 pad_left = pixel_value(cell_style.getPropertyValue("padding-left"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6120 pad_right = pixel_value(cell_style.getPropertyValue("padding-right"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6121 colw[c] = cell.clientWidth - pad_left - pad_right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6122 if (typeof colw[c] !== "number" || colw[c] < 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6123 colw[c] = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6124 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6125 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6126
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6127 // set minimum table column widths on each row so later when we remove rows it still aligns
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6128 for (r = 0; r < tbl.tBodies[0].rows.length; r++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6129 row = tbl.tBodies[0].rows[r];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6130 for (c = 0; c < row.cells.length; c++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6131 row.cells[c].style.minWidth = colw[c] + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6132 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6133 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6134
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6135 // store the table column widths so we can create rows latter with the same minimums
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6136 container.data_colw = colw;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6137
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6138 // calculate the x offset for the buttons
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6139 row = tbl.tBodies[0].rows[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6140 container.data_more_x = coords(find_child(find_child(row, "motif_more"), "sym_btn"))[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6141 container.data_submit_x = coords(find_child(find_child(row, "motif_submit"), "sym_btn"))[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6142
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6143 draw_on_screen();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6144 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6145
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6146 function make_meme_block(container, max_seq_len, is_scan, site) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6147 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6148 var motif = data.motifs[site.motif];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6149 var block = make_block(container, max_seq_len, site.pos, motif.len,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6150 site.pvalue, site.rc, site.motif, is_scan);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6151 var handler = (is_scan ?
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6152 make_scan_popup(site, motif, block) :
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6153 make_block_popup(site, motif, block));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6154 block.addEventListener("mouseover", handler, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6155 block.addEventListener("mouseout", handler, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6156 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6157
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6158 function append_blocks_entries(tbody, seq_index, count) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6159 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6160 var i, end, j;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6161 var max_pvalue, max_block_height, max_seq_len, sequences;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6162 var sequence, sites, scans, scan;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6163 var container, plus, minus, rule, row;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6164 // define some constants
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6165 max_seq_len = data.sequence_db.max_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6166 // determine how many to load
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6167 end = Math.min(seq_index + count, data.sequence_db.sequences.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6168 for (i = seq_index; i < end; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6169 // get the sequence
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6170 sequence = data.sequence_db.sequences[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6171 // make the containers for the block diagram
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6172 container = make_block_container(current_alphabet.has_complement(),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6173 data.options.revcomp, max_seq_len, sequence.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6174 // create blocks for the motif sites
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6175 sites = sequence["sites"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6176 for (j = 0; j < sites.length; j++)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6177 make_meme_block(container, max_seq_len, false, sites[j]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6178 // create blocks for the scanned sites
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6179 scan = data.scan[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6180 for (j = 0; j < scan.sites.length; j++)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6181 make_meme_block(container, max_seq_len, true, scan.sites[j]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6182 // create a row for the sequence
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6183 row = tbody.insertRow(tbody.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6184 toggle_class(row, "empty_seq", sites.length == 0 && scan.sites.length == 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6185 toggle_class(row, "only_scan", sites.length == 0 && scan.sites.length > 0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6186 add_text_cell(row, (i + 1) + ".", "blockdiag_num");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6187 add_text_cell(row, sequence["name"], "blockdiag_name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6188 add_text_cell(row, scan["pvalue"].toExponential(2), "blockdiag_pvalue");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6189 add_cell(row, container, "block_td");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6190 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6191 return end;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6192 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6193
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6194 function make_blocks_entries() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6195 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6196 var region;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6197 region = this;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6198 if (region.data_blocks_index >= data["sequence_db"]["sequences"].length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6199 // all sites created
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6200 region.removeEventListener('scroll', make_blocks_entries, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6201 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6202 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6203 // if there's still 100 pixels to scroll then don't do anything yet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6204 if (region.scrollHeight - (region.scrollTop + region.offsetHeight) > 100) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6205 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6206 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6207
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6208 region.data_blocks_index = append_blocks_entries(
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6209 find_child(region, "blocks_tbl").tBodies[0],
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6210 region.data_blocks_index, 20
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6211 );
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6212 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6213
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6214 // Apply opacity alpha to color rgb with backrgound bkg.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6215 function RGBAtoRGB(rgb, bkg, opacity) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6216 var i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6217 var rgb_new = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6218 for (i=0; i<3; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6219 rgb_new[i] = Math.round(((1-opacity) * bkg[i]) + (opacity * rgb[i]));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6220 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6221 return rgb_new;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6222 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6223
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6224 // Function to measure the size of text on a canvas.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6225 var MeasureText = function(font, text) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6226 var image = document.createElement("canvas");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6227 var image_ctx = image.getContext('2d');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6228 image_ctx.save();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6229 image_ctx.font = font;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6230 var text_length = image_ctx.measureText(text).width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6231 image.remove();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6232 return text_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6233 } // MeasureText
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6234
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6235 // Functions to download the motif block diagram as a PDF or SVG file.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6236 function download_PDF_block_diagram() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6237 downloadBlockDiagram(true, 'bitbucket');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6238 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6239 function download_SVG_block_diagram() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6240 downloadBlockDiagram(false, 'bitbucket');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6241 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6242
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6243 // Helper function to create a script element for downloading javascript.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6244 function createScriptElement(url, file, integrity)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6245 {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6246 console.log('Downloading ' + file + ' from ' + url + '.');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6247 const script = document.createElement('script');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6248 script.setAttribute('src', url + '/' + file);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6249 if (integrity) script.setAttribute('integrity', integrity);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6250 script.setAttribute('crossorigin', 'anonymous');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6251 script.setAttribute('async', '');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6252 document.head.appendChild(script);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6253 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6254
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6255 // Helper function to download the motif block diagram as a PDF or SVG file.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6256 var downloadBlockDiagram = function(
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6257 make_pdf,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6258 next_source
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6259 ) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6260 var script_file, integrity_key;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6261 // Check if necessary javascript has been loaded.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6262 if ( (make_pdf && typeof jsPDF === 'undefined') ||
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6263 (!make_pdf && typeof d3 === 'undefined') ) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6264 if (next_source === 'bitbucket') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6265 if (make_pdf) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6266 script_file = 'jspdf.min.js';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6267 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6268 script_file = 'd3.v5.min.js';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6269 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6270 createScriptElement('https://memesuite.bitbucket.io/javascript', script_file);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6271 // Wait 3 seconds and then try to create the diagram.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6272 setTimeout(downloadBlockDiagram, 3000, make_pdf, 'cloudflare');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6273 } else if (next_source === 'cloudflare') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6274 if (make_pdf) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6275 script_file = 'jspdf/1.5.3/jspdf.min.js';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6276 integrity_key = 'sha512-ToRWKKOvhBSS8EtqSflysM/S7v9bB9V0X3B1+E7xo7XZBEZCPL3VX5SFIp8zxY19r7Sz0svqQVbAOx+QcLQSAQ=='
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6277 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6278 script_file = 'd3/5.16.0/d3.min.js';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6279 integrity_key = 'sha512-FHsFVKQ/T1KWJDGSbrUhTJyS1ph3eRrxI228ND0EGaEp6v4a/vGwPWd3Dtd/+9cI7ccofZvl/wulICEurHN1pg==';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6280 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6281 createScriptElement('https://cdnjs.cloudflare.com/ajax/libs', script_file, integrity_key);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6282 // Wait 3 seconds and then try to create the diagram.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6283 setTimeout(downloadBlockDiagram, 3000, make_pdf, 'none');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6284 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6285 // No more sources for javascript. Call so error message will be shown.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6286 downloadBlockDiagramMain(make_pdf);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6287 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6288 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6289 // Create the diagram.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6290 downloadBlockDiagramMain(make_pdf);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6291 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6292 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6293
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6294 // Main function to download the motif block diagram as a PDF or SVG file.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6295 var downloadBlockDiagramMain= function(
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6296 make_pdf
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6297 ) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6298 // Check that necessary javascript was downloaded.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6299 if ( (make_pdf && typeof jsPDF === 'undefined') ||
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6300 (!make_pdf && typeof d3 === 'undefined') ) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6301 var id = make_pdf ? $("pdfButton") : $("svgButton");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6302 help_popup(id, "pop_offline");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6303 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6304 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6305
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6306 // Determine which lines are visible in the HTML inner scroll window.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6307 var inner_tbl = $("blocks_scroll");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6308 var pix_per_sequence = 27; // (vertical) pixels per sequence diagram line
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6309 var first = Math.round(inner_tbl.scrollTop / pix_per_sequence) + 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6310 var last = first + Math.round(inner_tbl.offsetHeight / pix_per_sequence) - 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6311
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6312 // Get the contents of the HTML inner scroll window while saving the sequences to be printed.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6313 var numbers = document.getElementsByClassName("blockdiag_num");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6314 var bars = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6315 var visible_motifs = {};
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6316 var seq_index = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6317 var rgb;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6318 for (var i=0; i<numbers.length && seq_index < last; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6319 var row_node = numbers[i].parentNode;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6320 // Check if the sequence is displayed in the outer scrolling window.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6321 var seq_name = numbers[i].nextSibling.innerHTML;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6322 if (
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6323 ($("rdo_sites_only").checked && row_node.getAttribute("class").includes("only_scan"))
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6324 ||
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6325 (! $("rdo_all_seqs").checked && row_node.getAttribute("class").includes("empty_seq"))
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6326 ) { continue; }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6327 seq_index++;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6328
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6329 if (seq_index < first) { continue; } // sequence not in HTML inner scrolling window
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6330
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6331 var pvalue = numbers[i].nextSibling.nextSibling.innerHTML;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6332 var far = numbers[i].nextSibling.nextSibling.nextSibling.children[0].children;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6333 var seq_length = data.sequence_db.sequences[i].length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6334
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6335 var seqObj = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6336 seqObj["length"] = seq_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6337 seqObj["pvalue"] = pvalue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6338 seqObj["pn"] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6339 seqObj["width"] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6340 seqObj["left"] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6341 seqObj["height"] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6342 seqObj["color"] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6343 seqObj["opacity"] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6344 for (var x = 0; x < far.length; x++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6345 if ((far[x].getAttribute("style") != null)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6346 && (
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6347 ( $("rdo_sites_only").checked && ! far[x].getAttribute("class").includes("scanned"))
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6348 || ( $("rdo_sites_and_scan").checked || $("rdo_all_seqs").checked )
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6349 )
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6350 ) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6351 if (far[x].getAttribute("style").includes("rgb")) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6352 var compStyles = far[x].style;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6353 // Make scanned sites get displayed first so they will not "cover" regular sites.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6354 var site_pn = far[x].getAttribute("class").includes("top") ? "+" : "-";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6355 var site_width = parseFloat(compStyles.width.slice(0, -1));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6356 var site_left = parseFloat(compStyles.left.slice(0, -1));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6357 var site_height = parseFloat(compStyles.height.slice(0, -2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6358 var site_color = compStyles.backgroundColor.slice(4, -1).replace(/ /g, "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6359 if (far[x].getAttribute("class").includes("scanned")) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6360 seqObj["pn"].unshift(site_pn);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6361 seqObj["width"].unshift(site_width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6362 seqObj["left"].unshift(site_left);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6363 seqObj["height"].unshift(site_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6364 seqObj["color"].unshift(site_color);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6365 seqObj["opacity"].unshift(0.3);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6366 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6367 seqObj["pn"].push(site_pn);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6368 seqObj["width"].push(site_width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6369 seqObj["left"].push(site_left);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6370 seqObj["height"].push(site_height);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6371 seqObj["color"].push(site_color);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6372 seqObj["opacity"].push(1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6373 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6374 visible_motifs[far[x].getAttribute("data-colour-index")] = site_color;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6375 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6376 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6377 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6378 // Save the sequence data if it has motifs (or rdo_all_seqs is checked)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6379 if ($("rdo_all_seqs").checked || seqObj["width"].length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6380 bars[seq_name] = seqObj;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6381 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6382 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6383
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6384 // jsPDF coordinates are always in points.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6385 var font_size = 13;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6386 var nbars = Object.keys(bars).length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6387 var legend_font_size = 0.8 * font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6388
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6389 // Initialize field widths in points by measuring header text.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6390 var font = "bold " + font_size + "pt Helvetica, sans-serif";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6391 var max_name_width = MeasureText(font, "Name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6392 var max_pvalue_width = MeasureText(font, "p-value");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6393
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6394 var max_seq_length = 0; // in characters
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6395 var has_complement = current_alphabet.has_complement();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6396 var revcomp = data.options["revcomp"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6397
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6398 // Measure text of numbers, names and p-values, convert to points and save the max.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6399 font = font_size + "pt Helvetica, sans-serif";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6400 var seq_name;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6401 for (seq_name in bars) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6402 var seq_name_width = MeasureText(font, seq_name);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6403 var pvalue_width = MeasureText(font, pvalue);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6404 var seq_length = bars[seq_name]["length"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6405 if (seq_length > max_seq_length) { max_seq_length = seq_length; }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6406 if (seq_name_width > max_name_width) { max_name_width = seq_name_width; }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6407 if (pvalue_width > max_pvalue_width) { max_pvalue_width = pvalue_width; }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6408 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6409
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6410 // Get the length in characters of the longest visible motif.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6411 var max_motif_length = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6412 var motif_index, motif_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6413 for (motif_index in visible_motifs) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6414 motif_length = data.motifs[motif_index].len;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6415 if (motif_length > max_motif_length) { max_motif_length = motif_length; }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6416 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6417
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6418 // Sort the motif indices.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6419 var motif_indices = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6420 var sorted_motif_indices = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6421 for (motif_index in visible_motifs) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6422 motif_indices.push(Number(motif_index));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6423 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6424 sorted_motif_indices = motif_indices.sort(function(a, b){return a-b;});
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6425
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6426 // Set up values for main section.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6427 var height = (nbars+1) * (2.6*font_size);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6428 var nmotifs = Object.keys(visible_motifs).length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6429 var name_field_width = max_name_width + font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6430 var pvalue_field_width = max_pvalue_width + font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6431 var plus_minus_field_width = has_complement ? 2*font_size : font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6432 var non_diagram_width = name_field_width + pvalue_field_width + plus_minus_field_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6433 var diagram_width = 47 * font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6434 var pix_per_char = diagram_width/max_seq_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6435 var x_scale_factor = data.sequence_db.max_length/100; // Scale factor comes from function make_block().
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6436 var diagram_line_height = (height-2*font_size)/nbars;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6437 var doc_width = diagram_width + non_diagram_width + 2*font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6438 var doc_height = height + 0.5*font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6439
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6440 // Set up values for the legend.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6441 var tmp_font = legend_font_size + "pt Courier, normal";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6442 var courier_width = MeasureText(tmp_font, "A");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6443
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6444 var legend_line_height = 1.2 * legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6445 var index_field_width = 3 * legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6446 var symbol_field_width = 5 * legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6447 var legend_non_consensus_width = index_field_width + symbol_field_width + 3*legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6448 var legend_hdr_font = legend_font_size + "pt Helvetica, sans-serif";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6449 var consensus_hdr_width = MeasureText(legend_hdr_font, "Motif Consensus");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6450 var consensus_field_width = doc_width - legend_non_consensus_width - legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6451 // Get number of characters that will fit in legend consensus field.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6452 var legend_split_length = Math.floor(consensus_field_width/courier_width);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6453 // Get number of lines in legend.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6454 var n_legend_lines = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6455 for (motif_index in visible_motifs) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6456 motif_length = data.motifs[motif_index].len;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6457 n_legend_lines += Math.ceil(motif_length/legend_split_length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6458 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6459 if (n_legend_lines > 0) { n_legend_lines += 3; } // header line + 2*space
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6460 var legend_width = legend_non_consensus_width + Math.min(legend_split_length, max_motif_length)*courier_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6461 var legend_height = n_legend_lines * legend_line_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6462 doc_height += legend_height + 1*font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6463
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6464 if (make_pdf) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6465 // Now create the PDF document.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6466 // This next line is necessary because jsPDF silently swaps width and height.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6467 var orient = doc_width > doc_height ? 'landscape' : 'portrait';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6468 doc = new jsPDF(
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6469 {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6470 orientation: orient,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6471 unit: 'pt',
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6472 format: [doc_width, doc_height]
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6473 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6474 );
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6475
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6476 // Set the font size for the PDF.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6477 doc.setFontSize(1.33*font_size);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6478
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6479 // Create the header.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6480 var offset = font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6481 var liney = 1.5*font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6482 // .. Name hdr ..
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6483 doc.setFont("Helvetica", "bold");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6484 doc.text("Name", offset, liney);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6485 offset += name_field_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6486
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6487 // p-value hdr
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6488 doc.setFont("Helvetica", "bolditalic");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6489 doc.text("p", offset + font_size, liney);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6490 doc.setFont("Helvetica", "bold");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6491 doc.text("-value", offset + 2*font_size, liney);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6492 offset += pvalue_field_width + plus_minus_field_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6493
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6494 // Motif Location hdr
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6495 doc.text("Motif Locations", offset, liney);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6496
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6497 // Generate the data object for the PDF.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6498 liney -= 0.5*font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6499 var dy = font_size/3.5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6500 for (var seq_name in bars) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6501 liney += diagram_line_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6502 offset = font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6503
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6504 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6505 // Generate the text fields.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6506 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6507 doc.setFont("Helvetica", "normal");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6508
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6509 // Sequence name text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6510 doc.text(seq_name, offset, liney + dy);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6511 offset += name_field_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6512
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6513 // p-value text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6514 doc.text(bars[seq_name]["pvalue"], offset + pvalue_field_width, liney + dy, {align: "right"});
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6515 offset += pvalue_field_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6516
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6517 // +/- text (optional)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6518 if (has_complement) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6519 doc.text("+", offset+font_size, liney + dy - font_size/2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6520 if (revcomp) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6521 doc.text("-", offset+1.15*font_size, liney + dy + font_size/2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6522 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6523 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6524 offset += plus_minus_field_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6525
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6526 // Generate the base line.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6527 doc.setLineWidth(0.35);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6528 doc.line(offset, liney, offset + (bars[seq_name]["length"] * pix_per_char), liney);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6529
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6530 // Generate the blocks.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6531 for (var i = 0; i < bars[seq_name]["width"].length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6532 if (bars[seq_name]["pn"][i] == undefined) { continue; }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6533 rgb = bars[seq_name]["color"][i].split(",").map(Number);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6534 var opacity = bars[seq_name]["opacity"][i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6535 if (opacity != 1) { rgb = RGBAtoRGB(rgb, [255,255,255], opacity); }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6536 var bar_x = offset + (bars[seq_name]["left"][i] * x_scale_factor * pix_per_char);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6537 var bar_y = (bars[seq_name]["pn"][i] == "+") ? (liney - 0.1*font_size*bars[seq_name]["height"][i]) : liney;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6538 doc.setFillColor(rgb[0], rgb[1], rgb[2]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6539 doc.rect(bar_x, bar_y, bars[seq_name]["width"][i] * x_scale_factor * pix_per_char, 0.1*font_size*bars[seq_name]["height"][i], 'FD');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6540 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6541 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6542
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6543 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6544 // Generate the legend.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6545 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6546 if (n_legend_lines > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6547 doc.setFontSize(1.33*legend_font_size);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6548 dy = 0.8 * legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6549
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6550 // The legend header.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6551 var legend_top = liney + 2*legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6552 liney += 4.5*legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6553 offset = legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6554 doc.setFont("Helvetica", "bold");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6555 doc.text("Motif", offset, liney);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6556 offset += index_field_width + legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6557 doc.text("Symbol", offset, liney);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6558 offset += symbol_field_width + legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6559 doc.text("Motif Consensus", offset, liney);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6560 liney -= 0.5*legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6561 liney += legend_line_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6562
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6563 for (var i=0; i<motif_indices.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6564 motif_index = sorted_motif_indices[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6565 offset = legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6566
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6567 // Motif Name
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6568 doc.setFont("Helvetica", "normal");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6569 var motif_index_string = (motif_index+1).toString();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6570 motif_index_string = motif_index_string + ".";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6571 var dx = 3 * legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6572 doc.text(motif_index_string, offset+dx, liney+dy, {align: "right"});
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6573 offset += index_field_width + legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6574
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6575 // Motif Symbol
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6576 motif_length = data.motifs[motif_index].len;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6577 rgb = visible_motifs[motif_index].split(",").map(Number);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6578 var bar_x = offset;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6579 var bar_y = liney;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6580 doc.setFillColor(rgb[0], rgb[1], rgb[2]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6581 doc.rect(bar_x, bar_y, symbol_field_width*(motif_length/max_motif_length), legend_font_size, 'FD');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6582 offset += symbol_field_width + legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6583
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6584 // Motif Consensus Sequence
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6585 doc.setFont("Courier", "normal");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6586 var motif_consensus = data.motifs[motif_index].id;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6587 doc.text(motif_consensus, offset, liney+dy, {maxWidth: legend_split_length*courier_width});
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6588 liney += Math.ceil(motif_length/legend_split_length) * legend_line_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6589 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6590
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6591 // Draw box around legend.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6592 doc.rect(
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6593 0.5*legend_font_size,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6594 legend_top + 0.5*legend_font_size,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6595 Math.max(legend_width, legend_non_consensus_width + consensus_hdr_width + courier_width),
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6596 legend_height
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6597 );
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6598 } // legend
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6599
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6600 doc.save('motif_locations.pdf');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6601
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6602 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6603 // Download an SVG document.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6604 var body = d3.select("#blocks").append("svg")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6605 .attr("width", (diagram_width + non_diagram_width) + "pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6606 .attr("height", (doc_height+legend_font_size).toString())
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6607 .attr("background-color", "lightgrey")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6608 .attr("id", "memeSVG")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6609 .attr("xmlns", "http://www.w3.org/2000/svg");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6610
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6611 // Create the header.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6612 var x = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6613 var offset = font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6614 var liney = 1.5*font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6615
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6616 // .. Name hdr ..
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6617 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6618 .attr("x", offset)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6619 .attr("y", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6620 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6621 .attr("font-size", font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6622 .attr("font-weight", "bold")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6623 .text("Name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6624 offset += name_field_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6625
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6626 // p-value hdr
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6627 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6628 .attr("x", offset + 2*font_size)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6629 .attr("y", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6630 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6631 .attr("font-size", font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6632 .attr("font-weight", "bold")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6633 .attr("font-style", "italic")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6634 .text("p");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6635 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6636 .attr("x", offset + 3*font_size)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6637 .attr("y", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6638 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6639 .attr("font-size", font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6640 .attr("font-weight", "bold")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6641 .text("-value");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6642 offset += pvalue_field_width + plus_minus_field_width + font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6643
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6644 // Motif Location hdr
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6645 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6646 .attr("x", offset)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6647 .attr("y", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6648 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6649 .attr("font-size", font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6650 .attr("font-weight", "bold")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6651 .text("Motif Locations");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6652
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6653 // Generate the data for the SVG.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6654 liney -= 0.5*font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6655 var dy = font_size/3.5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6656 for (var seq_name in bars) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6657 liney += diagram_line_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6658 offset = font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6659
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6660 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6661 // Generate the text fields.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6662 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6663
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6664 // Sequence name text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6665 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6666 .attr("x", offset)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6667 .attr("y", liney + dy)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6668 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6669 .attr("font-size", font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6670 .text(seq_name);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6671 offset += name_field_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6672
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6673 // p-value text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6674 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6675 .attr("x", offset + font_size+ pvalue_field_width)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6676 .attr("y", liney + dy)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6677 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6678 .attr("font-size", font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6679 .attr("text-anchor", "end")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6680 .text(bars[seq_name]["pvalue"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6681 offset += pvalue_field_width + font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6682
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6683 // +/- text (optional)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6684 if (has_complement) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6685 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6686 .attr("x", offset+font_size)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6687 .attr("y", liney + dy - font_size/2)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6688 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6689 .attr("font-size", font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6690 .text("+");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6691 if (revcomp) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6692 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6693 .attr("x", offset+1.15*font_size)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6694 .attr("y", liney + dy + font_size/2)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6695 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6696 .attr("font-size", font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6697 .text("-");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6698 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6699 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6700 offset += plus_minus_field_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6701
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6702 // Generate the base line.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6703 body.append("line")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6704 .attr("x1", offset)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6705 .attr("x2", offset + (bars[seq_name]["length"] * pix_per_char))
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6706 .attr("y1", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6707 .attr("y2", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6708 .attr("stroke-width", 0.5)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6709 .attr("stroke","black");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6710
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6711 // Generate the blocks.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6712 for (var i = 0; i < bars[seq_name]["width"].length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6713 if (bars[seq_name]["pn"][i] == undefined) { continue; }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6714 body.append("rect")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6715 .attr("x", offset + (bars[seq_name]["left"][i] * x_scale_factor * pix_per_char) )
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6716 .attr("y", (bars[seq_name]["pn"][i] == "+") ? (liney - 0.1*font_size*bars[seq_name]["height"][i]) : liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6717 .attr("width", bars[seq_name]["width"][i] * x_scale_factor * pix_per_char)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6718 .attr("height", 0.1*font_size*bars[seq_name]["height"][i])
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6719 .attr("fill", "rgb("+bars[seq_name]["color"][i] + ")")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6720 .attr("fill-opacity", bars[seq_name]["opacity"][i])
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6721 .attr("stroke-width", 0.5)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6722 .attr("stroke","black");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6723 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6724 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6725
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6726 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6727 // Generate the legend.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6728 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6729 if (n_legend_lines > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6730 dy = 0.8 * legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6731
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6732 // The legend header.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6733 var legend_top = liney + 2*legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6734 liney += 4.5*legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6735 offset = legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6736 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6737 .attr("x", offset)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6738 .attr("y", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6739 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6740 .attr("font-size", legend_font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6741 .attr("font-weight", "bold")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6742 .text("Motif");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6743 offset += index_field_width + legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6744 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6745 .attr("x", offset)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6746 .attr("y", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6747 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6748 .attr("font-size", legend_font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6749 .attr("font-weight", "bold")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6750 .text("Symbol");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6751 offset += symbol_field_width + legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6752 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6753 .attr("x", offset)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6754 .attr("y", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6755 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6756 .attr("font-size", legend_font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6757 .attr("font-weight", "bold")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6758 .text("Motif Consensus");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6759 liney -= 0.5*legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6760 liney += legend_line_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6761
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6762 for (var i=0; i<motif_indices.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6763 motif_index = sorted_motif_indices[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6764 offset = legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6765
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6766 // Motif Name
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6767 var motif_index_string = (motif_index+1).toString();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6768 motif_index_string = motif_index_string + ".";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6769 var dx = 3.3 * legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6770 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6771 .attr("x", offset+dx)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6772 .attr("y", liney+dy)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6773 .attr("font-family", "Helvetica, sans-serif")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6774 .attr("font-size", legend_font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6775 .attr("text-anchor", "end")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6776 .text(motif_index_string);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6777 offset += index_field_width + legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6778
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6779 // Motif Symbol
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6780 motif_length = data.motifs[motif_index].len;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6781 var bar_x = offset;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6782 var bar_y = liney;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6783 body.append("rect")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6784 .attr("x", bar_x )
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6785 .attr("y", liney)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6786 .attr("width", symbol_field_width*(motif_length/max_motif_length))
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6787 .attr("height", legend_font_size)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6788 .attr("fill", "rgb("+ visible_motifs[motif_index] + ")")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6789 .attr("stroke-width", 0.5)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6790 .attr("stroke","black");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6791 offset += symbol_field_width + legend_font_size;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6792
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6793 // Motif Consensus Sequence
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6794 var motif_consensus = data.motifs[motif_index].id;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6795 var cons_length = motif_consensus.length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6796 var start_index = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6797 while (start_index < cons_length) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6798 body.append("text")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6799 .attr("x", offset)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6800 .attr("y", liney+dy)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6801 .attr("font-family", "Courier")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6802 .attr("font-size", legend_font_size+"pt")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6803 .text(motif_consensus.slice(start_index, Math.min(cons_length, start_index+legend_split_length)))
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6804 liney += legend_line_height;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6805 start_index += legend_split_length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6806 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6807 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6808
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6809 // Draw box around legend.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6810 body.append("rect")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6811 .attr("x", 0.5*legend_font_size)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6812 .attr("y", legend_top + 0.5*legend_font_size)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6813 .attr("width", Math.max(legend_width, legend_non_consensus_width + consensus_hdr_width + courier_width))
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6814 .attr("height", legend_height)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6815 .attr("fill", "none")
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6816 .attr("stroke-width", 1)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6817 .attr("stroke", "black");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6818
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6819 } // legend
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6820
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6821 var svg = document.getElementsByTagName("svg")[0].outerHTML;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6822 var svgBlob = new Blob([svg], {type:"image/svg+xml;charset=utf-8"});
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6823 var svgUrl = URL.createObjectURL(svgBlob);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6824 var downloadLink = document.createElement("a");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6825 downloadLink.href = svgUrl;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6826 downloadLink.download = "meme-motif-locations.svg";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6827 document.getElementById("sites_sec").appendChild(downloadLink);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6828 downloadLink.click();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6829 downloadLink.remove();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6830 document.getElementById("memeSVG").remove();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6831
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6832 } // SVG
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6833
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6834 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6835
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6836 function make_blocks() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6837 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6838 function add_seqs_filter(container, id, checked, label_text, help_topic) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6839 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6840 var label, radio;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6841 radio = document.createElement("input");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6842 radio.type = "radio";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6843 radio.name = "seqs_display";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6844 radio.id = id;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6845 radio.checked = checked;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6846 radio.addEventListener('click', action_seqs_filter, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6847 label = document.createElement("label");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6848 label.appendChild(document.createTextNode(label_text));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6849 label.htmlFor = id;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6850 container.appendChild(radio);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6851 container.appendChild(label);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6852 if (help_topic) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6853 container.appendChild(document.createTextNode("\xA0"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6854 container.appendChild(help_button(help_topic));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6855 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6856 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6857 function add_block_diagram_button(container, id, buttonText, help_topic) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6858 var button, label;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6859 button = document.createElement("button");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6860 button.id = id;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6861 label = document.createTextNode(buttonText);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6862 button.appendChild(label);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6863 button.onclick = (id === "pdfButton") ? download_PDF_block_diagram : download_SVG_block_diagram;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6864 container.appendChild(document.createTextNode(" "));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6865 container.appendChild(button);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6866 if (help_topic) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6867 container.appendChild(document.createTextNode("\xA0"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6868 container.appendChild(help_button(help_topic));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6869 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6870 //var new_icon = document.createElement("img");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6871 //new_icon.src = new_icon_src;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6872 //new_icon.alt = "NEW";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6873 //container.appendChild(document.createTextNode(" "));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6874 //container.appendChild(new_icon);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6875 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6876 function add_blocks_header(row, title, nopad, help_topic) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6877 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6878 var div, divcp, th;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6879 th = document.createElement("th");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6880 div = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6881 div.className = "blocks_th_inner";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6882 if (typeof title !== "object") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6883 title = document.createTextNode("" + title);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6884 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6885 div.appendChild(title);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6886 if (help_topic) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6887 div.appendChild(document.createTextNode("\xA0"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6888 div.appendChild(help_button(help_topic));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6889 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6890 divcp = div.cloneNode(true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6891 divcp.className = "blocks_th_hidden";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6892 th.appendChild(div);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6893 th.appendChild(divcp);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6894 if (nopad) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6895 th.className = "nopad";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6896 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6897 row.appendChild(th);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6898 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6899 var container;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6900 var page, view_height, outer_tbl, inner_tbl, tbl, thead, tbody, rhead;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6901 var in_view, i, seq_count;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6902
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6903 page = (document.compatMode === "CSS1Compat") ? document.documentElement : document.body;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6904 view_height = Math.max(page.clientHeight - 300, 300);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6905
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6906 container = $("blocks");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6907 toggle_class(container, "hide_empty_seqs", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6908 toggle_class(container, "hide_only_scan", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6909 container.innerHTML = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6910 add_seqs_filter(container, "rdo_sites_only", true, "Only Motif Sites", "pop_motif_sites");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6911 add_seqs_filter(container, "rdo_sites_and_scan", false, "Motif Sites+Scanned Sites", "pop_scanned_sites");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6912 add_seqs_filter(container, "rdo_all_seqs", false, "All Sequences", "pop_all_sequences");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6913 add_block_diagram_button(container, "pdfButton", "Download PDF", "pop_download_pdf_motif_locations");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6914 add_block_diagram_button(container, "svgButton", "Download SVG", "pop_download_svg_motif_locations");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6915
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6916 outer_tbl = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6917 outer_tbl.className = "blocks_outer";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6918
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6919 inner_tbl = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6920 inner_tbl.id = "blocks_scroll";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6921 inner_tbl.className = "blocks_inner";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6922 inner_tbl.style.maxHeight = view_height + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6923 outer_tbl.appendChild(inner_tbl);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6924
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6925 tbl = document.createElement("table");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6926 tbl.className = "blocks_tbl";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6927 inner_tbl.appendChild(tbl);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6928
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6929 thead = document.createElement("thead");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6930 tbl.appendChild(thead);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6931 tbody = document.createElement("tbody");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6932 tbl.appendChild(tbody);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6933
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6934 rhead = thead.insertRow(thead.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6935 add_blocks_header(rhead, "", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6936 add_blocks_header(rhead, "Name", false, "pop_seq_name");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6937 add_blocks_header(rhead, make_pv_text(), false, "pop_seq_pvalue");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6938 add_blocks_header(rhead, "Motif Locations", false, "pop_motif_location");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6939
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6940 container.appendChild(outer_tbl);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6941
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6942 seq_count = data["sequence_db"]["sequences"].length;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6943 in_view = Math.max(Math.ceil(view_height / 25), 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6944 i = append_blocks_entries(tbody, 0, in_view);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6945
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6946 while (i < seq_count && inner_tbl.scrollHeight - (inner_tbl.scrollTop + inner_tbl.offsetHeight) < 400) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6947 i = append_blocks_entries(tbody, i, 20);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6948 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6949 inner_tbl.data_blocks_index = i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6950 if (i < seq_count) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6951 inner_tbl.addEventListener('scroll', make_blocks_entries, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6952 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6953 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6954
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6955 function make_scan_popup(site, motif) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6956 return function (e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6957 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6958 var pop, xy, padding, edge_padding, pop_left, pop_top, page_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6959 var lflank, match, rflank, pspm;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6960 if (!e) var e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6961 pop = make_scan_popup.pop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6962 if (e.type === "mouseover") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6963 if (pop) return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6964 pop = clone_template("tmpl_scan_info");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6965 pspm = new Pspm(motif.pwm);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6966 if (site.rc) pspm.reverse_complement(current_alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6967 set_tvar(pop, "tvar_logo", make_small_logo(current_alphabet, pspm, {"className": "scan_logo"}));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6968 set_tvar(pop, "tvar_motif", motif.id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6969 set_tvar(pop, "tvar_pvalue", site.pvalue.toExponential(2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6970 set_tvar(pop, "tvar_start", site.pos + 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6971 set_tvar(pop, "tvar_end", site.pos + motif.len);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6972
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6973 document.body.appendChild(pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6974 position_popup(this, pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6975 make_scan_popup.pop = pop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6976 } else if (e.type === "mouseout") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6977 if (pop) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6978 pop.parentNode.removeChild(pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6979 make_scan_popup.pop = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6980 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6981 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6982 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6983 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6984
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6985 function make_block_popup(site, motif, block) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6986 return function (e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6987 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6988 var pop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6989 var lflank, match, rflank, pspm, ruler, match_seq, match_width;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6990 if (!e) var e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6991 pop = make_block_popup.pop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6992 if (e.type === "mouseover") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6993 if (pop) return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6994 pop = clone_template("tmpl_block_info");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6995 pspm = new Pspm(motif.pwm);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6996 if (site.rc) { // must be dna
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6997 pspm.reverse_complement(current_alphabet);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6998 lflank = current_alphabet.invcomp_seq(site.rflank);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
6999 match = current_alphabet.invcomp_seq(site.match);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7000 rflank = current_alphabet.invcomp_seq(site.lflank);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7001 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7002 lflank = site.lflank;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7003 match = site.match;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7004 rflank = site.rflank;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7005 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7006 ruler = document.getElementById("measure_match");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7007 match_seq = make_seq(current_alphabet, match);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7008 ruler.innerHTML = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7009 ruler.appendChild(match_seq);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7010 match_width = ruler.clientWidth;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7011 ruler.removeChild(match_seq);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7012 set_tvar(pop, "tvar_lflank", lflank);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7013 set_tvar(pop, "tvar_match", match_seq);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7014 set_tvar(pop, "tvar_rflank", rflank);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7015 set_tvar(pop, "tvar_logo_pad", lflank);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7016 set_tvar(pop, "tvar_logo", make_small_logo(current_alphabet, pspm, {"width": match_width}));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7017 set_tvar(pop, "tvar_motif", motif.id);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7018 set_tvar(pop, "tvar_pvalue", site.pvalue.toExponential(2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7019 set_tvar(pop, "tvar_start", site.pos + 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7020 set_tvar(pop, "tvar_end", site.pos + motif.len);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7021
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7022 document.body.appendChild(pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7023 position_popup(block, pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7024 make_block_popup.pop = pop;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7025 } else if (e.type === "mouseout") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7026 if (pop) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7027 pop.parentNode.removeChild(pop);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7028 make_block_popup.pop = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7029 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7030 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7031 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7032 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7033
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7034 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7035 // action_show_more
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7036 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7037 // Show more information on the motif.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7038 ///
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7039 function action_show_more(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7040 var node, tr, tbody, table, container, motif, ordinal;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7041 var expanded_motif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7042 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7043 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7044 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7045 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7046 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7047 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7048 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7049 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7050 // find the row that contains the cell
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7051 node = this;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7052 do {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7053 if (node.tagName === "TR") break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7054 } while (node = node.parentNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7055 if (!node) throw new Error("Expected to find row!?");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7056 tr = node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7057 // get info
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7058 motif = tr.data_motif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7059 ordinal = tr.data_ordinal;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7060 // find tbody
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7061 do {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7062 if (node.tagName === "TBODY") break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7063 } while (node = node.parentNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7064 if (!node) throw new Error("Expected to find tbody!?");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7065 tbody = node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7066 // find table
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7067 do {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7068 if (node.tagName === "TABLE") break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7069 } while (node = node.parentNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7070 if (!node) throw new Error("Expected to find table!?");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7071 table = node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7072 // find container
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7073 container = node.parentNode;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7074 // make a expanded motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7075 motif["expanded"] = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7076 expanded_motif = make_expanded_motif(current_alphabet, ordinal, motif,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7077 container.data_more_x, container.data_submit_x);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7078 // now determine how to place it
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7079 if (tbody.rows.length === 1) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7080 // only us in the table so the table can be replaced
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7081 container.replaceChild(expanded_motif, table);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7082 } else if (tbody.rows[0] === tr) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7083 // first row, so remove and insert an expanded motif before
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7084 table.deleteRow(tr.rowIndex);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7085 container.insertBefore(expanded_motif, table);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7086 } else if (tbody.rows[tbody.rows.length - 1] === tr) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7087 // last row, so remove and insert an expanded motif after
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7088 table.deleteRow(tr.rowIndex);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7089 container.insertBefore(expanded_motif, table.nextSibling);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7090 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7091 var table2, tbody2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7092 table2 = table.cloneNode(false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7093 table2.appendChild(table.tHead.cloneNode(true));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7094 tbody2 = table.tBodies[0].cloneNode(false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7095 table2.appendChild(tbody2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7096 container.insertBefore(table2, table.nextSibling);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7097 for (i = tbody.rows.length - 1; i >= 0; i--) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7098 row = tbody.rows[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7099 row.parentNode.removeChild(row);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7100 if (row === tr) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7101 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7102 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7103 tbody2.insertBefore(row, tbody2.rows[0]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7104 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7105 container.insertBefore(expanded_motif, table2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7106 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7107 find_child(expanded_motif, "tvar_less").focus();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7108 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7109
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7110 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7111 // action_show_less
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7112 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7113 // Show less information on the motif.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7114 ///
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7115 function action_show_less(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7116 var btn;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7117 var expanded_motif, container, motif, ordinal, colw, focus_target;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7118 var table, tbody, tbody2, row, table_before, table_after;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7119 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7120 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7121 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7122 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7123 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7124 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7125 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7126 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7127 btn = this;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7128 // find expanded motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7129 expanded_motif = find_parent(btn, "expanded_motif");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7130 if (!expanded_motif) throw new Error("Expected expanded motif.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7131 // find the container
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7132 container = expanded_motif.parentNode;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7133 // get data
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7134 motif = expanded_motif.data_motif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7135 ordinal = expanded_motif.data_ordinal;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7136 colw = container.data_colw;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7137 // get the table before
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7138 table_before = expanded_motif.previousSibling;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7139 if (table_before && table_before.tagName !== "TABLE") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7140 table_before = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7141 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7142 // get the table after
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7143 table_after = expanded_motif.nextSibling;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7144 if (table_after && table_after.tagName !== "TABLE") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7145 table_after = null;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7146 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7147 // see if there is a table below or above that we can put this in.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7148 // if there is a table both below and above then add this motif and
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7149 // all ones below to the above table
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7150 motif["expanded"] = false;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7151 if (table_before && table_after) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7152 tbody = table_before.tBodies[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7153 row = tbody.insertRow(tbody.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7154 make_motif_table_entry(row, current_alphabet, ordinal, motif, colw);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7155 focus_target = find_child(row.cells[5], "sym_btn");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7156 container.removeChild(expanded_motif);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7157 tbody2 = table_after.tBodies[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7158 while (tbody2.rows.length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7159 row = tbody2.rows[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7160 row.parentNode.removeChild(row);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7161 tbody.appendChild(row);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7162 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7163 container.removeChild(table_after);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7164 } else if (table_before) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7165 tbody = table_before.tBodies[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7166 row = tbody.insertRow(tbody.rows.length);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7167 make_motif_table_entry(row, current_alphabet, ordinal, motif, colw);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7168 focus_target = find_child(row.cells[5], "sym_btn");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7169 container.removeChild(expanded_motif);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7170 } else if (table_after) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7171 tbody = table_after.tBodies[0];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7172 row = tbody.insertRow(0);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7173 make_motif_table_entry(row, current_alphabet, ordinal, motif, colw);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7174 focus_target = find_child(row.cells[5], "sym_btn");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7175 container.removeChild(expanded_motif);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7176 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7177 //no table above or below!
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7178 // make a new table
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7179 table = make_motifs_table(current_alphabet, ordinal, [motif], colw, data["stop_reason"]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7180 focus_target = find_child(table.tBodies[0].rows[0].cells[5], "sym_btn");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7181 container.replaceChild(table, expanded_motif);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7182 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7183 focus_target.focus();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7184 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7185
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7186 //TODO -- can we delete this junk?
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7187 //function action_show_outpop(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7188 function fred_action_show_outpop(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7189 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7190 function init() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7191 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7192 var close_btn, next_btn, prev_btn, cancel_btn, do_btn;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7193 var tab1, tab2, tab3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7194 var pnl1, pnl2, pnl3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7195 var format_list;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7196 var tbl_submit, inputs, i, default_prog;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7197 close_btn = $("outpop_close");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7198 close_btn.addEventListener("click", action_hide_outpop, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7199 close_btn.addEventListener("keydown", action_hide_outpop, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7200 next_btn = $("outpop_next");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7201 next_btn.addEventListener("click", action_outpop_next, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7202 next_btn.addEventListener("keydown", action_outpop_next, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7203 prev_btn = $("outpop_prev");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7204 prev_btn.addEventListener("click", action_outpop_prev, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7205 prev_btn.addEventListener("keydown", action_outpop_prev, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7206 cancel_btn = $("outpop_cancel");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7207 cancel_btn.addEventListener("click", action_hide_outpop, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7208 do_btn = $("outpop_do");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7209 do_btn.addEventListener("click", action_outpop_submit, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7210 tab1 = $("outpop_tab_1");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7211 tab1.tabIndex = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7212 tab1.addEventListener("click", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7213 tab1.addEventListener("keydown", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7214 tab2 = $("outpop_tab_2");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7215 tab2.tabIndex = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7216 tab2.addEventListener("click", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7217 tab2.addEventListener("keydown", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7218 tab3 = $("outpop_tab_3");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7219 tab3.tabIndex = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7220 tab3.addEventListener("click", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7221 tab3.addEventListener("keydown", action_outpop_tab, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7222 pnl1 = $("outpop_pnl_1");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7223 pnl2 = $("outpop_pnl_2");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7224 pnl3 = $("outpop_pnl_3");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7225 toggle_class(tab1, "activeTab", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7226 toggle_class(tab2, "activeTab", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7227 toggle_class(tab3, "activeTab", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7228 pnl1.style.display = "block";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7229 pnl2.style.display = "none";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7230 pnl3.style.display = "none";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7231 format_list = $("text_format");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7232 format_list.addEventListener("change", action_outpop_format, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7233 // setup program selection
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7234 tbl_submit = $("programs");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7235 // when not dna, hide the inputs for programs that require dna motifs
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7236 toggle_class(tbl_submit, "alphabet_dna", current_alphabet.has_complement());//TODO alphabet_dna is a bad name for a field when allowing custom alphabets
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7237 // add a click listener for the radio buttons
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7238 inputs = tbl_submit.querySelectorAll("input[type='radio']");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7239 for (i = 0; i < inputs.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7240 inputs[i].addEventListener("click", action_outpop_program, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7241 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7242 // ensure that a default program option is selected for DNA and Protein
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7243 default_prog = document.getElementById(current_alphabet.has_complement() ? "submit_tomtom" : "submit_fimo"); //TODO Tomtom might require a more strict definition of DNA
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7244 default_prog.checked = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7245 action_outpop_program.call(default_prog);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7246 // disable reverse-complement when not DNA
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7247 $("logo_rc_option").disabled = !current_alphabet.has_complement();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7248 // set errorbars on when ssc is on
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7249 $("logo_ssc").addEventListener("change", action_outpop_ssc, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7250 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7251 var node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7252 // store the focused element
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7253 action_hide_outpop.last_active = document.activeElement;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7254 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7255 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7256 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7257 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7258 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7259 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7260 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7261 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7262 // hide the help popup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7263 help_popup();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7264 // on first load initilize the popup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7265 if (!action_show_outpop.ready) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7266 init();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7267 action_show_outpop.ready = true;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7268 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7269 // load the motif logo
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7270 node = this;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7271 do {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7272 if (/\bexpanded_motif\b/.test(node.className) || node.tagName === "TR") break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7273 } while (node = node.parentNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7274 if (node === null) throw new Error("Expected node!");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7275 update_outpop_motif(node.data_ordinal - 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7276 // display the download popup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7277 $("grey_out_page").style.display = "block";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7278 $("download").style.display = "block";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7279 $("outpop_close").focus();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7280 } // fred_action_show_outpop
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7281
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7282 function action_btn_rc(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7283 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7284 var node, tr, motif, box, logo_box, tab_st, tab_rc, rc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7285 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7286 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7287 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7288 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7289 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7290 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7291 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7292 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7293 node = this;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7294 do {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7295 if (node.tagName === "TR") break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7296 } while (node = node.parentNode);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7297 if (!node) throw new Error("Expected to find row!?");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7298 tr = node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7299 // get info
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7300 motif = tr.data_motif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7301 box = find_parent(this, "preview_box");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7302 logo_box = find_child(box, "preview_logo_box");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7303 tab_st = find_child(box, "plus");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7304 tab_rc = find_child(box, "minus");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7305 rc = (this === tab_rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7306 motif["rc"] = rc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7307 toggle_class(logo_box, "show_rc_logo", rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7308 toggle_class(tab_st, "active", !rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7309 toggle_class(tab_rc, "active", rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7310 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7311
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7312 function action_rc_tab(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7313 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7314 var box, logo_box, tab_st, tab_rc, rc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7315 if (!e) e = window.event;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7316 if (e.type === "keydown") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7317 if (e.keyCode !== 13 && e.keyCode !== 32) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7318 return;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7319 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7320 // stop a submit or something like that
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7321 e.preventDefault();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7322 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7323 box = find_parent(this, "expanded_motif");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7324 logo_box = find_child(box, "tvar_logo");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7325 tab_st = find_child(box, "tvar_tab");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7326 tab_rc = find_child(box, "tvar_tab_rc");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7327 rc = (this === tab_rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7328 box.data_motif["rc"] = rc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7329 toggle_class(logo_box, "show_rc_logo", rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7330 toggle_class(tab_st, "activeTab", !rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7331 toggle_class(tab_rc, "activeTab", rc);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7332 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7333
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7334 function action_seqs_filter() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7335 "use strict";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7336 var block_container;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7337 block_container = $("blocks");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7338 if ($("rdo_all_seqs").checked) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7339 toggle_class(block_container, "hide_empty_seqs", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7340 toggle_class(block_container, "hide_only_scan", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7341 } else if ($("rdo_sites_and_scan").checked) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7342 toggle_class(block_container, "hide_empty_seqs", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7343 toggle_class(block_container, "hide_only_scan", false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7344 } else if ($("rdo_sites_only").checked) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7345 toggle_class(block_container, "hide_empty_seqs", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7346 toggle_class(block_container, "hide_only_scan", true);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7347 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7348 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7349
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7350 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7351 // page_loaded
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7352 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7353 // Called when the page has loaded for the first time.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7354 ///
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7355 function page_loaded() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7356 post_load_setup();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7357 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7358
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7359 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7360 // page_loaded
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7361 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7362 // Called when a cached page is reshown.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7363 ///
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7364 function page_shown(e) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7365 if (e.persisted) post_load_setup();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7366 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7367
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7368 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7369 // page_loaded
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7370 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7371 // Called when the page is resized
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7372 ///
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7373 function page_resized() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7374 var page, blocks_scroll;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7375 update_scroll_pad();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7376 page = (document.compatMode === "CSS1Compat") ? document.documentElement : document.body;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7377 blocks_scroll = $("blocks_scroll");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7378 if (blocks_scroll) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7379 blocks_scroll.style.maxHeight = Math.max(page.clientHeight - 300, 300) + "px";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7380 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7381 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7382
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7383 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7384 // pre_load_setup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7385 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7386 // Run before the page is displayed
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7387 ///
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7388 function pre_load_setup() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7389 var start, hue, sat, light, divisions;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7390 var i, j, motifs, motif, sites, site, sequences, sequence;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7391 var max_seq_len;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7392 motifs = data["motifs"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7393 sequences = data["sequence_db"]["sequences"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7394 max_seq_len = 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7395 if (sequences) { // no sequences if -brief
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7396 for (i = 0; i < sequences.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7397 sequence = sequences[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7398 sequence["sites"] = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7399 if (sequence["length"] > max_seq_len) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7400 max_seq_len = sequence["length"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7401 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7402 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7403 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7404 data["sequence_db"]["max_length"] = max_seq_len;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7405 // use hsl colours
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7406 start = 0; //red
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7407 sat = 100;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7408 light = 50;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7409 for (i = 0; i < motifs.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7410 motif = motifs[i];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7411 // give the motif a colour
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7412 divisions = 1 << Math.ceil(Math.log(i + 1) / Math.LN2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7413 hue = start + (360 / divisions) * ((i - (divisions >> 1)) * 2 + 1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7414 motif["colour"] = "hsl(" + hue + ", " + sat + "%, " + light + "%)";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7415 // associate sites with sequences as well
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7416 // to make generating the block diagram easier
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7417 sites = motif["sites"];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7418 for (j = 0; j < sites.length; j++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7419 site = sites[j];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7420 sequence = sequences[site["seq"]];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7421 // record the motif index
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7422 site["motif"] = i;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7423 // add the site to the sequence
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7424 sequence["sites"].push(site);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7425 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7426 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7427 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7428
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7429 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7430 // post_load_setup
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7431 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7432 // Run when the page has loaded, or been reloaded.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7433 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7434 function post_load_setup() {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7435 update_scroll_pad();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7436 if (data["motifs"].length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7437 make_motifs();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7438 if (data.sequence_db.primary_count > data.options.brief) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7439 if (data.options.brief == 1000) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7440 $("blocks").innerHTML = "<p>Output of sites suppressed because there were more than 1000 (primary) sequences.</p>";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7441 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7442 $("blocks").innerHTML = "<p>Output of motif locations suppressed by -brief option.</p>";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7443 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7444 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7445 make_blocks();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7446 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7447 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7448 $("motifs").innerHTML = "<p>No significant motifs found!</p>"; // clear content
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7449 $("motifs").innerHTML += "<p><b>" + data["stop_reason"] + "</b></p>";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7450 $("blocks").innerHTML = "<p>No significant motifs found!</p>";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7451 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7452 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7453
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7454 pre_load_setup();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7455 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7456 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7457 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7458 // template.js
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7459 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7460
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7461 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7462 * Fill in a template variable
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7463 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7464 function set_tvar(template, tvar, value) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7465 var node;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7466 node = find_child(template, tvar);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7467 if (node === null) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7468 throw new Error("Template does not contain variable " + tvar);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7469 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7470 node.innerHTML = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7471 if (typeof value !== "object") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7472 node.appendChild(document.createTextNode(value));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7473 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7474 node.appendChild(value);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7475 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7476 } // set_tvar
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7477
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7478 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7479 * Get the text contained within the element.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7480 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7481 function elem_text(elem, separator) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7482 if (separator === undefined) separator = '';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7483 return text_nodes(elem).map(node_text).join(separator);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7484 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7485
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7486 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7487 * Get the text out of a specific text node.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7488 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7489 function node_text(node) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7490 if (node === undefined) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7491 return '';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7492 } else if (node.textContent) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7493 return node.textContent;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7494 } else if (node.innerText) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7495 return node.innerText;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7496 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7497 return '';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7498 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7499 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7500
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7501 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7502 * Find all text nodes in the given container.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7503 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7504 function text_nodes(container) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7505 var textNodes = [];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7506 var stack = [container];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7507 // depth first search to maintain ordering when flattened
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7508 while (stack.length > 0) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7509 var node = stack.pop();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7510 if (node.nodeType == Node.TEXT_NODE) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7511 textNodes.push(node);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7512 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7513 for (var i = node.childNodes.length-1; i >= 0; i--) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7514 stack.push(node.childNodes[i]);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7515 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7516 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7517 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7518 return textNodes;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7519 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7520
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7521 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7522 * Create a button designed to contain a single symbol
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7523 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7524 function make_sym_btn(symbol, title, action) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7525 var box, sbox;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7526 box = document.createElement("div");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7527 box.tabIndex = 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7528 box.className = "sym_btn";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7529 sbox = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7530 if (typeof symbol === "string") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7531 sbox.appendChild(document.createTextNode(symbol));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7532 } else {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7533 sbox.appendChild(symbol);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7534 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7535 box.appendChild(sbox);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7536 box.title = title;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7537 box.addEventListener('click', action, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7538 box.addEventListener('keydown', action, false);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7539 return box;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7540 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7541
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7542 /*
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7543 * Create a pair of text spans with different classes.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7544 * This is useful when using CSS to only display one of them.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7545 */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7546 function text_pair(txt1, cls1, txt2, cls2) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7547 var container, part1, part2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7548 container = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7549 part1 = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7550 part1.appendChild(document.createTextNode(txt1));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7551 part1.className = cls1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7552 container.appendChild(part1);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7553 part2 = document.createElement("span");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7554 part2.appendChild(document.createTextNode(txt2));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7555 part2.className = cls2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7556 container.appendChild(part2);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7557 return container;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7558 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7559 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7560 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7561 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7562 // citation.js
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7563 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7564 function get_citation_text(doc_type, extra) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7565 var html;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7566
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7567 switch (doc_type) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7568 case 'AMA':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7569 return(get_citation_text("GOMo", extra));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7570 case 'AME':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7571 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7572 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7573 Robert C. McLeay and Timothy L. Bailey,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7574 &quot;Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7575 <i>BMC Bioinformatics</i>, <b>11</b>:165, 2010.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7576 <a href="http://www.biomedcentral.com/1471-2105/11/165">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7577 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7578 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7579 case 'CentriMo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7580 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7581 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7582 Timothy L. Bailey and Philip Machanick,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7583 &quot;Inferring direct DNA binding from ChIP-seq&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7584 <i>Nucleic Acids Research</i>, <b>40</b>:e128, 2012.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7585 <a href="http://nar.oxfordjournals.org/content/40/17/e128">[Full Text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7586 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7587 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7588 case 'DREME':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7589 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7590 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7591 Timothy L. Bailey,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7592 &quot;DREME: Motif discovery in transcription factor ChIP-seq data&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7593 <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7594 <a href="http://bioinformatics.oxfordjournals.org/content/27/12/1653">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7595 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7596 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7597 case 'FIMO':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7598 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7599 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7600 Charles E. Grant, Timothy L. Bailey and William Stafford Noble,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7601 &quot;FIMO: Scanning for occurrences of a given motif&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7602 <i>Bioinformatics</i> <b>27</b>(7):1017-1018, 2011.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7603 <a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7604 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7605 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7606 case 'GLAM2':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7607 case 'GLAM2SCAN':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7608 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7609 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7610 Martin C. Frith, Neil F. W. Saunders, Bostjan Kobe and Timothy L. Bailey,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7611 &quot;Discovering sequence motifs with arbitrary insertions and deletions&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7612 <i>PLoS Computational Biology</i>, <b>4</b>(5):e1000071, 2008.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7613 <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000071">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7614 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7615 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7616 case 'GOMo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7617 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7618 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7619 Fabian A. Buske, Mikael Bod&eacute;n, Denis C. Bauer and Timothy L. Bailey,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7620 &quot;Assigning roles to DNA regulatory motifs using comparative genomics&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7621 <i>Bioinformatics</i>, <b>26</b>(7), 860-866, 2010.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7622 <a href="http://bioinformatics.oxfordjournals.org/cgi/content/full/26/7/860">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7623 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7624 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7625 case 'MAST':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7626 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7627 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7628 Timothy L. Bailey and Michael Gribskov,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7629 &quot;Combining evidence using p-values: application to sequence homology searches&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7630 <i>Bioinformatics</i>, <b>14</b>(1):48-54, 1998.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7631 <a href="http://bioinformatics.oxfordjournals.org/content/14/1/48">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7632 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7633 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7634 case 'MCAST':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7635 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7636 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7637 Timothy Bailey and William Stafford Noble,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7638 &quot;Searching for statistically significant regulatory modules&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7639 <i>Bioinformatics (Proceedings of the European Conference on Computational Biology)</i>,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7640 <b>19</b>(Suppl. 2):ii16-ii25, 2003.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7641 <a href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/suppl_2/ii16">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7642 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7643 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7644 case 'Meta-MEME':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7645 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7646 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7647 William N. Grundy, Timothy L. Bailey, Charles P. Elkan and Michael E. Baker.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7648 &quot;Meta-MEME: Motif-based Hidden Markov Models of Protein Families&quot;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7649 <i>Computer Applications in the Biological Sciences (CABIOS)</i>,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7650 <b>13</b>(4):397-406, 1997.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7651 <a href="http://bioinformatics.oxfordjournals.org/content/13/4/397">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7652 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7653 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7654 case 'MEME':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7655 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7656 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7657 Timothy L. Bailey and Charles Elkan,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7658 &quot;Fitting a mixture model by expectation maximization to
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7659 discover motifs in biopolymers&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7660 <em>Proceedings of the Second International Conference on Intelligent Systems
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7661 for Molecular Biology</em>, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7662 <a href="http://www.aaai.org/Papers/ISMB/1994/ISMB94-004.pdf">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7663 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7664 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7665 case 'MEME-ChIP':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7666 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7667 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7668 Philip Machanick and Timothy L. Bailey,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7669 &quot;MEME-ChIP: motif analysis of large DNA datasets&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7670 <i>Bioinformatics</i> <b>27</b>(12):1696-1697, 2011.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7671 <a href="http://bioinformatics.oxfordjournals.org/content/27/12/1696.full">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7672 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7673 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7674 case 'MEME_SUITE':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7675 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7676 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7677 Timothy L. Bailey, James Johnson, Charles E. Grant, William S. Noble,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7678 &quot;The MEME Suite&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7679 <i>Nucleic Acids Research</i>, <b>43</b>(W1):W39-W49, 2015.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7680 <a href="https://academic.oup.com/nar/article/43/W1/W39/2467905">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7681 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7682 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7683 case 'MoMo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7684 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7685 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7686 Alice Cheng, Charles Grant, Timothy L. Bailey and William Noble,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7687 &quot;MoMo: Discovery of statistically significant post-translational modification motifs&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7688 <i>Bioinformatics</i>, <b>35</b>(16):2774-2782, 2018.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7689 <a href="https://doi.org/10.1093/bioinformatics/bty1058">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7690 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7691 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7692 case 'PSPs':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7693 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7694 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7695 Timothy L. Bailey, Mikael Bod&eacute;n, Tom Whitington and Philip Machanick,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7696 &quot;The value of position-specific priors in motif discovery using MEME&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7697 <i>BMC Bioinformatics</i>, <b>11</b>(1):179, 2010.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7698 <a href="http://www.biomedcentral.com/1471-2105/11/179">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7699 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7700 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7701 case 'SEA':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7702 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7703 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7704 Timothy L. Bailey and Charles E. Grant, &quot;SEA: Simple Enrichment Analysis of motifs&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7705 <i>BioRxiv</i>, August 24, 2021.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7706 <a href="https://www.biorxiv.org/content/10.1101/2021.08.23.457422v1">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7707 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7708 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7709 case 'SpaMo':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7710 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7711 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7712 Tom Whitington, Martin C. Frith, James Johnson and Timothy L. Bailey
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7713 &quot;Inferring transcription factor complexes from ChIP-seq data&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7714 <i>Nucleic Acids Res.</i> <b>39</b>(15):e98, 2011.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7715 <a href="http://nar.oxfordjournals.org/content/39/15/e98">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7716 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7717 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7718 case 'STREME':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7719 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7720 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7721 Timothy L. Bailey,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7722 &quot;STREME: accurate and versatile sequence motif discovery&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7723 <i>Bioinformatics</i>, Mar. 24, 2021.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7724 <a href="https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab203/6184861" >[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7725 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7726 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7727 case 'Tomtom':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7728 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7729 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7730 Shobhit Gupta, JA Stamatoyannopolous, Timothy Bailey and William Stafford Noble,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7731 &quot;Quantifying similarity between motifs&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7732 <i>Genome Biology</i>, <b>8</b>(2):R24, 2007.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7733 <a href="http://genomebiology.com/2007/8/2/R24">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7734 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7735 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7736 case 'T-Gene':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7737 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7738 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7739 Timothy O'Connor, Charles E. Grant, Mikael Bod&eacute;n, Timothy L. Bailey,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7740 &quot;T-Gene: Improved target gene prediction&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7741 <i>Bioinformatics</i>, <b>36</b>(12):3902-3904, 2020.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7742 <a href="https://academic.oup.com/bioinformatics/article/36/12/3902/5815978?guestAccessKey=aa625a49-a2aa-4d7a-858e-8bc82867a534">[Full Text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7743 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7744 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7745 case 'XSTREME':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7746 return(extra + `
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7747 <span class="citation">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7748 Charles E. Grant and Timothy L. Bailey, &quot;XSTREME: comprehensive motif analysis of biological sequence datasets&quot;,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7749 <i>BioRxiv</i>, September 3, 2021.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7750 <a href="https://www.biorxiv.org/content/10.1101/2021.09.02.458722v1">[full text]</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7751 </span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7752 `);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7753 default:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7754 return("Unknown program: " + doc_type);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7755 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7756 } // get_citation_text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7757
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7758 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7759 // Function to replace the innerHTML of element "id" with an HTML paragraph
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7760 // containing the text for 'program', which is known to function get_citation_text.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7761 // If "id" is either "citation" or "reference" some extra text is printed.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7762 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7763 function print_citation(id, program) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7764 var extra;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7765 switch (id) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7766 case 'citation':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7767 extra = "If you use " + program + " in your research, please cite the following paper:<br>";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7768 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7769 case 'reference':
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7770 extra = "<h5>Reference</h5>";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7771 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7772 default:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7773 extra = "";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7774 break;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7775 };
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7776 var html = get_citation_text(program, extra);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7777 document.getElementById(id).insertAdjacentHTML('beforeend', html);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7778 } // print_citation
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7779
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7780 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7781 // Function to convert a citation for a program to a C #define statement.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7782 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7783 function print_citation_define(lang, pgm) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7784 var citation = get_citation_text(pgm, '');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7785 citation = citation.replace(/<[^>]*>/g, '');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7786 citation = citation.replace(/\[.*\]/g, '');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7787 citation = citation.replace(/\n\s*/g, '\\n');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7788 citation = citation.replace(/&quot;/g, '\\"');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7789 citation = citation.replace(/&eacute;/g, 'e');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7790 citation = citation.replace(/^\\n/, '');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7791 pgm = pgm.replace(/-/, '');
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7792 citation = "If you use this program in your research, please cite:\\n\\n" + citation;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7793 if (lang == "C") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7794 citation = "#define " + pgm + '_CITE "' + citation + '"';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7795 } else if (lang == "perl") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7796 citation = '"' + pgm + '" => "' + citation + '",';
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7797 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7798 return(citation);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7799 } // print_citation_define
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7800
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7801 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7802 // Main program (for use with nodejs "node" javascript engine)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7803 // to create citation.js.h and citation.pm from citation.js.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7804 // The command line:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7805 // node citation.js C > citation.js.h
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7806 // will output the C #define statements for each of the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7807 // programs listed below, defining macros <program>_CITE.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7808 // The command line:
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7809 // node citation.js perl > citation.js.pm
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7810 // will output perl hash <program> => text
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7811 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7812 //
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7813 if (typeof process !== 'undefined') {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7814 var lang = process.argv[2];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7815 var programs = ['AMA', 'AME', 'CentriMo', 'DREME', 'FIMO', 'GLAM2',
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7816 'GLAM2SCAN', 'GOMo', 'MAST', 'MCAST', 'Meta-MEME', 'MEME',
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7817 'MEME-ChIP', 'MEME_SUITE', 'MoMo', 'PSPs', 'SEA', 'SpaMo',
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7818 'STREME', 'Tomtom', 'T-Gene', 'XSTREME'];
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7819
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7820 if (lang == "C") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7821 console.log("// Do not edit this file. It is created from etc/citation.js.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7822 console.log("#ifndef citation_js_h\n#define citation_js_h\n");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7823 for (var i=0; i<programs.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7824 console.log(print_citation_define(lang, programs[i]));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7825 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7826 console.log("\n#endif");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7827 } else if (lang == "perl") {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7828 console.log("# Do not edit this file. It is created from etc/citation.js.");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7829 console.log("package Citation;");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7830 console.log("sub cite {\n my ($pgm) = @_;\n return $citation{$pgm};\n}");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7831 console.log("%citation = (");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7832 for (var i=0; i<programs.length; i++) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7833 console.log(print_citation_define(lang, programs[i]));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7834 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7835 console.log(");");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7836 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7837 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7838 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7839 <style>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7840 /* The following is the content of meme.css */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7841 body { background-color:white; font-size: 12px; font-family: Verdana, Arial, Helvetica, sans-serif;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7842
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7843 div.help {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7844 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7845 margin: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7846 padding: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7847 width: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7848 height: 13px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7849 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7850 background-image: url(data:image/gif;base64,R0lGODlhDAANAIABANR0AP///yH5BAEAAAEALAAAAAAMAA0AAAIdhI8Xy22MIFgv1DttrrJ7mlGNNo4c+aFg6SQuUAAAOw==);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7851 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7852
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7853 div.help:hover {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7854 background-image: url(data:image/gif;base64,R0lGODlhDAANAKEAANR0AP///9R0ANR0ACH+EUNyZWF0ZWQgd2l0aCBHSU1QACH5BAEAAAIALAAAAAAMAA0AAAIdDGynCe3PgoxONntvwqz2/z2K2ImjR0KhmSIZUgAAOw==);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7855 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7856
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7857 p.spaced { line-height: 1.8em;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7858
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7859 span.citation { font-family: "Book Antiqua", "Palatino Linotype", serif; color: #004a4d;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7860
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7861 p.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7862
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7863 td.jump { font-size: 13px; color: #ffffff; background-color: #00666a;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7864 font-family: Georgia, "Times New Roman", Times, serif;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7865
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7866 a.jump { margin: 15px 0 0; font-style: normal; font-variant: small-caps;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7867 font-weight: bolder; font-family: Georgia, "Times New Roman", Times, serif;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7868
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7869 h2.mainh {font-size: 1.5em; font-style: normal; margin: 15px 0 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7870 font-variant: small-caps; font-family: Georgia, "Times New Roman", Times, serif;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7871
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7872 h2.line {border-bottom: 1px solid #CCCCCC; font-size: 1.5em; font-style: normal;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7873 margin: 15px 0 0; padding-bottom: 3px; font-variant: small-caps;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7874 font-family: Georgia, "Times New Roman", Times, serif;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7875
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7876 h4 {border-bottom: 1px solid #CCCCCC; font-size: 1.2em; font-style: normal;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7877 margin: 10px 0 0; padding-bottom: 3px; font-family: Georgia, "Times New Roman", Times, serif;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7878
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7879 h5 {margin: 0px}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7880
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7881 a.help { font-size: 9px; font-style: normal; text-transform: uppercase;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7882 font-family: Georgia, "Times New Roman", Times, serif;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7883
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7884 div.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7885
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7886 div.pad1 { margin: 10px 5px;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7887
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7888 div.pad2 { margin: 25px 5px 5px;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7889 h2.pad2 { padding: 25px 5px 5px;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7890
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7891 div.pad3 { padding: 5px 0px 10px 30px;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7892
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7893 div.box { border: 2px solid #CCCCCC; padding:10px; overflow: hidden;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7894
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7895 div.bar { border-left: 7px solid #00666a; padding:5px; margin-top:25px; }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7896
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7897 div.subsection {margin:25px 0px;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7898
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7899 img {border:0px none;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7900
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7901 th.majorth {text-align:left;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7902 th.minorth {font-weight:normal; text-align:left; width:8em; padding: 3px 0px;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7903 th.actionth {font-weight:normal; text-align:left;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7904
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7905 .explain h5 {font-size:1em; margin-left: 1em;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7906
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7907 div.doc {margin-left: 2em; margin-bottom: 3em;}
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7908
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7909 th.trainingset {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7910 border-bottom: thin dashed black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7911 font-weight:normal;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7912 padding:0px 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7913 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7914 div.pop_content {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7915 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7916 z-index:50;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7917 width:300px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7918 padding: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7919 background: #E4ECEC;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7920 font-size: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7921 font-family: Arial;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7922 border-style: double;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7923 border-width: 3px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7924 border-color: #AA2244;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7925 display:none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7926 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7927 div.pop_content_wide {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7928 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7929 z-index:1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7930 width:700px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7931 padding: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7932 background: #E4ECEC;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7933 font-size: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7934 font-family: Arial;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7935 border-style: double;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7936 border-width: 3px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7937 border-color: #AA2244;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7938 display:none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7939 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7940
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7941 div.pop_content > *:first-child {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7942 margin-top: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7943 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7944
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7945 div.pop_content h1, div.pop_content h2, div.pop_content h3, div.pop_content h4,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7946 div.pop_content h5, div.pop_content h6, div.pop_content p {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7947 margin: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7948 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7949
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7950 div.pop_content p + h1, div.pop_content p + h2, div.pop_content p + h3,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7951 div.pop_content p + h4, div.pop_content p + h5, div.pop_content p + h6 {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7952 margin-top: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7953 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7954
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7955 div.pop_content p + p {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7956 margin-top: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7957 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7958
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7959 div.pop_content > *:last-child {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7960 margin-bottom: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7961 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7962
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7963 div.pop_content div.pop_close {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7964 /* old definition */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7965 float:right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7966 bottom: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7967 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7968
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7969 div.pop_content span.pop_close, div.pop_content span.pop_back {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7970 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7971 border: 2px outset #661429;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7972 background-color: #CCC;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7973 padding-left: 1px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7974 padding-right: 1px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7975 padding-top: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7976 padding-bottom: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7977 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7978 color: #AA2244; /*#661429;*/
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7979 font-weight: bold;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7980 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7981
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7982 div.pop_content span.pop_close:active, div.pop_content span.pop_back:active {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7983 border-style: inset;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7984 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7985
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7986 div.pop_content span.pop_close {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7987 float:right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7988 /*border: 2px outset #AA002B;*/
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7989 /*color: #AA2244;*/
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7990 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7991
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7992 div.pop_content:not(.nested) .nested_only {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7993 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7994 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7995
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7996 div.pop_back_sec {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7997 margin-bottom: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7998 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
7999
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8000 div.pop_close_sec {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8001 margin-top: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8002 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8003
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8004 table.hide_advanced tr.advanced {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8005 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8006 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8007 span.show_more {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8008 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8009 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8010 table.hide_advanced span.show_more {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8011 display: inline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8012 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8013 table.hide_advanced span.show_less {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8014 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8015 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8016
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8017
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8018 /*****************************************************************************
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8019 * Program logo styling
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8020 ****************************************************************************/
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8021 div.prog_logo {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8022 border-bottom: 0.25em solid #0f5f60;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8023 height: 4.5em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8024 width: 25em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8025 display:inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8026 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8027 div.prog_logo img {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8028 float:left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8029 width: 4em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8030 border-style: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8031 margin-right: 0.2em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8032 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8033 div.prog_logo h1, div.prog_logo h1:hover, div.prog_logo h1:active, div.prog_logo h1:visited {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8034 margin:0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8035 padding:0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8036 font-family: Arial, Helvetica, sans-serif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8037 font-size: 3.2em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8038 line-height: 1em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8039 vertical-align: top;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8040 display: block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8041 color: #026666;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8042 letter-spacing: -0.06em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8043 text-shadow: 0.04em 0.06em 0.05em #666;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8044 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8045 div.prog_logo h2, div.prog_logo h2:hover, div.prog_logo h2:active, div.prog_logo h2:visited {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8046 display: block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8047 margin:0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8048 padding:0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8049 font-family: Helvetica, sans-serif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8050 font-size: 0.9em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8051 line-height: 1em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8052 letter-spacing: -0.06em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8053 color: black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8054 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8055 div.prog_logo h3, div.prog_logo h3:hover, div.prog_logo h3:active, div.prog_logo h3:visited {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8056 display: block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8057 margin:0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8058 padding:0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8059 font-family: Helvetica, sans-serif;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8060 font-size: 0.9em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8061 line-height: 1.5em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8062 letter-spacing: -0.06em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8063 color: black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8064 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8065
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8066 div.big.prog_logo {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8067 font-size: 18px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8068 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8069
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8070 /* These are for centered columns in tables */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8071 td.ctr {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8072 text-align: center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8073 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8074
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8075 /* These are for the navigation bars at the top of outputs. */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8076 table.navigation {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8077 margin-top: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8078 border-collapse:collapse;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8079 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8080 table.navigation * td
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8081 {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8082 padding-left: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8083 padding-right: 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8084 padding-top: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8085 padding-bottom: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8086 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8087 </style>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8088 <style>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8089 .block_td {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8090 height:25px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8091 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8092 .block_container {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8093 position:relative;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8094 box-sizing: border-box;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8095 height: 25px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8096 padding: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8097 margin: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8098 margin-left: 1em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8099 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8100 .block_label {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8101 position: absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8102 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8103 padding: 3px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8104 z-index: 4;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8105 top: 6px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8106 height: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8107 line-height: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8108 font-size: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8109 background-color: white;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8110 border: 1px solid black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8111 -moz-border-radius: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8112 -webkit-border-radius: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8113 border-radius: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8114 transform: translateX(-50%);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8115 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8116 .block_motif {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8117 position: absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8118 z-index: 3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8119 top: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8120 box-sizing: border-box;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8121 border: 1px solid black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8122 height: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8123 background-color: cyan;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8124 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8125 .block_motif.top {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8126 border-bottom-width: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8127 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8128 .block_motif.bottom {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8129 border-top-width: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8130 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8131 .block_motif.scanned_site {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8132 opacity: 0.3;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8133 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8134 .block_motif.scanned_site.active {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8135 opacity: 0.9;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8136 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8137 .block_region {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8138 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8139 z-index:6;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8140 height:25px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8141 top:0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8142 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8143 .block_region.main {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8144 z-index:8;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8145 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8146 .block_region.scanned_site {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8147 z-index:5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8148 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8149 .block_region.scanned_site.main {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8150 z-index:7;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8151 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8152 .block_region.top {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8153 height:13px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8154 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8155 .block_region.bottom {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8156 height:13px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8157 top:12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8158 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8159 .block_rule {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8160 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8161 z-index:2;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8162 width:100%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8163 height:1px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8164 top:12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8165 left:0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8166 background-color:gray;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8167 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8168 .block_plus_sym {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8169 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8170 z-index:4;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8171 line-height:12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8172 top:0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8173 left:-1em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8174 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8175 .block_minus_sym {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8176 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8177 z-index:4;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8178 line-height:12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8179 top:13px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8180 left:-1em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8181 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8182
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8183 .tic_major {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8184 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8185 top:0em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8186 height:0.5em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8187 width: 2px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8188 margin-left: -1px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8189 background-color: blue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8190 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8191 .tic_minor {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8192 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8193 top:0em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8194 height:0.2em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8195 width: 1px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8196 margin-left: -0.5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8197 background-color: blue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8198 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8199 .tic_label {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8200 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8201 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8202 top:0.5em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8203 height: 1em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8204 color: blue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8205 transform: translateX(-50%);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8206 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8207
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8208 .block_needle {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8209 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8210 z-index:4;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8211 height:30px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8212 width:1px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8213 top:-2px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8214 background-color:gray;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8215 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8216 .block_needle.right {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8217 height: 60px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8218 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8219 .block_handle {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8220 position: absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8221 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8222 z-index: 5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8223 top: 27px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8224 min-width: 3ex;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8225 text-align: center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8226 font-size: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8227 line-height: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8228 transform: translateX(-50%);
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8229 background-color: LightGrey;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8230 border:3px outset grey;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8231 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8232 -webkit-user-select: none; /* Chrome/Safari */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8233 -moz-user-select: none; /* Firefox */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8234 -ms-user-select: none; /* IE10+ */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8235 /* Rules below not implemented in browsers yet */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8236 -o-user-select: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8237 user-select: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8238 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8239 .block_handle.right {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8240 top: 47px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8241 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8242
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8243 .legend_container {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8244 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8245 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8246 .legend_entry {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8247 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8248 padding: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8249 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8250 div.legend_swatch {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8251 box-sizing: border-box;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8252 width: 15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8253 height: 15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8254 border: 1px solid black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8255 background-color: cyan;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8256 float: left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8257 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8258 div.legend_swatch input {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8259 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8260 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8261 .legend_text {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8262 line-height: 15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8263 margin-left: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8264 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8265 </style>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8266 <style>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8267 /* meme output specific css */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8268
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8269 div.pop_block {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8270 position:absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8271 z-index:5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8272 padding: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8273 border: 1px solid black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8274 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8275 background-color: white;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8276 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8277
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8278 #measure_match {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8279 position: absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8280 visibility: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8281 height: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8282 width: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8283 white-space: nowrap;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8284 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8285
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8286 div.template {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8287 position: absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8288 z-index: 1;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8289 left: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8290 top: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8291 visibility: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8292 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8293
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8294 table.block_information {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8295 margin-left: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8296 margin-right: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8297 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8298
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8299 table.block_information * th {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8300 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8301 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8302
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8303 *.hide_empty_seqs * tr.empty_seq {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8304 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8305 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8306
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8307 *.hide_only_scan * tr.only_scan {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8308 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8309 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8310
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8311 *.hide_only_scan * div.scanned_site {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8312 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8313 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8314
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8315 td.symaction {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8316 text-align: center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8317 text-decoration: underline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8318 font-size: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8319 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8320 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8321 div.sym_btn {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8322 display:inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8323 text-decoration: underline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8324 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8325 font-size: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8326 line-height:20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8327 text-align: center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8328 width: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8329 height: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8330 color: blue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8331 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8332 div.sym_btn:hover {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8333 color: white;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8334 background-color: blue;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8335 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8336
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8337 div.sym_btn.positioned {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8338 position: absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8339 top: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8340 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8341
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8342 div.actionbutton {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8343 display:inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8344 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8345 font-size: 18px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8346 line-height:20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8347 padding: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8348 margin: 10px 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8349 border: 1px solid black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8350 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8351
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8352 div.actionbutton:hover {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8353 color:#FFF;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8354 background-color:#000;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8355 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8356
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8357 div.param_box {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8358 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8359 margin-right: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8360 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8361
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8362 span.param {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8363 font-weight: bold;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8364 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8365
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8366 div.box + div.box {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8367 margin-top: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8368 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8369
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8370 div.sites_outer {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8371 position: relative;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8372 padding-top: 20px; /* height of header */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8373 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8374 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8375
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8376 div.sites_inner {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8377 overflow-x: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8378 overflow-y: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8379 max-height: 200px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8380 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8381 table.sites_tbl {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8382 border-collapse: collapse;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8383 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8384
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8385 div.sites_th_inner {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8386 position: absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8387 top: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8388 line-height: 20px; /* height of header */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8389 text-align: left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8390 padding-left: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8391 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8392 th.nopad div.sites_th_inner {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8393 padding-left: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8394 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8395 div.sites_th_hidden {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8396 visibility: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8397 height: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8398 padding: 0 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8399 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8400 th.nopad div.sites_th_hidden {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8401 padding: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8402 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8403 div.sites_inner * th {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8404 height: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8405 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8406
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8407 table.sites_tbl {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8408 overflow-x: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8409 overflow-y: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8410 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8411
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8412 .site_num {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8413 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8414 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8415 .site_name {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8416 padding:0px 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8417 text-align:left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8418 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8419 .site_strand {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8420 padding:0px 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8421 text-align:center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8422 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8423 .norc .site_strand, .norc .site_strand_title {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8424 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8425 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8426 .site_start {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8427 padding:0px 15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8428 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8429 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8430 .site_pvalue {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8431 text-align:center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8432 padding:0px 15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8433 text-align:right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8434 white-space: nowrap;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8435 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8436 .lflank, .rflank, .match, .alpha_symbol {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8437 font-weight:bold;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8438 font-size:15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8439 font-family: 'Courier New', Courier, monospace;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8440 color:gray;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8441 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8442
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8443 .site.lflank {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8444 text-align:right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8445 padding-right:5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8446 color:gray;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8447 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8448 .site.match {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8449 text-align:center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8450 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8451 .site.rflank {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8452 text-align:left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8453 padding-left:5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8454 padding-right: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8455 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8456
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8457 th.stop_reason {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8458 text-align: left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8459 padding-right: 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8460 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8461
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8462 th.motif_ordinal {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8463
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8464 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8465 td.motif_ordinal {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8466 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8467 padding-right: 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8468 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8469 th.motif_logo {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8470 padding-right: 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8471 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8472 td.motif_logo {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8473 padding-right: 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8474 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8475 th.motif_evalue {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8476 text-align:right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8477 padding-right: 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8478 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8479 td.motif_evalue {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8480 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8481 white-space: nowrap;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8482 padding-right: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8483 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8484 th.motif_nsites {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8485 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8486 padding-right: 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8487 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8488 td.motif_nsites {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8489 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8490 padding-right: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8491 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8492 th.motif_width {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8493 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8494 padding-right: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8495 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8496 td.motif_width {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8497 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8498 padding-right: 15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8499 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8500 th.motif_more {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8501 padding: 0 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8502 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8503 td.motif_more {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8504 text-align: center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8505 padding: 0 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8506 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8507 th.motif_submit {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8508 padding: 0 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8509 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8510 td.motif_submit {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8511 text-align: center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8512 padding: 0 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8513 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8514 th.motif_download {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8515 padding-left: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8516 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8517 td.motif_download {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8518 text-align: center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8519 padding-left: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8520 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8521
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8522
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8523 div.tabArea {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8524 font-size: 80%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8525 font-weight: bold;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8526 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8527
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8528 .norc div.tabArea {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8529 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8530 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8531
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8532 span.tab, span.tab:visited {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8533 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8534 color: #888;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8535 background-color: #ddd;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8536 border: 2px solid #ccc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8537 padding: 2px 1em;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8538 text-decoration: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8539 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8540 span.tab.middle {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8541 border-left-width: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8542 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8543 div.tabArea.base span.tab {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8544 border-top-width: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8545 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8546 div.tabArea.top span.tab {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8547 border-bottom-width: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8548 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8549
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8550 span.tab:hover {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8551 background-color: #bbb;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8552 border-color: #bbb;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8553 color: #666;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8554 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8555 span.tab.activeTab, span.tab.activeTab:hover, span.tab.activeTab:visited {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8556 background-color: white;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8557 color: black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8558 cursor: default;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8559 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8560 div.tabMain {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8561 border: 2px solid #ccc;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8562 background-color: white;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8563 padding: 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8564 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8565 div.tabMain.base {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8566 margin-top: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8567 display: inline-block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8568 max-width: 98%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8569 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8570
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8571 div.tabMain.top {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8572 margin-bottom: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8573 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8574
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8575 div.tabCenter {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8576 max-width: 100%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8577 overflow-x: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8578 height: 200px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8579 overflow-y: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8580 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8581
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8582 canvas.logo_rc {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8583 display:none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8584 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8585 .show_rc_logo > canvas {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8586 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8587 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8588 .show_rc_logo > canvas.logo_rc {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8589 display: block;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8590 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8591
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8592 canvas.scan_logo {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8593 margin-left: 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8594 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8595
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8596 div.blocks_outer {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8597 position: relative;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8598 padding-top: 20px; /* height of header */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8599 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8600
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8601 div.blocks_inner {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8602 overflow-x: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8603 overflow-y: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8604 max-height: 200px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8605 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8606 table.blocks_tbl {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8607 border-collapse: collapse;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8608 width: 100%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8609 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8610
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8611 table.blocks_tbl .blockdiag_name {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8612 white-space: nowrap
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8613 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8614
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8615 div.blocks_th_inner {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8616 position: absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8617 top: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8618 line-height: 20px; /* height of header */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8619 text-align: left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8620 padding-left: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8621 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8622 th.nopad div.blocks_th_inner {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8623 padding-left: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8624 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8625 div.blocks_th_hidden {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8626 visibility: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8627 height: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8628 padding: 0 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8629 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8630 th.nopad div.blocks_th_hidden {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8631 padding: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8632 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8633 div.blocks_inner * th {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8634 height: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8635 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8636
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8637 table.blocks_tbl {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8638 overflow-x: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8639 overflow-y: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8640 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8641 td.block_td {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8642 width: 99%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8643 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8644
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8645 *.blockdiag_num {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8646 text-align: right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8647 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8648
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8649 td.blockdiag_name {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8650 text-align: left;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8651 padding:0px 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8652 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8653
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8654 td.blockdiag_pvalue {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8655 padding:0px 10px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8656 text-align:right;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8657 white-space: nowrap;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8658 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8659
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8660 div.preview_btn {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8661 border: 2px solid white;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8662 height: 16px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8663 width: 16px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8664 font-size: 12px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8665 line-height: 16px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8666 text-align: center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8667 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8668 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8669 div.preview_btn + div.preview_btn {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8670 margin-top: 3px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8671 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8672
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8673 div.preview_btn.active {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8674 border: 2px solid black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8675 cursor: default;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8676 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8677
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8678 div.preview_btn:hover {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8679 background-color: black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8680 color: white;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8681 border-color: black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8682 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8683
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8684 div.preview_btn.active:hover {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8685 background-color: white;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8686 color: black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8687 border-color: black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8688 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8689
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8690
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8691 div.preview_btn_box {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8692 position: absolute;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8693 left: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8694 top: 0px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8695 padding: 3px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8696 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8697
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8698 div.preview_logo_box {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8699 height: 50px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8700 overflow-y: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8701 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8702
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8703 div.preview_btn_box + div.preview_logo_box {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8704 margin-left: 25px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8705 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8706
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8707 div.preview_box {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8708 position: relative;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8709 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8710
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8711 div.grey_background {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8712 position:fixed;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8713 z-index: 8;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8714 background-color: #000;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8715 -ms-filter: "progid:DXImageTransform.Microsoft.Alpha(Opacity=50)";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8716 opacity: 0.5;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8717 left: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8718 top: 0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8719 width: 100%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8720 height: 100%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8721 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8722
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8723 div.popup_wrapper {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8724 position:fixed;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8725 z-index:9;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8726 width:100%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8727 height:0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8728 top:50%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8729 left:0;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8730 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8731
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8732 div.popup {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8733 width: 600px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8734 z-index:9;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8735 margin-left: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8736 margin-right: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8737 padding: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8738 background-color: #FFF;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8739 border-style: double;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8740 border-width: 5px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8741 border-color: #00666a;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8742 position:relative;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8743 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8744 div.close {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8745 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8746 border: 1px solid black;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8747 width:15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8748 height:15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8749 line-height:15px; /* this causes vertical centering */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8750 text-align:center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8751 background-color:#FFF;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8752 color:#000;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8753 font-size:15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8754 font-family:monospace;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8755 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8756
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8757 div.close:hover {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8758 color:#FFF;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8759 background-color:#000;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8760 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8761
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8762 div.navnum {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8763 width:100%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8764 height:20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8765 line-height:20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8766 text-align:center;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8767 font-size:medium;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8768 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8769
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8770 div.navarrow {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8771 font-size: 30px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8772 text-decoration:none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8773 cursor: pointer;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8774 -moz-user-select: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8775 -webkit-user-select: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8776 -ms-user-select: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8777 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8778
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8779 div.navarrow > span.inactive {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8780 display: inline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8781 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8782 div.navarrow > span.active {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8783 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8784 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8785
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8786 div.navarrow:hover > span.active {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8787 display: inline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8788 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8789 div.navarrow:hover > span.inactive {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8790 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8791 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8792
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8793 table.programs {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8794 width: 100%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8795 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8796
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8797 table.programs tr {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8798 background-color: #EFE;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8799 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8800
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8801 table.programs tr.selected {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8802 background-color: #262;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8803 color: #FFF;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8804 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8805
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8806 table.programs tr.dna_only {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8807 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8808 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8809
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8810 table.programs.alphabet_dna tr.dna_only {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8811 display: table-row;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8812 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8813
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8814 div.programs_scroll {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8815 width: 100%;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8816 height: 90px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8817 overflow-y: auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8818 overflow-x: hidden;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8819 margin: 0 auto;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8820 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8821 table.inputs, table.alpha_bg_table {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8822 margin-top: 20px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8823 border-collapse:collapse;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8824 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8825 table.inputs * td, table.inputs * th, table.alpha_bg_table * td, table.alpha_bg_table * th {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8826 padding-left: 15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8827 padding-right: 15px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8828 padding-top: 1px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8829 padding-bottom: 1px;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8830 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8831
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8832 table.hide_psp td.col_psp, table.hide_psp th.col_psp {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8833 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8834 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8835
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8836 table.hide_control td.col_control, table.hide_control th.col_control {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8837 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8838 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8839
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8840 /* program settings */
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8841 span.mod_oops, span.mod_zoops, span.mod_anr {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8842 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8843 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8844 td.oops span.mod_oops,td.zoops span.mod_zoops, td.anr span.mod_anr {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8845 display: inline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8846 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8847 span.strand_none, span.strand_given, span.strand_both {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8848 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8849 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8850 td.none span.strand_none, td.given span.strand_given, td.both span.strand_both {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8851 display: inline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8852 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8853 span.spmap_uni, span.spmap_pam {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8854 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8855 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8856 td.uni span.spmap_uni, td.pam span.spmap_pam {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8857 display: inline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8858 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8859 span.prior_dirichlet, span.prior_dmix, span.prior_mega, span.prior_megap, span.prior_addone {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8860 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8861 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8862 td.dirichlet span.prior_dirichlet, td.dmix span.prior_dmix, td.mega span.prior_mega,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8863 td.megap span.prior_megap, td.addone span.prior_addone {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8864 display: inline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8865 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8866 span.noendgaps_on, span.noendgaps_off {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8867 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8868 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8869 td.on span.noendgaps_on, td.off span.noendgaps_off {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8870 display: inline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8871 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8872 span.substring_on, span.substring_off {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8873 display: none;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8874 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8875 td.on span.substring_on, td.off span.substring_off {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8876 display: inline;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8877 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8878 </style>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8879 </head>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8880 <body onload="page_loaded()" onpageshow="page_shown(event)" onresize="page_resized()">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8881 <!-- -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8882 <div id="grey_out_page" class="grey_background" style="display:none;">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8883 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8884 <!-- Help popups -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8885 <div class="pop_content" id="pop_results_txt">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8886 <p>MEME results in plain text format.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8887 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8888 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8889 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8890 <div class="pop_content" id="pop_results_xml">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8891 <p>MEME results in XML format.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8892 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8893 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8894 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8895 <div class="pop_content" id="pop_">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8896 <p>Help poup.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8897 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8898 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8899 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8900 <div class="pop_content" id="pop_logo">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8901 <script>print_doc_para("pop_logo", "discovery", "motif_logo", site_url);</script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8902 Click on the "+" or "-" buttons to the left of the motif to see
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8903 the forward or reverse complement of the motif if available.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8904 <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8905 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8906 <div class="pop_content" id="pop_ev">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8907 <p>The statistical significance of the motif. MEME usually finds the most
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8908 statistically significant (low E-value) motifs first. It is unusual to
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8909 consider a motif with an E-value larger than 0.05 significant so, as an
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8910 additional indicator, MEME displays these greyed out.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8911 <p>The E-value of a motif is based on its log likelihood ratio, width,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8912 sites, the background letter frequencies (given in the command line
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8913 summary), and the size of the training set.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8914 <p>The E-value is an estimate of the expected number of motifs with the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8915 given log likelihood ratio (or higher), and with the same width and site
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8916 count, that one would find in a similarly sized set of random
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8917 sequences (sequences where each position is independent and letters are
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8918 chosen according to the background letter frequencies).</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8919 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8920 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8921 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8922 <div class="pop_content" id="pop_sites">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8923 <p>The number of sites contributing to the construction of the motif.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8924 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8925 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8926 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8927 <div class="pop_content" id="pop_width">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8928 <p>The width of the motif. Each motif describes a pattern of a fixed
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8929 width, as no gaps are allowed in MEME motifs.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8930 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8931 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8932 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8933 <div class="pop_content" id="pop_more">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8934 <script>print_doc_para("pop_more", "discovery", "more");</script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8935 <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8936 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8937 <div class="pop_content" id="pop_submit_dl">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8938 <script>print_doc_para("pop_submit_dl", "discovery", "submit_dl", "https://meme-suite.org/meme");</script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8939 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8940 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8941 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8942 <div class="pop_content" id="pop_llr">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8943 <p>The log likelihood ratio of the motif. The log likelihood ratio is the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8944 logarithm of the ratio of the probability of the occurrences of the motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8945 given the motif model (likelihood given the motif) versus their
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8946 probability given the background model (likelihood given the null model).
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8947 (Normally the background model is a 0-order Markov model using the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8948 background letter frequencies, but higher order Markov models may be
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8949 specified via the -bfile option to MEME.).</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8950 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8951 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8952 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8953 <div class="pop_content" id="pop_ic">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8954 <p>The information content of the motif in bits. It is equal to the sum
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8955 of the uncorrected information content, R(), in the columns of the motif.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8956 This is equal relative entropy of the motif relative to a uniform
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8957 background frequency model.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8958 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8959 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8960 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8961 <div class="pop_content" id="pop_re">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8962 <p>The relative entropy of the motif.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8963
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8964 <p style="font-family: monospace;">re = llr / (sites * ln(2))</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8965 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8966 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8967 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8968 <div class="pop_content" id="pop_bt">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8969 <p>The Bayes Threshold.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8970 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8971 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8972 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8973 <div class="pop_content" id="pop_site_strand">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8974 <p>The strand used for the motif site.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8975 <dl>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8976 <dt>+</dt>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8977 <dd>The motif site was found in the sequence as it was supplied.</dd>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8978 <dt>-</dt>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8979 <dd>The motif site was found in the reverse complement of the supplied sequence.</dd>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8980 </dl>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8981 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8982 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8983 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8984 <div class="pop_content" id="pop_site_start">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8985 <p>The position in the sequence where the motif site starts. If a motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8986 started right at the beginning of a sequence it would be described as
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8987 starting at position 1.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8988 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8989 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8990 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8991 <div class="pop_content" id="pop_site_pvalue">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8992 <p>The probability that an equal or better site would be found in a
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8993 random sequence of the same length conforming to the background letter
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8994 frequencies.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8995 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8996 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8997 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8998 <div class="pop_content" id="pop_site_match">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
8999 <p>A motif site with the 10 flanking letters on either side.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9000 <p>When the site is not on the given strand then the site
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9001 and both flanks are reverse complemented so they align.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9002 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9003 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9004 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9005
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9006 <div class="pop_content" id="pop_seq_name">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9007 <p>The name of the sequences as given in the FASTA file.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9008 <p>The number to the left of the sequence name is the position
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9009 of the sequence in the input sequence file.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9010 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9011 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9012 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9013
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9014 <div class="pop_content" id="pop_motif_sites">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9015 <p>These are the motif sites predicted by MEME and used to build the motif.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9016 <p>These sites are shown in solid color and hovering the cursor
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9017 over a site will reveal details about the site. Only sequences
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9018 that contain a motif site are shown.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9019 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9020 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9021 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9022
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9023 <div class="pop_content" id="pop_scanned_sites">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9024 <p>These are the motif sites predicted by MEME plus
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9025 any additional sites detected using a motif scanning
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9026 algorithm.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9027 <p>These MEME sites are shown in solid color and
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9028 additional scanned sites are shown greyed out.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9029 Hovering the cursor over a site will reveal details about the site.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9030 Only sequences containing a predicted or scanned motif site are shown.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9031 <p>The scanned sites are predicted using a
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9032 log-odds scoring matrix constructed from the MEME sites.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9033 Only scanned sites with position <i>p</i>-values less
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9034 than 0.0001 are shown.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9035 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9036 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9037 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9038
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9039 <div class="pop_content" id="pop_all_sequences">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9040 <p>These are the same sites as shown by selecting the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9041 "Motif Sites + Scanned Sites" button except that all
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9042 sequences, including those with no sites, are included
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9043 in the diagram.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9044 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9045 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9046 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9047
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9048 <div class="pop_content" id="pop_seq_pvalue">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9049 <p>This is the combined match <i>p</i>-value.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9050 <p>The combined match <i>p</i>-value is defined as the probability that a
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9051 random sequence (with the same length and conforming to the background)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9052 would have position <i>p</i>-values such that the product is smaller
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9053 or equal to the value calculated for the sequence under test.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9054 <p>The position <i>p</i>-value is defined as the probability that a
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9055 random sequence (with the same length and conforming to the background)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9056 would have a match to the motif under test with a score greater or equal
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9057 to the largest found in the sequence under test.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9058 <p>Hovering your mouse over a motif site in the motif location
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9059 block diagram will show its position <i>p</i>-value and other information
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9060 about the site.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9061 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9062 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9063 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9064
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9065 <div class="pop_content" id="pop_download_pdf_motif_locations">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9066 <p>Use this button to download the "Motif Locations" block diagrams
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9067 as a PDF image suitable for publication.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9068 </p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9069 <p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9070 Only the block diagrams currently visible in the inner scrolling
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9071 window (below) will be included in the image, and the numbers to
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9072 the left of each sequence name will not be included in the image.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9073 You can change the size of the inner scrolling by moving the bottom
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9074 of the main document window up and down. You can display more
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9075 diagrams by making your browser's font size smaller.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9076 </p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9077 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9078 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9079 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9080
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9081 <div class="pop_content" id="pop_download_svg_motif_locations">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9082 <p>Use this button to download the "Motif Locations" block diagrams
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9083 as a SVG image use in HTML documents.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9084 </p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9085 <p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9086 Only the block diagrams currently visible in the inner scrolling
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9087 window (below) will be included in the image, and the numbers to
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9088 the left of each sequence name will not be included in the image.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9089 You can change the size of the inner scrolling by moving the bottom
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9090 of the main document window up and down. You can display more
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9091 diagrams by making your browser's font size smaller.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9092 </p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9093 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9094 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9095 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9096
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9097 <div class="pop_content" id="pop_offline">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9098 <p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9099 This button will only function if your browser was
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9100 connected to the internet when you loaded this page.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9101 </p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9102 <p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9103 To use this button, make sure your browser is connected to the internet
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9104 and then reload this page. (You may need to do a "hard refresh" to clear the cache.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9105 On Mac, hold down the Shift key and click the Reload button.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9106 On Windows/Linux, hold down Ctrl and press F5.)
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9107 </p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9108 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9109 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9110 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9111
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9112 <div class="pop_content" id="pop_motif_location">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9113 <p>This diagram shows the location of motif sites.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9114 <p>Each block shows the position and strength of a motif
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9115 site. The height of a block gives an indication of the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9116 significance of the site as taller blocks are more significant.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9117 The height is calculated to be proportional to the negative
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9118 logarithm of the <i>p</i>-value of the site, truncated at
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9119 the height for a <i>p</i>-value of 1e-10.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9120 <p>For complementable alphabets (like DNA), sites on the
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9121 positive strand are shown above the line,
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9122 sites on the negative strand are shown below.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9123 <p>Placing the cursor
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9124 over a motif site will reveal more information about the site
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9125 including its position <i>p</i>-value. (See the help
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9126 for the <i>p</i>-value column for an explanation of position
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9127 <i>p</i>-values.)</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9128 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9129 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9130 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9131
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9132 <div class="pop_content" id="pop_seq_source">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9133 <p>The name of the file(s) of sequences input to MEME.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9134 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9135 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9136 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9137 <div class="pop_content" id="pop_psp_source">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9138 <p>The position specific priors file used by MEME to find the motifs.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9139 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9140 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9141 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9142 <div class="pop_content" id="pop_seq_alph">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9143 <p>The alphabet used by the sequences.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9144 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9145 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9146 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9147 <div class="pop_content" id="pop_seq_count">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9148 <p>The number of FASTA sequences provided in this input file.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9149 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9150 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9151 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9152 <div class="pop_content" id="pop_num_positions">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9153 <p>The number of characters in the sequences provided in this FASTA input file.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9154 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9155 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9156 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9157
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9158 <div class="pop_content" id="pop_alph_name">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9159 <p>The name of the alphabet symbol.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9160 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9161 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9162 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9163 <div class="pop_content" id="pop_alph_freq">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9164 <p>The frequency of the alphabet symbol in the dataset.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9165 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9166 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9167 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9168 <div class="pop_content" id="pop_alph_bg">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9169 <p>The frequency of the alphabet symbol as defined by the background model.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9170 <div style="float:right; bottom:0px;">[
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9171 <a href="javascript:help_popup()">close</a> ]</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9172 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9173
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9174 <!-- templates -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9175 <div id="measure_match" class="match"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9176 <div class="template pop_block" id="tmpl_block_info">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9177 <div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9178 <span class="tvar_logo_pad lflank" style="visibility:hidden;"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9179 <span class="tvar_logo"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9180 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9181 <div class="block_sequence_fragment">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9182 <span class="tvar_lflank lflank"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9183 <span class="tvar_match match"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9184 <span class="tvar_rflank rflank"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9185 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9186 <table class="block_information">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9187 <tr><th>Motif</th><td class="tvar_motif">1</td></tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9188 <tr><th><i>p</i>-value</th><td class="tvar_pvalue">8.23e-7</td></tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9189 <tr><th>Start</th><td class="tvar_start">23</td></tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9190 <tr><th>End</th><td class="tvar_end">33</td></tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9191 </table>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9192 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9193
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9194 <div class="template pop_block" id="tmpl_scan_info">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9195 <h5>Scanned Site</h5>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9196 <div class="tvar_logo"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9197 <table class="block_information">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9198 <tr><th>Motif</th><td class="tvar_motif">1</td></tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9199 <tr><th><i>p</i>-value</th><td class="tvar_pvalue">8.23e-7</td></tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9200 <tr><th>Start</th><td class="tvar_start">23</td></tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9201 <tr><th>End</th><td class="tvar_end">33</td></tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9202 </table>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9203 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9204
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9205 <div class="template box expanded_motif" id="tmpl_motif_expanded">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9206 <div style="position: relative; min-height: 20px">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9207 <div class="param_box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9208 <span class="param"><span class="tvar_ordinal"></span>.</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9209 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9210 <div class="sym_btn positioned tvar_less" tabindex="0"
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9211 title="Show less information.">&#8613;</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9212 <div class="sym_btn positioned tvar_submit" tabindex="0"
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9213 title="Submit the motif to another MEME Suite program or download it.">&#8674;</div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9214 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9215 <div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9216 <div class="param_box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9217 <span class="param"><i>E</i>-value:</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9218 <span class="tvar_evalue"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9219 <div class="help" data-topic="pop_ev"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9220 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9221 <div class="param_box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9222 <span class="param">Site Count:</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9223 <span class="tvar_site_count"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9224 <div class="help" data-topic="pop_sites"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9225 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9226 <div class="param_box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9227 <span class="param">Width:</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9228 <span class="tvar_width"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9229 <div class="help" data-topic="pop_width"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9230 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9231 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9232 <div class="tabMain base">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9233 <div class="tabCenter tvar_logo"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9234 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9235 <div class="tabArea base">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9236 <span class="tvar_tab tab" tabindex="0">Standard</span><span
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9237 class="tvar_tab_rc tab middle" tabindex="0">Reverse
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9238 Complement</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9239 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9240 <div style="padding: 10px 0">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9241 <div class="param_box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9242 <span class="param">Log Likelihood Ratio:</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9243 <span class="tvar_llr"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9244 <div class="help" data-topic="pop_llr"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9245 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9246 <div class="param_box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9247 <span class="param">Information Content:</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9248 <span class="tvar_ic"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9249 <div class="help" data-topic="pop_ic"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9250 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9251 <div class="param_box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9252 <span class="param">Relative Entropy:</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9253 <span class="tvar_re"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9254 <div class="help" data-topic="pop_re"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9255 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9256 <div class="param_box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9257 <span class="param">Bayes Threshold:</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9258 <span class="tvar_bt"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9259 <div class="help" data-topic="pop_bt"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9260 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9261 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9262 <div class="tvar_sites"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9263 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9264
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9265 <div id="tab_submit_or_download_motif"></div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9266 <script> make_submit_or_download_motif_form("tab_submit_or_download_motif", site_url, "MEME"); </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9267
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9268 <!-- Page starts here -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9269 <div id="top" class="pad1">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9270 <div class="prog_logo big">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9271 <img src="data:image/png;base64,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" alt="MEME Logo">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9272 <h1>MEME</h1>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9273 <h2>Multiple Em for Motif Elicitation</h2>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9274 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9275 <p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9276 For further information on how to interpret these results please access
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9277 <a href="https://meme-suite.org/meme/doc/meme.html">https://meme-suite.org/meme/doc/meme.html</a>. <br />
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9278 To get a copy of the MEME software please access
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9279 <a href="https://meme-suite.org">https://meme-suite.org</a>.
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9280 </p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9281 <p id="citation"> <script>print_citation("citation", "MEME");</script></p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9282 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9283 <!-- navigation -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9284 <div class="pad2">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9285 <a class="jump" href="#motifs_sec">Discovered Motifs</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9286 &nbsp;&nbsp;|&nbsp;&nbsp;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9287 <a class="jump" href="#sites_sec">Motif Locations</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9288 &nbsp;&nbsp;|&nbsp;&nbsp;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9289 <a class="jump" href="#inputs_sec">Inputs &amp; Settings</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9290 &nbsp;&nbsp;|&nbsp;&nbsp;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9291 <a class="jump" href="#info_sec">Program Information</a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9292 &nbsp;&nbsp;|&nbsp;&nbsp;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9293 <a class="jump" href="meme.txt">Results in Text Format</a>&nbsp;<span id="results_txt_help"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9294 &nbsp;&nbsp;|&nbsp;&nbsp;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9295 <a class="jump" href="meme.xml">Results in XML Format</a>&nbsp;<span id="results_xml_help"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9296 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9297 make_help_button($("results_txt_help"), "pop_results_txt");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9298 make_help_button($("results_xml_help"), "pop_results_xml");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9299 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9300 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9301 <!-- alert the user when their browser is not up to the task -->
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9302 <noscript><h1 style="color:red">Javascript is required to view these results!</h1></noscript>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9303 <h1 id="html5_warning" style="color:red; display:none;">Your browser does not support canvas!</h1>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9304 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9305 if (!window.HTMLCanvasElement) $("html5_warning").style.display = "block";
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9306 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9307 <h2 class="mainh pad2" id="motifs_sec">Discovered Motifs</h2>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9308 <div id="motifs" class="box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9309 <p>Please wait... Loading...</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9310 <p>If the page has fully loaded and this message does not disappear then an error may have occurred.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9311 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9312 <h2 class="mainh pad2" id="sites_sec">Motif Locations</h2>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9313 <div id="blocks" class="box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9314 <p>Please wait... Loading...</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9315 <p>If the page has fully loaded and this message does not disappear then an error may have occurred.</p>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9316 </div>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9317 <h2 class="mainh pad2" id="inputs_sec">Inputs &amp; Settings</h2>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9318 <div class="box">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9319 <h4>Sequences</h4>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9320 <table id="seq_info" class="inputs">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9321 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9322 <th>Role <div class="help" data-topic="pop_seq_role"></div></th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9323 <th>Source <div class="help" data-topic="pop_seq_source"></div></th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9324 <th class="col_psp">PSP Source <div class="help" data-topic="pop_psp_source"></div></th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9325 <th>Alphabet <div class="help" data-topic="pop_seq_alph"></div></th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9326 <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9327 <th>Total Size <div class="help" data-topic="pop_num_positions"></div></th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9328 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9329 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9330 <td>Primary Sequences</td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9331 <td id="ins_seq_source"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9332 <td id="ins_seq_psp" class="col_psp"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9333 <td id="ins_seq_alphabet"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9334 <td id="ins_seq_count"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9335 <td id="ins_num_positions"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9336 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9337 <tr class="col_control">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9338 <td class="col_control">Control Sequences</td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9339 <td id="ins_control_source" class="col_control"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9340 <td id="ins_control_psp" class="col_control col_psp"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9341 <td id="ins_control_alphabet" class="col_control"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9342 <td id="ins_control_count" class="col_control"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9343 <td id="ins_control_positions" class="col_control"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9344 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9345 </table>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9346 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9347 {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9348 var db = data.sequence_db;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9349 $("ins_seq_source").innerHTML = db.primary_source;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9350 $("ins_seq_alphabet").innerHTML = current_alphabet.get_alphabet_name();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9351 $("ins_seq_count").innerHTML = db.primary_count;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9352 $("ins_num_positions").innerHTML = db.primary_positions;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9353 $("ins_control_source").innerHTML = db.control_source;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9354 $("ins_control_alphabet").innerHTML = current_alphabet.get_alphabet_name();
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9355 $("ins_control_count").innerHTML = db.control_count;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9356 $("ins_control_positions").innerHTML = db.control_positions;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9357 if (db.psp_source) {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9358 $("ins_seq_psp").innerHTML = db.psp_source;
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9359 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9360 toggle_class($("seq_info"), "hide_psp", !(db.psp_source));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9361 toggle_class($("seq_info"), "hide_control", (db.control_source == "--none--"));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9362 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9363 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9364 <h4>Background Model</h4>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9365 <span id="bg_source"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9366 <span id="bg_order"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9367 <span id="alpha_bg"></span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9368 <script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9369 {
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9370 $("bg_source").appendChild(make_background_source("Source", data.background.source, false));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9371 $("bg_order").innerHTML = "&nbsp;&nbsp;&nbsp;&nbsp;<b>Order:</b> " + data.background.order +
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9372 (data.background.order>0 ? " (only order-0 shown)" : "");
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9373 $("alpha_bg").appendChild(make_alpha_bg_table(current_alphabet, data.sequence_db.freqs));
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9374 }
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9375 </script>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9376 <h4>Other Settings</h4>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9377 <table id="tbl_settings" class="inputs hide_advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9378 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9379 <th>Motif Site Distribution</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9380 <td id="opt_mod">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9381 <span class="mod_zoops">ZOOPS: Zero or one site per sequence</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9382 <span class="mod_oops">OOPS: Exactly one site per sequence</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9383 <span class="mod_anr">ANR: Any number of sites per sequence</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9384 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9385 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9386 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9387 <th>Objective Function</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9388 <td id=opt_objfun></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9389 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9390 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9391 <th>Starting Point Function</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9392 <td id=opt_spfun></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9393 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9394 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9395 <th>Site Strand Handling</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9396 <td id="opt_strand">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9397 <span class="strand_none">This alphabet only has one strand</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9398 <span class="strand_given">Sites must be on the given strand</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9399 <span class="strand_both">Sites may be on either strand</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9400 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9401 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9402 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9403 <th>Maximum Number of Motifs</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9404 <td id="opt_nmotifs"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9405 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9406 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9407 <th>Motif E-value Threshold</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9408 <td id="opt_evt"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9409 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9410 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9411 <th>Minimum Motif Width</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9412 <td id="opt_minw"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9413 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9414 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9415 <th>Maximum Motif Width</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9416 <td id="opt_maxw"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9417 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9418 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9419 <th>Minimum Sites per Motif</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9420 <td id="opt_minsites"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9421 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9422 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9423 <th>Maximum Sites per Motif</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9424 <td id="opt_maxsites"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9425 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9426 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9427 <th>Bias on Number of Sites</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9428 <td id="opt_wnsites"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9429 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9430 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9431 <th>Sequence Prior</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9432 <td id="opt_prior">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9433 <span class="prior_dirichlet">Simple Dirichlet</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9434 <span class="prior_dmix">Dirichlet Mixture</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9435 <span class="prior_mega">Mega-weight Dirichlet Mixture</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9436 <span class="prior_megap">Mega-weight Dirichlet Mixture Plus</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9437 <span class="prior_addone">Add One</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9438 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9439 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9440 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9441 <th>Sequence Prior Source</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9442 <td id="opt_prior_source"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9443 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9444 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9445 <th>Sequence Prior Strength</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9446 <td id="opt_b"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9447 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9448 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9449 <th>EM Starting Point Source</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9450 <td id="opt_substring">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9451 <span class="substring_on">From substrings in input sequences</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9452 <span class="substring_off">From strings on command line (-cons)</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9453 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9454 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9455 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9456 <th>EM Starting Point Map Type</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9457 <td id="opt_spmap">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9458 <span class="spmap_uni">Uniform</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9459 <span class="spmap_pam">Point Accepted Mutation</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9460 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9461 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9462 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9463 <th>EM Starting Point Fuzz</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9464 <td id="opt_spfuzz"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9465 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9466 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9467 <th>EM Maximum Iterations</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9468 <td id="opt_maxiter"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9469 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9470 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9471 <th>EM Improvement Threshold</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9472 <td id="opt_distance"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9473 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9474 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9475 <th>Maximum Search Size</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9476 <td id="opt_searchsize"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9477 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9478 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9479 <th>Maximum Number of Sites for E-values</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9480 <td id="opt_csites"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9481 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9482 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9483 <th>Trim Gap Open Cost</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9484 <td id="opt_wg"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9485 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9486 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9487 <th>Trim Gap Extend Cost</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9488 <td id="opt_ws"></td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9489 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9490 <tr class="advanced">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9491 <th>End Gap Treatment</th>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9492 <td id="opt_noendgaps">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9493 <span class="noendgaps_on">No cost</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9494 <span class="noendgaps_off">Same cost as other gaps</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9495 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9496 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9497 <tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9498 <td colspan="2" style="text-align: center">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9499 <a href="javascript:toggle_class(document.getElementById('tbl_settings'), 'hide_advanced')">
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9500 <span class="show_more">Show Advanced Settings</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9501 <span class="show_less">Hide Advanced Settings</span>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9502 </a>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9503 </td>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9504 </tr>
613c75eee7bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 89ee0af6e955ff964b7984d77ad536e0a9154278
iuc
parents: 18
diff changeset
9505 </table>
18
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9506 <script>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9507 {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9508 $("opt_mod").className = data.options.mod;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9509 $("opt_objfun").textContent = data.options.objfun;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9510 $("opt_spfun").textContent = data.options.spfun;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9511 $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9512 $("opt_nmotifs").textContent = data.options.nmotifs;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9513 $("opt_evt").textContent = (typeof data.options.evt === "number" ? data.options.evt : "no limit");
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9514 $("opt_minw").textContent = data.options.minw;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9515 $("opt_maxw").textContent = data.options.maxw;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9516 $("opt_minsites").textContent = data.options.minsites;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9517 $("opt_maxsites").textContent = data.options.maxsites;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9518 $("opt_wnsites").textContent = data.options.wnsites;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9519 $("opt_spmap").className = data.options.spmap;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9520 $("opt_spfuzz").textContent = data.options.spfuzz;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9521 $("opt_prior").className = data.options.prior;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9522 if (data.options.prior == "dirichlet") {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9523 $("opt_prior_source").textContent = make_background_source("Source", data.background.source, true);
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9524 } else {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9525 $("opt_prior_source").textContent = (data.options.prior == "addone") ? "motif observed frequencies" : data.options.priors_source;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9526 }
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9527 $("opt_b").textContent = (data.options.b < 0) ? "not applicable" : (data.options.b == 0) ? "intrinsic strength" : data.options.b;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9528 $("opt_maxiter").textContent = data.options.maxiter;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9529 $("opt_distance").textContent = data.options.distance;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9530 $("opt_searchsize").textContent = data.options.searchsize;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9531 if (typeof data.options.csites != "undefined") {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9532 $("opt_csites").textContent = data.options.csites;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9533 } else {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9534 $("opt_csites").parentElement.style.display = "none"
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9535 }
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9536 if (typeof data.options.wg != "undefined") {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9537 $("opt_wg").textContent = data.options.wg;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9538 } else {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9539 $("opt_wg").parentElement.style.display = "none"
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9540 }
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9541 if (typeof data.options.ws != "undefined") {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9542 $("opt_ws").textContent = data.options.ws;
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9543 }
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9544 else {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9545 $("opt_ws").parentElement.style.display = "none"
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9546 }
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9547 if (typeof data.options.noendgaps != "undefined") {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9548 $("opt_noendgaps").className = (data.options.noendgaps ? "on" : "off");
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9549 }
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9550 else {
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9551 $("opt_noendgaps").parentElement.style.display = "none"
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9552 }
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9553 $("opt_substring").className = (data.options.substring ? "on" : "off");
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9554 }
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9555 </script>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9556 </div>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9557 <!-- list information on this program -->
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9558 <div id="info_sec" class="bar">
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9559 <div class="subsection">
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9560 <h5 id="version">MEME version</h5>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9561 <span id="ins_version"></span>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9562 (Release date: <span id="ins_release"></span>)<br>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9563 </div>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9564 <script>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9565 $("ins_version").innerHTML = data["version"];
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9566 $("ins_release").innerHTML = data["release"];
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9567 </script>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9568 <div class="subsection" id="reference"> <script>print_citation("reference", "MEME");</script></div>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9569 <div class="subsection">
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9570 <h5 id="command">Command line</h5>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9571 <textarea id="cmd" rows="5" style="width:100%;" readonly="readonly">
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9572 </textarea>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9573 <script>$("cmd").value = data["cmd"].join(" ");</script>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9574 </div>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9575 </div>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9576
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9577 </body>
c5209f38700d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 03235f29be6368f58bc730a20d87a13cf215310f"
iuc
parents: 15
diff changeset
9578 </html>