meme_psp_gen: test-data/dreme_output

comparison test-data/dreme_output_test2.html @ 3:ff2f53a32d0e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"

author	iuc
date	Wed, 11 Dec 2019 18:04:34 -0500
parents	b48e673af4e8
children	5f95d385a33c

comparison

equal deleted inserted replaced

-:b48e673af4e8
+:ff2f53a32d0e
 <title>DREME</title>
 <script>
 // @JSON_VAR data
 var data = {
 "program": "dreme",
-"version": "4.12.0",
+"version": "5.0.5",
-"release": "Tue Jun 27 16:22:50 2017 -0700",
+"release": "Mon Mar 18 20:12:19 2019 -0700",
 "cmd": [
-"dreme", "-o", "./dreme_test2_out", "-p", "dreme_test_sites.fa",
+"dreme", "-o", "./dreme_out", "-p",
 "-norc", "-rna", "-s", "1", "-e", "1e-05", "-g", "100", "-mink",
 "4", "-maxk", "10"
 ],
 "options": {
 "revcomp": false,
 "colour": "CC0000"
 }, {
 "symbol": "C",
 "name": "Cytosine",
 "colour": "0000CC"
-}, {
 "symbol": "G",
 "name": "Guanine",
 "colour": "FFB300"
-}, {
 "symbol": "U",
 "aliases": "T",
 "name": "Uracil",
 "colour": "008000"
-}, {
 "symbol": "N",
 "aliases": "X.",
 "name": "Any base",
 "equals": "ACGU"
-}, {
 "symbol": "V",
 "name": "Not U",
 "equals": "ACG"
-}, {
 "symbol": "H",
 "name": "Not G",
 "equals": "ACU"
-}, {
 "symbol": "D",
 "name": "Not C",
 "equals": "AGU"
-}, {
 "symbol": "B",
 "name": "Not A",
 "equals": "CGU"
-}, {
 "symbol": "M",
 "name": "Amino",
 "equals": "AC"
-}, {
 "symbol": "R",
 "name": "Purine",
 "equals": "AG"
-}, {
 "symbol": "W",
 "name": "Weak",
 "equals": "AU"
-}, {
 "symbol": "S",
 "name": "Strong",
 "equals": "CG"
-}, {
 "symbol": "Y",
 "name": "Pyrimidine",
 "equals": "CU"
-}, {
 "symbol": "K",
 "name": "Keto",
 "equals": "GU"
-}
-]
-},
 "background": {
 "freqs": [0.221, 0.245, 0.221, 0.312]
-},
 "sequence_db": {
-"name": "dreme test sites",
-"file": "dreme_test_sites.fa",
-"lmod": "Thu Apr 26 15:09:03 CEST 2018",
 "count": 1000
-},
 "control_db": {
 "name": "shuffled positive sequences",
 "from": "shuffled",
 "count": 1000,
 "freqs": [0.221, 0.245, 0.221, 0.312]
-},
 "motifs": [
-{
 "db": 0,
 "id": "UUYUCY",
 "alt": "DREME-1",
 "len": 6,
 "nsites": 459,
 [0.000000, 0.000000, 0.000000, 1.000000],
 [0.000000, 0.294118, 0.000000, 0.705882],
 [0.000000, 0.000000, 0.000000, 1.000000],
 [0.000000, 1.000000, 0.000000, 0.000000],
 [0.000000, 0.474946, 0.000000, 0.525054]
-],
 "matches": [
-{
 "seq": "UUUUCC",
 "p": 147,
 "n": 75,
 "pvalue": "1.8e-007",
 "evalue": "2.2e-002"
-}, {
-"seq": "UUUUCU",
-"p": 155,
-"n": 94,
-"pvalue": "2.2e-005",
-"evalue": "2.8e+000"
-}, {
-"seq": "UUCUCU",
-"p": 94,
-"n": 51,
-"pvalue": "1.3e-004",
-"evalue": "1.7e+001"
-}, {
-"seq": "UUCUCC",
-"p": 75,
-"n": 42,
-"pvalue": "1.1e-003",
-"evalue": "1.4e+002"
-}
-]
-}, {
-"db": 0,
-"id": "YAGG",
-"alt": "DREME-2",
-"len": 4,
-"nsites": 793,
-"evalue": "1.4e-011",
-"p": 600,
-"n": 416,
-"pvalue": "1.1e-016",
-"unerased_evalue": "6.3e-012",
-"pwm": [
-[0.000000, 0.692308, 0.000000, 0.307692],
-[1.000000, 0.000000, 0.000000, 0.000000],
-[0.000000, 0.000000, 1.000000, 0.000000],
-[0.000000, 0.000000, 1.000000, 0.000000]
-],
-"matches": [
-{
-"seq": "CAGG",
-"p": 441,
-"n": 304,
-"pvalue": "1.5e-010",
-"evalue": "1.8e-005"
-}, {
-"seq": "UAGG",
-"p": 232,
-"n": 165,
-"pvalue": "1.1e-004",
-"evalue": "1.3e+001"
-}
-]
-}
-],
-"runtime": {
-"host": "ThinkPad-T450s",
-"when": "Thu May 03 13:22:11 CEST 2018",
-"cpu": 15.97,
-"real": 15.97,
-"stop": "evalue"
-}
-};
 </script>
-<script>
 var site_url = "http://meme-suite.org";
-</script>
-<script>
-/*
-* $
-*
-* Shorthand function for getElementById
-*/
-function $(el) {
-return document.getElementById(el);
-}
-/*
-* See http://stackoverflow.com/a/5450113/66387
-* Does string multiplication like the perl x operator.
-*/
-function string_mult(pattern, count) {
-if (count < 1) return '';
-var result = '';
-while (count > 1) {
-if (count & 1) result += pattern;
-count >>= 1, pattern += pattern;
-}
-return result + pattern;
-}
-/*
-* See http://stackoverflow.com/questions/814613/how-to-read-get-data-from-a-url-using-javascript
-* Slightly modified with information from
-* https://developer.mozilla.org/en/DOM/window.location
-*/
-function parse_params() {
-"use strict";
-var search, queryStart, queryEnd, query, params, nvPairs, i, nv, n, v;
-search = window.location.search;
-queryStart = search.indexOf("?") + 1;
-queryEnd   = search.indexOf("#") + 1 || search.length + 1;
-query      = search.slice(queryStart, queryEnd - 1);
-if (query === search || query === "") return {};
-params  = {};
-nvPairs = query.replace(/\+/g, " ").split("&");
-for (i = 0; i < nvPairs.length; i++) {
-nv = nvPairs[i].split("=");
-n  = decodeURIComponent(nv[0]);
-v  = decodeURIComponent(nv[1]);
-// allow a name to be used multiple times
-// storing each value in the array
-if (!(n in params)) {
-params[n] = [];
-}
-params[n].push(nv.length === 2 ? v : null);
-}
-return params;
-}
-/*
-* coords
-*
-* Calculates the x and y offset of an element.
-* From http://www.quirksmode.org/js/findpos.html
-* with alterations to take into account scrolling regions
-*/
-function coords(elem) {
-var myX = myY = 0;
-if (elem.getBoundingClientRect) {
-var rect;
-rect = elem.getBoundingClientRect();
-myX = rect.left + ((typeof window.pageXOffset !== "undefined") ?
-window.pageXOffset : document.body.scrollLeft);
-myY = rect.top + ((typeof window.pageYOffset !== "undefined") ?
-window.pageYOffset : document.body.scrollTop);
-} else {
-// this fall back doesn't properly handle absolutely positioned elements
-// inside a scrollable box
-var node;
-if (elem.offsetParent) {
-// subtract all scrolling
-node = elem;
-do {
-myX -= node.scrollLeft ? node.scrollLeft : 0;
-myY -= node.scrollTop ? node.scrollTop : 0;
-} while (node = node.parentNode);
-// this will include the page scrolling (which is unwanted) so add it back on
-myX += (typeof window.pageXOffset !== "undefined") ? window.pageXOffset : document.body.scrollLeft;
-myY += (typeof window.pageYOffset !== "undefined") ? window.pageYOffset : document.body.scrollTop;
-// sum up offsets
-node = elem;
-do {
-myX += node.offsetLeft;
-myY += node.offsetTop;
-} while (node = node.offsetParent);
-}
-}
-return [myX, myY];
-}
-/*
-* position_popup
-*
-* Positions a popup relative to an anchor element.
-*
-* The avaliable positions are:
-* 0 - Centered below the anchor.
-*/
-function position_popup(anchor, popup, position) {
-"use strict";
-var a_x, a_y, a_w, a_h, p_x, p_y, p_w, p_h;
-var a_xy, spacer, margin, scrollbar, page_w;
-// define constants
-spacer = 5;
-margin = 15;
-scrollbar = 15;
-// define the positions and widths
-a_xy = coords(anchor);
-a_x = a_xy[0];
-a_y = a_xy[1];
-a_w = anchor.offsetWidth;
-a_h = anchor.offsetHeight;
-p_w = popup.offsetWidth;
-p_h = popup.offsetHeight;
-page_w = null;
-if (window.innerWidth) {
-page_w = window.innerWidth;
-} else if (document.body) {
-page_w = document.body.clientWidth;
-}
-// check the position type is defined
-if (typeof position !== "number") {
-position = 0;
-}
-// calculate the popup position
-switch (position) {
-case 1:
-p_x = a_x + a_w + spacer;
-p_y = a_y + (a_h / 2) - (p_h / 2);
-break;
-case 0:
-default:
-p_x = a_x + (a_w / 2) - (p_w / 2);
-p_y = a_y + a_h + spacer;
-break;
-}
-// constrain the popup position
-if (p_x < margin) {
-p_x = margin;
-} else if (page_w != null && (p_x + p_w) > (page_w - margin - scrollbar)) {
-p_x = page_w - margin - scrollbar - p_w;
-}
-if (p_y < margin) {
-p_y = margin;
-}
-// position the popup
-popup.style.left = p_x + "px";
-popup.style.top = p_y + "px";
-}
-function lookup_help_popup(popup_id) {
-var _body, pop, info;
-pop = document.getElementById(popup_id);
-if (pop == null) {
-_body = document.getElementsByTagName("body")[0];
-pop = document.createElement("div");
-pop.className = "pop_content";
-pop.id = popup_id;
-pop.style.backgroundColor = "#FFC";
-pop.style.borderColor = "black";
-info = document.createElement("p");
-info.style.fontWeight = "bold";
-info.appendChild(document.createTextNode("Error: No popup for topic \"" + popup_id + "\"."));
-pop.appendChild(info);
-// this might cause problems with the menu, but as this only happens
-// when something is already wrong I don't think that's too much of a problem
-_body.insertBefore(pop, _body.firstChild);
-}
-if (document.getElementsByTagName('body')[0].hasAttribute("data-autobtns")) {
-if (!/\bauto_buttons\b/.test(pop.className)) {
-pop.className += " auto_buttons";
-var back_btn_sec = document.createElement("div");
-back_btn_sec.className = "nested_only pop_back_sec";
-var back_btn = document.createElement("span");
-back_btn.className = "pop_back";
-back_btn.appendChild(document.createTextNode("<< back"));
-back_btn.addEventListener("click", function(e) {
-help_return();
-}, false);
-back_btn_sec.appendChild(back_btn);
-pop.insertBefore(back_btn_sec, pop.firstChild);
-var close_btn_sec = document.createElement("div");
-close_btn_sec.className = "pop_close_sec";
-var close_btn = document.createElement("span");
-close_btn.className = "pop_close";
-close_btn.appendChild(document.createTextNode("close"));
-close_btn.addEventListener("click", function(e) {
-help_popup();
-}, false);
-close_btn_sec.appendChild(close_btn);
-pop.appendChild(close_btn_sec);
-}
-}
-return pop;
-}
-/*
-* help_popup
-*
-* Moves around help pop-ups so they appear
-* below an activator.
-*/
-function help_popup(activator, popup_id) {
-"use strict";
-var pop;
-// set default values
-if (typeof help_popup.popup === "undefined") {
-help_popup.popup = [];
-}
-if (typeof help_popup.activator === "undefined") {
-help_popup.activator = null;
-}
-var last_pop = (help_popup.popup.length > 0 ? help_popup.popup[help_popup.popup.length - 1] : null);
-if (typeof(activator) == "undefined") { // no activator so hide
-if (last_pop != null) {
-last_pop.style.display = 'none';
-help_popup.popup = [];
-}
-return;
-}
-pop = lookup_help_popup(popup_id);
-if (pop == last_pop) {
-if (activator == help_popup.activator) {
-//hide popup (as we've already shown it for the current help button)
-last_pop.style.display = 'none';
-help_popup.popup = [];
-return; // toggling complete!
-}
-} else if (last_pop != null) {
-//activating different popup so hide current one
-last_pop.style.display = 'none';
-}
-help_popup.popup = [pop];
-help_popup.activator = activator;
-toggle_class(pop, "nested", false);
-//must make the popup visible to measure it or it has zero width
-pop.style.display = 'block';
-position_popup(activator, pop);
-}
-/*
-* help_refine
-*
-* Intended for links within a help popup. Stores a stack of state so
-* you can go back.
-*/
-function help_refine(popup_id) {
-if (help_popup.popup == null || help_popup.popup.length == 0 || help_popup.activator == null) {
-throw new Error("Can not refine a help popup when one is not shown!");
-}
-var pop = lookup_help_popup(popup_id);
-var last_pop = help_popup.popup[help_popup.popup.length - 1];
-if (pop == last_pop) return; // slightly odd, but no real cause for alarm
-help_popup.popup.push(pop);
-toggle_class(pop, "nested", true);
-last_pop.style.display = "none";
-//must make the popup visible to measure it or it has zero width
-pop.style.display = "block";
-position_popup(help_popup.activator, pop);
-}
-/*
-* help_return
-*
-* Intended for links within a help popup. Stores a stack of state so
-* you can go back.
-*/
-function help_return() {
-if (help_popup.popup == null || help_popup.popup.length == 0 || help_popup.activator == null) {
-throw new Error("Can not return to a earlier help popup when one is not shown!");
-}
-var last_pop = help_popup.popup.pop();
-last_pop.style.display = "none";
-var pop = (help_popup.popup.length > 0 ? help_popup.popup[help_popup.popup.length - 1] : null);
-if (pop != null) {
-toggle_class(pop, "nested", help_popup.popup.length > 1);
-pop.style.display = "block";
-position_popup(help_popup.activator, pop);
-} else {
-help_popup.activator = null;
-}
-}
-/*
-* update_scroll_pad
-*
-* Creates padding at the bottom of the page to allow
-* scrolling of anything into view.
-*/
-function update_scroll_pad() {
-var page, pad;
-page = (document.compatMode === "CSS1Compat") ? document.documentElement : document.body;
-pad = $("scrollpad");
-if (pad === null) {
-pad = document.createElement("div");
-pad.id = 'scrollpad';
-document.getElementsByTagName('body')[0].appendChild(pad);
-}
-pad.style.height = Math.abs(page.clientHeight - 100) + "px";
-}
-function substitute_classes(node, remove, add) {
-"use strict";
-var list, all, i, cls, classes;
-list = node.className.split(/\s+/);
-all = {};
-for (i = 0; i < list.length; i++) {
-if (list[i].length > 0) all[list[i]] = true;
-}
-for (i = 0; i < remove.length; i++) {
-if (all.hasOwnProperty(remove[i])) {
-delete all[remove[i]];
-}
-}
-for (i = 0; i < add.length; i++) {
-all[add[i]] = true;
-}
-classes = "";
-for (cls in all) {
-classes += cls + " ";
-}
-node.className = classes;
-}
-/*
-* toggle_class
-*
-* Adds or removes a class from the node. If the parameter 'enabled' is not
-* passed then the existence of the class will be toggled, otherwise it will be
-* included if enabled is true.
-*/
-function toggle_class(node, cls, enabled) {
-var classes = node.className;
-var list = classes.replace(/^\s+/, '').replace(/\s+$/, '').split(/\s+/);
-var found = false;
-for (var i = 0; i < list.length; i++) {
-if (list[i] == cls) {
-list.splice(i, 1);
-i--;
-found = true;
-}
-}
-if (typeof enabled == "undefined") {
-if (!found) list.push(cls);
-} else {
-if (enabled) list.push(cls);
-}
-node.className = list.join(" ");
-}
-/*
-* find_child
-*
-* Searches child nodes in depth first order and returns the first it finds
-* with the className specified.
-* TODO replace with querySelector
-*/
-function find_child(node, className) {
-var pattern;
-if (node == null || typeof node !== "object") {
-return null;
-}
-if (typeof className === "string") {
-pattern = new RegExp("\\b" + className + "\\b");
-} else {
-pattern = className;
-}
-if (node.nodeType == Node.ELEMENT_NODE &&
-pattern.test(node.className)) {
-return node;
-} else {
-var result = null;
-for (var i = 0; i < node.childNodes.length; i++) {
-result = find_child(node.childNodes[i], pattern);
-if (result != null) break;
-}
-return result;
-}
-}
-/*
-* find_parent
-*
-* Searches parent nodes outwards from the node and returns the first it finds
-* with the className specified.
-*/
-function find_parent(node, className) {
-var pattern;
-pattern = new RegExp("\\b" + className + "\\b");
-do {
-if (node.nodeType == Node.ELEMENT_NODE &&
-pattern.test(node.className)) {
-return node;
-}
-} while (node = node.parentNode);
-return null;
-}
-/*
-* find_parent_tag
-*
-* Searches parent nodes outwards from the node and returns the first it finds
-* with the tag name specified. HTML tags should be specified in upper case.
-*/
-function find_parent_tag(node, tag_name) {
-do {
-if (node.nodeType == Node.ELEMENT_NODE && node.tagName == tag_name) {
-return node;
-}
-} while (node = node.parentNode);
-return null;
-}
-/*
-* __toggle_help
-*
-* Uses the 'topic' property of the this object to
-* toggle display of a help topic.
-*
-* This function is not intended to be called directly.
-*/
-function __toggle_help(e) {
-if (!e) e = window.event;
-if (e.type === "keydown") {
-if (e.keyCode !== 13 && e.keyCode !== 32) {
-return;
-}
-// stop a submit or something like that
-e.preventDefault();
-}
-help_popup(this, this.getAttribute("data-topic"));
-}
-function setup_help_button(button) {
-"use strict";
-var topic;
-if (button.hasAttribute("data-topic")) {
-topic = button.getAttribute("data-topic");
-if (document.getElementById(topic) != null) {
-button.tabIndex = "0"; // make keyboard selectable
-button.addEventListener("click", function() {
-help_popup(button, topic);
-}, false);
-button.addEventListener("keydown", function(e) {
-// toggle only on Enter or Spacebar, let other keys do their thing
-if (e.keyCode !== 13 && e.keyCode !== 32) return;
-// stop a submit or something like that
-e.preventDefault();
-help_popup(button, topic);
-}, false);
-} else {
-button.style.visibility = "hidden";
-}
-}
-button.className += " active";
-}
-/*
-* help_button
-*
-* Makes a help button for the passed topic.
-*/
-function help_button(topic) {
-var btn = document.createElement("div");
-btn.className = "help";
-btn.setAttribute("data-topic", topic);
-setup_help_button(btn);
-return btn;
-}
-/*
-* prepare_download
-*
-* Sets the attributes of a link to setup a file download using the given content.
-* If no link is provided then create one and click it.
-*/
-function prepare_download(content, mimetype, filename, link) {
-"use strict";
-// if no link is provided then create one and click it
-var click_link = false;
-if (!link) {
-link = document.createElement("a");
-click_link = true;
-}
-try {
-// Use a BLOB to convert the text into a data URL.
-// We could do this manually with a base 64 conversion.
-// This will only be supported on modern browsers,
-// hence the try block.
-var blob = new Blob([content], {type: mimetype});
-var reader = new FileReader();
-reader.onloadend = function() {
-// If we're lucky the browser will also support the download
-// attribute which will let us suggest a file name to save the link.
-// Otherwise it is likely that the filename will be unintelligible.
-link.setAttribute("download", filename);
-link.href = reader.result;
-if (click_link) {
-// must add the link to click it
-document.body.appendChild(link);
-link.click();
-document.body.removeChild(link);
-}
-}
-reader.readAsDataURL(blob);
-} catch (error) {
-if (console && console.log) console.log(error);
-// probably an old browser
-link.href = "";
-link.visible = false;
-}
-}
-/*
-* add_cell
-*
-* Add a cell to the table row.
-*/
-function add_cell(row, node, cls, click_action) {
-var cell = row.insertCell(row.cells.length);
-if (node) cell.appendChild(node);
-if (cls && cls !== "") cell.className = cls;
-if (click_action) cell.addEventListener("click", click_action, false);
-}
-/*
-* add_header_cell
-*
-* Add a header cell to the table row.
-*/
-function add_header_cell(row, node, help_topic, cls, colspan) {
-var th = document.createElement("th");
-if (node) th.appendChild(node);
-if (help_topic && help_topic !== "") th.appendChild(help_button(help_topic));
-if (cls && cls !== "") th.className = cls;
-if (typeof colspan == "number" && colspan > 1) th.colSpan = colspan;
-row.appendChild(th);
-}
-/*
-* add_text_cell
-*
-* Add a text cell to the table row.
-*/
-function add_text_cell(row, text, cls, action) {
-var node = null;
-if (typeof(text) != 'undefined') node = document.createTextNode(text);
-add_cell(row, node, cls, action);
-}
-/*
-* add_text_header_cell
-*
-* Add a text header cell to the table row.
-*/
-function add_text_header_cell(row, text, help_topic, cls, action, colspan) {
-var node = null;
-if (typeof(text) != 'undefined') {
-var nbsp = (help_topic ? "\u00A0" : "");
-var str = "" + text;
-var parts = str.split(/\n/);
-if (parts.length === 1) {
-if (action) {
-node = document.createElement("span");
-node.appendChild(document.createTextNode(str + nbsp));
-} else {
-node = document.createTextNode(str + nbsp);
-}
-} else {
-node = document.createElement("span");
-for (var i = 0; i < parts.length; i++) {
-if (i !== 0) {
-node.appendChild(document.createElement("br"));
-}
-node.appendChild(document.createTextNode(parts[i]));
-}
-}
-if (action) {
-node.addEventListener("click", action, false);
-node.style.cursor = "pointer";
-}
-}
-add_header_cell(row, node, help_topic, cls, colspan);
-}
-function setup_help() {
-"use strict";
-var help_buttons, i;
-help_buttons = document.querySelectorAll(".help:not(.active)");
-for (i = 0; i < help_buttons.length; i++) {
-setup_help_button(help_buttons[i]);
-}
-}
-function setup_scrollpad() {
-"use strict";
-if (document.getElementsByTagName('body')[0].hasAttribute("data-scrollpad") && document.getElementById("scrollpad") == null) {
-window.addEventListener("resize", update_scroll_pad, false);
-update_scroll_pad();
-}
-}
-// anon function to avoid polluting global scope
-(function() {
-"use strict";
-window.addEventListener("load", function load(evt) {
-window.removeEventListener("load", load, false);
-setup_help();
-setup_scrollpad();
-}, false);
-})();
-/*
-*  make_link
-*
-*  Creates a text node and if a URL is specified it surrounds it with a link.
-*  If the URL doesn't begin with "http://" it automatically adds it, as
-*  relative links don't make much sense in this context.
-*/
-function make_link(text, url) {
-var textNode = null;
-var link = null;
-if (typeof text !== "undefined" && text !== null) textNode = document.createTextNode(text);
-if (typeof url === "string") {
-if (url.indexOf("//") == -1) {
-url = "http://" + url;
-}
-link = document.createElement('a');
-link.href = url;
-if (textNode) link.appendChild(textNode);
-return link;
-}
-return textNode;
-}
-</script>
-<script>
-function motif_logo_template(inputs) {
-function _input(name) {
-if (typeof inputs[name] === "undefined") {
-throw new Error("Missing template variable: " + name);
-}
-return inputs[name];
-}
-return (
-"%!PS-Adobe-3.0 EPSF-3.0\n" +
-"%%Title: Sequence Logo : " + _input("TITLE") + "\n" +
-"%%Creator: " + _input("CREATOR") + "\n" +
-"%%CreationDate: " + _input("CREATIONDATE") + "\n" +
-"%%BoundingBox:   0  0  " + _input("BOUNDINGWIDTH") + " " + _input("BOUNDINGHEIGHT") + " \n" +
-"%%Pages: 0\n" +
-"%%DocumentFonts: \n" +
-"%%EndComments\n" +
-"\n" +
-"% ---- CONSTANTS ----\n" +
-"\/cmfactor 72 2.54 div def % defines points -> cm conversion\n" +
-"\/cm {cmfactor mul} bind def % defines centimeters\n" +
-"\n" +
-"% ---- VARIABLES ----\n" +
-"\n" +
-"% NA = Nucleic Acid, AA = Amino Acid\n" +
-"\/logoType (" + _input("LOGOTYPE") + ") def \n" +
-"\n" +
-"\/logoTitle (" + _input("TITLE") + ") def\n" +
-"\n" +
-"% Dimensions in cm\n" +
-"\/logoWidth " + _input("LOGOWIDTH") + " cm def\n" +
-"\/logoHeight " + _input("LOGOLINEHEIGHT") + " cm def\n" +
-"\/totalHeight " + _input("LOGOHEIGHT") + " cm def\n" +
-"\n" +
-"\/yaxis " + _input("YAXIS") + " def\n" +
-"\/yaxisLabel (" + _input("YAXISLABEL") + ") def\n" +
-"\/yaxisBits  " + _input("BARBITS") + " def % bits\n" +
-"\/yaxisTicBits " + _input("TICBITS") + " def\n" +
-"\n" +
-"\/xaxis " + _input("NUMBERING") + " def\n" +
-"\/xaxisLabel (" + _input("XAXISLABEL") + ") def\n" +
-"\/showEnds (" + _input("SHOWENDS") + ") def \n" +
-"\n" +
-"\/showFineprint true def\n" +
-"\/fineprint (" + _input("FINEPRINT") + ") def\n" +
-"\n" +
-"\/charsPerLine " + _input("CHARSPERLINE") + " def\n" +
-"\n" +
-"\/showingBox " + _input("SHOWINGBOX") + " def    \n" +
-"\/shrinking false def   % true falses\n" +
-"\/shrink  1.0 def\n" +
-"\/outline " + _input("OUTLINE") + " def\n" +
-"\n" +
-"\/IbeamFraction  " + _input("ERRORBARFRACTION") + " def\n" +
-"\/IbeamGray      0.50 def\n" +
-"\/IbeamLineWidth 0.5 def\n" +
-"\n" +
-"\/fontsize       " + _input("FONTSIZE") + " def\n" +
-"\/titleFontsize  " + _input("TITLEFONTSIZE") + " def\n" +
-"\/smallFontsize  " + _input("SMALLFONTSIZE") + " def\n" +
-"\n" +
-"\/topMargin      " + _input("TOPMARGIN") + " cm def\n" +
-"\/bottomMargin   " + _input("BOTTOMMARGIN") + " cm def\n" +
-"\n" +
-"\/defaultColor [0 0 0] def \n" +
-"\n" +
-_input("COLORDICT") + "\n" +
-"\n" +
-"\/colorDict fullColourDict def\n" +
-"\n" +
-"% ---- DERIVED PARAMETERS ----\n" +
-"\n" +
-"\/leftMargin\n" +
-"  fontsize 3.5 mul\n" +
-"\n" +
-"def \n" +
-"\n" +
-"\/rightMargin \n" +
-"  %Add extra room if showing ends\n" +
-"  showEnds (false) eq { fontsize}{fontsize 1.5 mul} ifelse\n" +
-"def\n" +
-"\n" +
-"\/yaxisHeight \n" +
-"  logoHeight \n" +
-"  bottomMargin sub  \n" +
-"  topMargin sub\n" +
-"def\n" +
-"\n" +
-"\/ticWidth fontsize 2 div def\n" +
-"\n" +
-"\/pointsPerBit yaxisHeight yaxisBits div  def\n" +
-"\n" +
-"\/stackMargin 1 def\n" +
-"\n" +
-"% Do not add space aroung characters if characters are boxed\n" +
-"\/charRightMargin \n" +
-"  showingBox { 0.0 } {stackMargin} ifelse\n" +
-"def\n" +
-"\n" +
-"\/charTopMargin \n" +
-"  showingBox { 0.0 } {stackMargin} ifelse\n" +
-"def\n" +
-"\n" +
-"\/charWidth\n" +
-"  logoWidth\n" +
-"  leftMargin sub\n" +
-"  rightMargin sub\n" +
-"  charsPerLine div\n" +
-"  charRightMargin sub\n" +
-"def\n" +
-"\n" +
-"\/charWidth4 charWidth 4 div def\n" +
-"\/charWidth2 charWidth 2 div def\n" +
-"\n" +
-"\/stackWidth \n" +
-"  charWidth charRightMargin add\n" +
-"def\n" +
-" \n" +
-"\/numberFontsize \n" +
-"  fontsize charWidth lt {fontsize}{charWidth} ifelse\n" +
-"def\n" +
-"\n" +
-"% movements to place 5'\/N and 3'\/C symbols\n" +
-"\/leftEndDeltaX  fontsize neg         def\n" +
-"\/leftEndDeltaY  fontsize 1.5 mul neg def\n" +
-"\/rightEndDeltaX fontsize 0.25 mul     def\n" +
-"\/rightEndDeltaY leftEndDeltaY        def\n" +
-"\n" +
-"% Outline width is proporional to charWidth, \n" +
-"% but no less that 1 point\n" +
-"\/outlinewidth \n" +
-"  charWidth 32 div dup 1 gt  {}{pop 1} ifelse\n" +
-"def\n" +
-"\n" +
-"\n" +
-"% ---- PROCEDURES ----\n" +
-"\n" +
-"\/StartLogo { \n" +
-"  % Save state\n" +
-"  save \n" +
-"  gsave \n" +
-"\n" +
-"  % Print Logo Title, top center \n" +
-"  gsave \n" +
-"    SetStringFont\n" +
-"\n" +
-"    logoWidth 2 div\n" +
-"    logoTitle\n" +
-"    stringwidth pop 2 div sub\n" +
-"    totalHeight\n" +
-"    titleFontsize sub\n" +
-"    moveto\n" +
-"\n" +
-"    logoTitle\n" +
-"    show\n" +
-"  grestore\n" +
-"\n" +
-"  % Print X-axis label, bottom center\n" +
-"  gsave\n" +
-"    SetStringFont\n" +
-"\n" +
-"    logoWidth 2 div\n" +
-"    xaxisLabel\n" +
-"    stringwidth pop 2 div sub\n" +
-"    0\n" +
-"    titleFontsize 3 div\n" +
-"    add\n" +
-"    moveto\n" +
-"\n" +
-"    xaxisLabel\n" +
-"    show\n" +
-"  grestore\n" +
-"\n" +
-"  % Show Fine Print\n" +
-"  showFineprint {\n" +
-"    gsave\n" +
-"      SetSmallFont\n" +
-"      logoWidth\n" +
-"        fineprint stringwidth pop sub\n" +
-"        smallFontsize sub\n" +
-"          smallFontsize 3 div\n" +
-"      moveto\n" +
-"    \n" +
-"      fineprint show\n" +
-"    grestore\n" +
-"  } if\n" +
-"\n" +
-"  % Move to lower left corner of last line, first stack\n" +
-"  leftMargin bottomMargin translate\n" +
-"\n" +
-"  % Move above first line ready for StartLine \n" +
-"  0 totalHeight translate\n" +
-"\n" +
-"  SetLogoFont\n" +
-"} bind def\n" +
-"\n" +
-"\/EndLogo { \n" +
-"  grestore \n" +
-"  showpage \n" +
-"  restore \n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/StartLine { \n" +
-"  % move down to the bottom of the line:\n" +
-"  0 logoHeight neg translate\n" +
-"  \n" +
-"  gsave \n" +
-"    yaxis { MakeYaxis } if\n" +
-"    xaxis { showEnds (true) eq {ShowLeftEnd} if } if\n" +
-"} bind def\n" +
-"\n" +
-"\/EndLine{ \n" +
-"    xaxis { showEnds (true) eq {ShowRightEnd} if } if\n" +
-"  grestore \n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/MakeYaxis {\n" +
-"  gsave    \n" +
-"    stackMargin neg 0 translate\n" +
-"    ShowYaxisBar\n" +
-"    ShowYaxisLabel\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/ShowYaxisBar { \n" +
-"  gsave  \n" +
-"    SetStringFont\n" +
-"\n" +
-"    \/str 10 string def % string to hold number  \n" +
-"    \/smallgap stackMargin 2 div def\n" +
-"\n" +
-"    % Draw first tic and bar\n" +
-"    gsave    \n" +
-"      ticWidth neg 0 moveto \n" +
-"      ticWidth 0 rlineto \n" +
-"      0 yaxisHeight rlineto\n" +
-"      stroke\n" +
-"    grestore\n" +
-"\n" +
-"   \n" +
-"    % Draw the tics\n" +
-"    % initial increment limit proc for\n" +
-"    0 yaxisTicBits yaxisBits abs %cvi\n" +
-"    {\/loopnumber exch def\n" +
-"\n" +
-"      % convert the number coming from the loop to a string\n" +
-"      % and find its width\n" +
-"      loopnumber 10 str cvrs\n" +
-"      \/stringnumber exch def % string representing the number\n" +
-"\n" +
-"      stringnumber stringwidth pop\n" +
-"      \/numberwidth exch def % width of number to show\n" +
-"\n" +
-"      \/halfnumberheight\n" +
-"         stringnumber CharBoxHeight 2 div\n" +
-"      def\n" +
-"\n" +
-"      numberwidth % move back width of number\n" +
-"      neg loopnumber pointsPerBit mul % shift on y axis\n" +
-"      halfnumberheight sub % down half the digit\n" +
-"\n" +
-"      moveto % move back the width of the string\n" +
-"\n" +
-"      ticWidth neg smallgap sub % Move back a bit more  \n" +
-"      0 rmoveto % move back the width of the tic  \n" +
-"\n" +
-"      stringnumber show\n" +
-"      smallgap 0 rmoveto % Make a small gap  \n" +
-"\n" +
-"      % now show the tic mark\n" +
-"      0 halfnumberheight rmoveto % shift up again\n" +
-"      ticWidth 0 rlineto\n" +
-"      stroke\n" +
-"    } for\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\/ShowYaxisLabel {\n" +
-"  gsave\n" +
-"    SetStringFont\n" +
-"\n" +
-"    % How far we move left depends on the size of\n" +
-"    % the tic labels.\n" +
-"    \/str 10 string def % string to hold number  \n" +
-"    yaxisBits yaxisTicBits div cvi yaxisTicBits mul \n" +
-"    str cvs stringwidth pop\n" +
-"    ticWidth 1.5 mul  add neg  \n" +
-"\n" +
-"\n" +
-"    yaxisHeight\n" +
-"    yaxisLabel stringwidth pop\n" +
-"    sub 2 div\n" +
-"\n" +
-"    translate\n" +
-"    90 rotate\n" +
-"    0 0 moveto\n" +
-"    yaxisLabel show\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/StartStack {  % <stackNumber> startstack\n" +
-"  xaxis {MakeNumber}{pop} ifelse\n" +
-"  gsave\n" +
-"} bind def\n" +
-"\n" +
-"\/EndStack {\n" +
-"  grestore\n" +
-"  stackWidth 0 translate\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"% Draw a character whose height is proportional to symbol bits\n" +
-"\/MakeSymbol{ % charbits character MakeSymbol\n" +
-"  gsave\n" +
-"    \/char exch def\n" +
-"    \/bits exch def\n" +
-"\n" +
-"    \/bitsHeight \n" +
-"       bits pointsPerBit mul \n" +
-"    def\n" +
-"\n" +
-"    \/charHeight \n" +
-"       bitsHeight charTopMargin sub\n" +
-"       dup \n" +
-"       0.0 gt {}{pop 0.0} ifelse % if neg replace with zero \n" +
-"    def \n" +
-" \n" +
-"    charHeight 0.0 gt {\n" +
-"      char SetColor\n" +
-"      charWidth charHeight char ShowChar\n" +
-"\n" +
-"      showingBox { % Unfilled box\n" +
-"        0 0 charWidth charHeight false ShowBox\n" +
-"      } if\n" +
-"\n" +
-"\n" +
-"    } if\n" +
-"\n" +
-"  grestore\n" +
-"\n" +
-"  0 bitsHeight translate \n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/ShowChar { % <width> <height> <char> ShowChar\n" +
-"  gsave\n" +
-"    \/tc exch def    % The character\n" +
-"    \/ysize exch def % the y size of the character\n" +
-"    \/xsize exch def % the x size of the character\n" +
-"\n" +
-"    \/xmulfactor 1 def \n" +
-"    \/ymulfactor 1 def\n" +
-"    \/limmulfactor 0.01 def\n" +
-"    \/drawable true def\n" +
-"\n" +
-"  \n" +
-"    % if ysize is negative, make everything upside down!\n" +
-"    ysize 0 lt {\n" +
-"      % put ysize normal in this orientation\n" +
-"      \/ysize ysize abs def\n" +
-"      xsize ysize translate\n" +
-"      180 rotate\n" +
-"    } if\n" +
-"\n" +
-"    shrinking {\n" +
-"      xsize 1 shrink sub 2 div mul\n" +
-"        ysize 1 shrink sub 2 div mul translate \n" +
-"\n" +
-"      shrink shrink scale\n" +
-"    } if\n" +
-"\n" +
-"    % Calculate the font scaling factors\n" +
-"    % Loop twice to catch small correction due to first scaling\n" +
-"    2 {\n" +
-"      gsave\n" +
-"        xmulfactor ymulfactor scale\n" +
-"      \n" +
-"        ysize % desired size of character in points\n" +
-"        tc CharBoxHeight \n" +
-"        dup 0.0 ne {\n" +
-"          div % factor by which to scale up the character\n" +
-"          \/ymulfactor exch def\n" +
-"        } % end if\n" +
-"        {pop pop}\n" +
-"        ifelse\n" +
-"\n" +
-"        xsize % desired size of character in points\n" +
-"        tc CharBoxWidth  \n" +
-"        dup 0.0 ne {\n" +
-"          div % factor by which to scale up the character\n" +
-"          \/xmulfactor exch def\n" +
-"        } % end if\n" +
-"        {pop pop}\n" +
-"        ifelse\n" +
-"      grestore\n" +
-"      % if the multiplication factors get too small we need to avoid a crash\n" +
-"      xmulfactor limmulfactor lt {\n" +
-"        \/xmulfactor 1 def\n" +
-"        \/drawable false def\n" +
-"      } if\n" +
-"      ymulfactor limmulfactor lt {\n" +
-"        \/ymulfactor 1 def\n" +
-"        \/drawable false def\n" +
-"      } if\n" +
-"    } repeat\n" +
-"\n" +
-"    % Adjust horizontal position if the symbol is an I\n" +
-"    tc (I) eq {\n" +
-"      charWidth 2 div % half of requested character width\n" +
-"      tc CharBoxWidth 2 div % half of the actual character\n" +
-"      sub 0 translate\n" +
-"      % Avoid x scaling for I \n" +
-"      \/xmulfactor 1 def \n" +
-"    } if\n" +
-"\n" +
-"\n" +
-"    % ---- Finally, draw the character\n" +
-"    drawable { \n" +
-"      newpath\n" +
-"      xmulfactor ymulfactor scale\n" +
-"\n" +
-"      % Move lower left corner of character to start point\n" +
-"      tc CharBox pop pop % llx lly : Lower left corner\n" +
-"      exch neg exch neg\n" +
-"      moveto\n" +
-"\n" +
-"      outline {  % outline characters:\n" +
-"        outlinewidth setlinewidth\n" +
-"        tc true charpath\n" +
-"        gsave 1 setgray fill grestore\n" +
-"        clip stroke\n" +
-"      } { % regular characters\n" +
-"        tc show\n" +
-"      } ifelse\n" +
-"    } if\n" +
-"\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/ShowBox { % x1 y1 x2 y2 filled ShowBox\n" +
-"  gsave\n" +
-"    \/filled exch def \n" +
-"    \/y2 exch def\n" +
-"    \/x2 exch def\n" +
-"    \/y1 exch def\n" +
-"    \/x1 exch def\n" +
-"    newpath\n" +
-"    x1 y1 moveto\n" +
-"    x2 y1 lineto\n" +
-"    x2 y2 lineto\n" +
-"    x1 y2 lineto\n" +
-"    closepath\n" +
-"\n" +
-"    clip\n" +
-"    \n" +
-"    filled {\n" +
-"      fill\n" +
-"    }{ \n" +
-"      0 setgray stroke   \n" +
-"    } ifelse\n" +
-"\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/MakeNumber { % number MakeNumber\n" +
-"  gsave\n" +
-"    SetNumberFont\n" +
-"    stackWidth 0 translate\n" +
-"    90 rotate % rotate so the number fits\n" +
-"    dup stringwidth pop % find the length of the number\n" +
-"    neg % prepare for move\n" +
-"    stackMargin sub % Move back a bit\n" +
-"    charWidth (0) CharBoxHeight % height of numbers\n" +
-"    sub 2 div %\n" +
-"    moveto % move back to provide space\n" +
-"    show\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/Ibeam{ % heightInBits Ibeam\n" +
-"  gsave\n" +
-"    % Make an Ibeam of twice the given height in bits\n" +
-"    \/height exch  pointsPerBit mul def \n" +
-"    \/heightDRAW height IbeamFraction mul def\n" +
-"\n" +
-"    IbeamLineWidth setlinewidth\n" +
-"    IbeamGray setgray \n" +
-"\n" +
-"    charWidth2 height neg translate\n" +
-"    ShowIbar\n" +
-"    newpath\n" +
-"      0 0 moveto\n" +
-"      0 heightDRAW rlineto\n" +
-"    stroke\n" +
-"    newpath\n" +
-"      0 height moveto\n" +
-"      0 height rmoveto\n" +
-"      currentpoint translate\n" +
-"    ShowIbar\n" +
-"    newpath\n" +
-"    0 0 moveto\n" +
-"    0 heightDRAW neg rlineto\n" +
-"    currentpoint translate\n" +
-"    stroke\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/ShowIbar { % make a horizontal bar\n" +
-"  gsave\n" +
-"    newpath\n" +
-"      charWidth4 neg 0 moveto\n" +
-"      charWidth4 0 lineto\n" +
-"    stroke\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/ShowLeftEnd {\n" +
-"  gsave\n" +
-"    SetStringFont\n" +
-"    leftEndDeltaX leftEndDeltaY moveto\n" +
-"    logoType (NA) eq {(5) show ShowPrime} if\n" +
-"    logoType (AA) eq {(N) show} if\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/ShowRightEnd { \n" +
-"  gsave\n" +
-"    SetStringFont\n" +
-"    rightEndDeltaX rightEndDeltaY moveto\n" +
-"    logoType (NA) eq {(3) show ShowPrime} if\n" +
-"    logoType (AA) eq {(C) show} if\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"\/ShowPrime {\n" +
-"  gsave\n" +
-"    SetPrimeFont\n" +
-"    (\\242) show \n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-" \n" +
-"\/SetColor{ % <char> SetColor\n" +
-"  dup colorDict exch known {\n" +
-"    colorDict exch get aload pop setrgbcolor\n" +
-"  } {\n" +
-"    pop\n" +
-"    defaultColor aload pop setrgbcolor\n" +
-"  } ifelse \n" +
-"} bind def\n" +
-"\n" +
-"% define fonts\n" +
-"\/SetTitleFont {\/Times-Bold findfont titleFontsize scalefont setfont} bind def\n" +
-"\/SetLogoFont  {\/Helvetica-Bold findfont charWidth  scalefont setfont} bind def\n" +
-"\/SetStringFont{\/Helvetica-Bold findfont fontsize scalefont setfont} bind def\n" +
-"\/SetPrimeFont {\/Symbol findfont fontsize scalefont setfont} bind def\n" +
-"\/SetSmallFont {\/Helvetica findfont smallFontsize scalefont setfont} bind def\n" +
-"\n" +
-"\/SetNumberFont {\n" +
-"    \/Helvetica-Bold findfont \n" +
-"    numberFontsize\n" +
-"    scalefont\n" +
-"    setfont\n" +
-"} bind def\n" +
-"\n" +
-"%Take a single character and return the bounding box\n" +
-"\/CharBox { % <char> CharBox <lx> <ly> <ux> <uy>\n" +
-"  gsave\n" +
-"    newpath\n" +
-"    0 0 moveto\n" +
-"    % take the character off the stack and use it here:\n" +
-"    true charpath \n" +
-"    flattenpath \n" +
-"    pathbbox % compute bounding box of 1 pt. char => lx ly ux uy\n" +
-"    % the path is here, but toss it away ...\n" +
-"  grestore\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"% The height of a characters bounding box\n" +
-"\/CharBoxHeight { % <char> CharBoxHeight <num>\n" +
-"  CharBox\n" +
-"  exch pop sub neg exch pop\n" +
-"} bind def\n" +
-"\n" +
-"\n" +
-"% The width of a characters bounding box\n" +
-"\/CharBoxWidth { % <char> CharBoxHeight <num>\n" +
-"  CharBox\n" +
-"  pop exch pop sub neg \n" +
-"} bind def\n" +
-"\n" +
-"% Set the colour scheme to be faded to indicate trimming\n" +
-"\/MuteColour {\n" +
-"  \/colorDict mutedColourDict def\n" +
-"} def\n" +
-"\n" +
-"% Restore the colour scheme to the normal colours\n" +
-"\/RestoreColour {\n" +
-"  \/colorDict fullColourDict def\n" +
-"} def\n" +
-"\n" +
-"% Draw the background for a trimmed section\n" +
-"% takes the number of columns as a parameter\n" +
-"\/DrawTrimBg { % <num> DrawTrimBox\n" +
-"  \/col exch def\n" +
-"  \n" +
-"  \/boxwidth \n" +
-"    col stackWidth mul \n" +
-"  def\n" +
-" \n" +
-"  gsave\n" +
-"    0.97 setgray\n" +
-"\n" +
-"    newpath\n" +
-"    0 0 moveto\n" +
-"    boxwidth 0 rlineto\n" +
-"    0 yaxisHeight rlineto\n" +
-"    0 yaxisHeight lineto\n" +
-"    closepath\n" +
-"    \n" +
-"    fill\n" +
-"  grestore\n" +
-"} def\n" +
-"\n" +
-"\/DrawTrimEdge {\n" +
-"  gsave\n" +
-"    0.2 setgray\n" +
-"    [2] 0 setdash\n" +
-"\n" +
-"    newpath\n" +
-"    0 0 moveto\n" +
-"    0 yaxisHeight lineto\n" +
-"    \n" +
-"    stroke\n" +
-"\n" +
-"} def\n" +
-"\n" +
-"\n" +
-"% Deprecated names\n" +
-"\/startstack {StartStack} bind  def\n" +
-"\/endstack {EndStack}     bind def\n" +
-"\/makenumber {MakeNumber} bind def\n" +
-"\/numchar { MakeSymbol }  bind def\n" +
-"\n" +
-"%%EndProlog\n" +
-"\n" +
-"%%Page: 1 1\n" +
-"StartLogo\n" +
-"\n" +
-_input("DATA") + "\n" +
-"\n" +
-"EndLogo\n" +
-"\n" +
-"%%EOF\n"
-);
-}</script>
-<script>
-//======================================================================
-// start Alphabet object
-//======================================================================
-var Alphabet = function(alphabet, background) {
-"use strict";
-var i, j, sym, aliases, complement, comp_e_sym, ambigs, generate_background;
-generate_background = (background == null);
-if (generate_background) {
-background = [];
-for (i = 0; i < alphabet.ncore; i++) background[i] = 1.0 / alphabet.ncore;
-} else if (alphabet.ncore != background.length) {
-throw new Error("The background length does not match the alphabet length.");
-}
-this.name = alphabet.name;
-this.like = (alphabet.like != null ? alphabet.like.toUpperCase() : null);
-this.ncore = alphabet.ncore;
-this.symbols = alphabet.symbols;
-this.background = background;
-this.genbg = generate_background;
-this.encode = {};
-this.encode2core = {};
-this.complement = {};
-// check if all symbols are same case
-var seen_uc = false;
-var seen_lc = false;
-var check_case = function (syms) {
-var s, sym;
-if (typeof syms === "string") {
-for (s = 0; s < syms.length; s++) {
-sym = syms.charAt(s);
-if (sym >= 'a' && sym <= 'z') seen_lc = true;
-else if (sym >= 'A' && sym <= 'Z') seen_uc = true;
-}
-}
-};
-for (i = 0; i < this.symbols.length; i++) {
-check_case(this.symbols[i].symbol);
-check_case(this.symbols[i].aliases);
-}
-// now map symbols to indexes
-var update_array = function(array, syms, index) {
-var s, sym;
-if (typeof syms === "string") {
-for (s = 0; s < syms.length; s++) {
-sym = syms.charAt(s);
-array[sym] = index;
-// when only a single case is used, then encode as case insensitive
-if (seen_uc != seen_lc) {
-if (sym >= 'a' && sym <= 'z') {
-array[sym.toUpperCase()] = index;
-} else if (sym >= 'A' && sym <= 'Z') {
-array[sym.toLowerCase()] = index;
-}
-}
-}
-}
-}
-// map core symbols to index
-for (i = 0; i < this.ncore; i++) {
-update_array(this.encode2core, this.symbols[i].symbol, i);
-update_array(this.encode, this.symbols[i].symbol, i);
-update_array(this.encode2core, this.symbols[i].aliases, i);
-update_array(this.encode, this.symbols[i].aliases, i);
-}
-// map ambigous symbols to index
-ambigs = {};
-for (i = this.ncore; i < this.symbols.length; i++) {
-update_array(this.encode, this.symbols[i].symbol, i);
-update_array(this.encode, this.symbols[i].aliases, i);
-ambigs[this.symbols[i].equals] = i;
-}
-// determine complements
-for (i = 0; i < this.ncore; i++) {
-complement = this.symbols[i].complement;
-if (typeof complement === "string") {
-this.complement[i] = this.encode2core[complement];
-}
-}
-next_symbol:
-for (i = this.ncore; i < this.symbols.length; i++) {
-complement = "";
-for (j = 0; j < this.symbols[i].equals.length; j++) {
-comp_e_sym = this.complement[this.encode2core[this.symbols[i].equals.charAt(j)]];
-if (typeof comp_e_sym !== "number") continue next_symbol;
-complement += this.symbols[comp_e_sym].symbol;
-}
-complement = complement.split("").sort().join("");
-if (typeof ambigs[complement] === "number") {
-this.complement[i] = ambigs[complement];
-}
-}
-// determine case insensitivity
-this.case_insensitive = true;
-if (seen_uc == seen_lc) {
-// when there is a mixture of cases it probably won't
-// be case insensitive but we still need to check
-loop:
-for (i = 0; i < this.symbols.length; i++) {
-sym = this.symbols[i].symbol;
-if (sym >= 'A' && sym <= 'Z') {
-if (this.encode[sym.toLowerCase()] != i) {
-this.case_insensitive = false;
-break loop;
-}
-} else if (sym >= 'a' && sym <= 'z') {
-if (this.encode[sym.toUpperCase()] != i) {
-this.case_insensitive = false;
-break loop;
-}
-}
-aliases = this.symbols[i].aliases;
-if (aliases != null) {
-for (j = 0; j < aliases.length; j++) {
-sym = aliases.charAt(j);
-if (sym >= 'A' && sym <= 'Z') {
-if (this.encode[sym.toLowerCase()] != i) {
-this.case_insensitive = false;
-break loop;
-}
-} else if (sym >= 'a' && sym <= 'z') {
-if (this.encode[sym.toUpperCase()] != i) {
-this.case_insensitive = false;
-break loop;
-}
-}
-}
-}
-}
-}
-// normalise aliases to remove the prime symbol and eliminate
-// the alternate cases when the alphabet is case insensitive
-var seen, out;
-for (i = 0; i < this.symbols.length; i++) {
-sym = this.symbols[i].symbol;
-aliases = this.symbols[i].aliases;
-if (typeof aliases != "string") aliases = "";
-seen = {};
-out = [];
-if (this.case_insensitive) {
-sym = sym.toUpperCase();
-aliases = aliases.toUpperCase();
-}
-seen[sym] = true;
-for (j = 0; j < aliases.length; j++) {
-if (!seen[aliases.charAt(j)]) {
-seen[aliases.charAt(j)] = true;
-out.push(aliases.charAt(j));
-}
-}
-this.symbols[i].aliases = out.sort().join("");
-}
-};
-// return the name of the alphabet
-Alphabet.prototype.get_alphabet_name = function() {
-return this.name;
-};
-// return if the alphabet can be complemented
-Alphabet.prototype.has_complement = function() {
-return (typeof this.symbols[0].complement === "string");
-};
-// return true if an uppercase letter has the same meaning as the lowercase form
-Alphabet.prototype.is_case_insensitive = function() {
-return this.case_insensitive;
-};
-// return the information content of an alphabet letter
-Alphabet.prototype.get_ic = function() {
-return Math.log(this.ncore) / Math.LN2;
-};
-// return the count of the core alphabet symbols
-Alphabet.prototype.get_size_core = function() {
-return this.ncore;
-};
-// return the count of all alphabet symbols
-Alphabet.prototype.get_size_full = function() {
-return this.symbols.length;
-};
-// return the symbol for the given alphabet index
-Alphabet.prototype.get_symbol = function(alph_index) {
-"use strict";
-if (alph_index < 0 || alph_index >= this.symbols.length) {
-throw new Error("Alphabet index out of bounds");
-}
-return this.symbols[alph_index].symbol;
-};
-// return the aliases for the given alphabet index
-Alphabet.prototype.get_aliases = function(alph_index) {
-"use strict";
-if (alph_index < 0 || alph_index >= this.symbols.length) {
-throw new Error("Alphabet index out of bounds");
-}
-var sym_obj = this.symbols[alph_index];
-return (sym_obj.aliases != null ? sym_obj.aliases : "");
-};
-// return the name for the given alphabet index
-Alphabet.prototype.get_name = function(alph_index) {
-"use strict";
-var sym;
-if (alph_index < 0 || alph_index >= this.symbols.length) {
-throw new Error("Alphabet index out of bounds");
-}
-sym = this.symbols[alph_index];
-return (typeof sym.name === "string" ? sym.name : sym.symbol);
-};
-// return the alphabet it is like or null
-Alphabet.prototype.get_like = function() {
-"use strict";
-return this.like;
-};
-// return the index of the complement for the given alphabet index
-Alphabet.prototype.get_complement = function(alph_index) {
-var comp_e_sym = this.complement[alph_index];
-if (typeof comp_e_sym === "number") {
-return comp_e_sym;
-} else {
-return -1;
-}
-};
-// return a string containing the core symbols
-Alphabet.prototype.get_symbols = function() {
-"use strict";
-var i, core_symbols;
-core_symbols = "";
-for (i = 0; i < this.ncore; i++) {
-core_symbols += this.symbols[i].symbol;
-}
-return core_symbols;
-};
-// return if the background was not a uniform generated background
-Alphabet.prototype.has_bg = function() {
-"use strict";
-return !this.genbg;
-};
-// get the background frequency for the index
-Alphabet.prototype.get_bg_freq = function(alph_index) {
-"use strict";
-var freq, i, symbols;
-if (alph_index >= 0) {
-if (alph_index < this.ncore) {
-return this.background[alph_index];
-} else if (alph_index < this.symbols.length) {
-freq = 0;
-symbols = this.symbols[alph_index].equals;
-for (i = 0; i < symbols.length; i++) {
-freq += this.background[this.encode2core[symbols.charAt(i)]];
-}
-return freq;
-}
-}
-throw new Error("The alphabet index is out of range.");
-};
-// get the colour of the index
-Alphabet.prototype.get_colour = function(alph_index) {
-"use strict";
-if (alph_index < 0 || alph_index >= this.symbols.length) {
-throw new Error("BAD_ALPHABET_INDEX");
-}
-if (typeof this.symbols[alph_index].colour != "string") {
-return "black";
-}
-return "#" + this.symbols[alph_index].colour;
-};
-// get the rgb componets of the colour at the index
-Alphabet.prototype.get_rgb = function(alph_index) {
-"use strict";
-if (alph_index < 0 || alph_index >= this.symbols.length) {
-throw new Error("BAD_ALPHABET_INDEX");
-}
-if (typeof this.symbols[alph_index].colour != "string") {
-return {"red": 0, "green": 0, "blue": 0};
-}
-var colour = this.symbols[alph_index].colour;
-var red = parseInt(colour.substr(0, 2), 16) / 255;
-var green = parseInt(colour.substr(2, 2), 16) / 255;
-var blue = parseInt(colour.substr(4, 2), 16) / 255;
-return {"red": red, "green": green, "blue": blue};
-};
-// convert a symbol into the index
-Alphabet.prototype.get_index = function(letter) {
-"use strict";
-var alph_index;
-alph_index = this.encode[letter];
-if (typeof alph_index === "undefined") {
-return -1;
-}
-return alph_index;
-};
-// convert a symbol into the list of core indexes that it equals
-Alphabet.prototype.get_indexes = function(letter) {
-"use strict";
-var alph_index, comprise_str, i, comprise_list;
-alph_index = this.encode[letter];
-if (typeof alph_index === "undefined") {
-throw new Error("Unknown letter");
-}
-comprise_str = this.symbols[alph_index].equals;
-comprise_list = [];
-if (typeof comprise_str == "string") {
-for (i = 0; i < comprise_str.length; i++) {
-comprise_list.push(this.encode2core[comprise_str.charAt(i)]);
-}
-} else {
-comprise_list.push(alph_index);
-}
-return comprise_list;
-};
-// check if a symbol is the primary way of representing the symbol in the alphabet
-Alphabet.prototype.is_prime_symbol = function(letter) {
-var alph_index;
-alph_index = this.encode[letter];
-if (alph_index == null) return false;
-if (this.is_case_insensitive()) {
-return (this.symbols[alph_index].symbol.toUpperCase() == letter.toUpperCase());
-} else {
-return (this.symbols[alph_index].symbol == letter);
-}
-};
-// compare 2 alphabets
-Alphabet.prototype.equals = function(other) {
-"use strict";
-var i, sym1, sym2;
-// first check that it's actually an alphabet object
-if (!(typeof other === "object" && other != null && other instanceof Alphabet)) {
-return false;
-}
-// second shortcircuit if it's the same object
-if (this === other) return true;
-// compare
-if (this.name !== other.name) return false;
-if (this.ncore !== other.ncore) return false;
-if (this.symbols.length !== other.symbols.length) return false;
-for (i = 0; i < this.symbols.length; i++) {
-sym1 = this.symbols[i];
-sym2 = other.symbols[i];
-if (sym1.symbol !== sym2.symbol) return false;
-if (sym1.aliases !== sym2.aliases) return false;
-if (sym1.name !== sym2.name) return false;
-if (typeof sym1.colour !== typeof sym2.colour ||
-(typeof sym1.colour === "string" && typeof sym2.colour === "string" &&
-parseInt(sym1.colour, 16) != parseInt(sym2.colour, 16))) {
-return false;
-}
-if (sym1.complement !== sym2.complement) return false;
-if (sym1.equals !== sym2.equals) return false;
-}
-return true;
-};
-Alphabet.prototype.check_core_subset = function(super_alph) {
-var complement_same = true;
-var seen_set = {};
-var sub_i, sub_symbol, super_i, super_symbol;
-for (sub_i = 0; sub_i < this.ncore; sub_i++) {
-sub_symbol = this.symbols[sub_i];
-super_i = super_alph.encode[sub_symbol.symbol];
-if (super_i == null) return 0;
-super_symbol = super_alph.symbols[super_i];
-if (seen_set[super_i]) return 0;
-seen_set[super_i] = true;
-// check complement
-if (sub_symbol.complement != null && super_symbol.complement != null) {
-if (super_alph.encode[sub_symbol.complement] != super_alph.encode[super_symbol.complement]) {
-complement_same = false;
-}
-} else if (sub_symbol.complement != null || super_symbol.complement != null) {
-complement_same = false;
-}
-}
-return (complement_same ? 1 : -1);
-};
-// convert a sequence to its reverse complement
-Alphabet.prototype.invcomp_seq = function(seq) {
-"use strict";
-var syms, i, e_sym, comp_e_sym;
-if (!this.has_complement()) throw new Error("Alphabet must be complementable");
-syms = seq.split("");
-for (i = 0; i < syms.length; i++) {
-e_sym = this.encode[syms[i]];
-if (typeof e_sym === "undefined") {
-e_sym = this.ncore; // wildcard
-}
-comp_e_sym = this.complement[e_sym];
-if (typeof comp_e_sym === "undefined") {
-comp_e_sym = e_sym; // not complementable
-}
-syms[i] = this.symbols[comp_e_sym].symbol;
-}
-return syms.reverse().join("");
-};
-// convert the alphabet to the text version
-Alphabet.prototype.as_text = function() {
-"use strict";
-function name_as_text(name) {
-var i, c, out;
-out = "\"";
-for (i = 0; i < name.length; i++) {
-c = name.charAt(i);
-if (c == "\"") {
-out += "\\\"";
-} else if (c == "/") {
-out += "\\/";
-} else if (c == "\\") {
-out += "\\\\";
-} else {
-out += c;
-}
-}
-out += "\"";
-return out;
-}
-function symbol_as_text(sym) {
-var out;
-out = sym.symbol;
-if (typeof sym.name === "string" && sym.name != sym.symbol) {
-out += " " + name_as_text(sym.name);
-}
-if (typeof sym.colour === "string") {
-out += " " + sym.colour;
-}
-return out;
-}
-var out, i, j, c, sym;
-out = "";
-// output core symbols with 2 way complements
-for (i = 0; i < this.ncore; i++) {
-c = this.complement[i];
-if (typeof c === "number" && i < c && this.complement[c] === i) {
-out += symbol_as_text(this.symbols[i]) + " ~ " + symbol_as_text(this.symbols[c]) + "\n";
-}
-}
-// output core symbols with no complement
-for (i = 0; i < this.ncore; i++) {
-if (typeof this.complement[i] === "undefined") {
-out += symbol_as_text(this.symbols[i]) + "\n";
-}
-}
-// output ambiguous symbols that have comprising characters
-for (i = this.ncore; i < this.symbols.length; i++) {
-if (this.symbols[i].equals.length == 0) break;
-out += symbol_as_text(this.symbols[i]) + " = " + this.symbols[i].equals + "\n";
-if (typeof this.symbols[i].aliases === "string") {
-for (j = 0; j < this.symbols[i].aliases.length; j++) {
-if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue;
-out += this.symbols[i].aliases.charAt(j) + " = " + this.symbols[i].equals + "\n";
-}
-}
-}
-// output aliases of core symbols
-for (i = 0; i < this.ncore; i++) {
-if (typeof this.symbols[i].aliases === "string") {
-for (j = 0; j < this.symbols[i].aliases.length; j++) {
-if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue;
-out += this.symbols[i].aliases.charAt(j) + " = " + this.symbols[i].symbol + "\n";
-}
-}
-}
-// output gap symbols
-i = this.symbols.length - 1;
-if (this.symbols[i].equals.length == 0) {
-out += symbol_as_text(this.symbols[i]) + " =\n";
-if (typeof this.symbols[i].aliases === "string") {
-for (j = 0; j < this.symbols[i].aliases.length; j++) {
-if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue;
-out += this.symbols[i].aliases.charAt(j) + " =\n";
-}
-}
-}
-return out;
-};
-// output the alphabet as it appears in minimal MEME format
-Alphabet.prototype.as_meme = function() {
-"use strict";
-function name_as_text(name) {
-var i, c, out;
-out = "\"";
-for (i = 0; i < name.length; i++) {
-c = name.charAt(i);
-if (c == "\"") {
-out += "\\\"";
-} else if (c == "/") {
-out += "\\/";
-} else if (c == "\\") {
-out += "\\\\";
-} else {
-out += c;
-}
-}
-out += "\"";
-return out;
-}
-if (this.equals(AlphStd.DNA)) {
-return "ALPHABET= ACGT\n";
-} else if (this.equals(AlphStd.PROTEIN)) {
-return "ALPHABET= ACDEFGHIKLMNPQRSTVWY\n";
-} else {
-return "ALPHABET" +
-(this.name != null ? " " + name_as_text(this.name) : "") +
-(this.like != null ? " " + this.like + "-LIKE" : "") + "\n" +
-this.as_text() + "END ALPHABET\n";
-}
-};
-// Returns a table showing all the letters in the alphabet
-Alphabet.prototype.as_table = function() {
-"use strict";
-var i, j, row, th, td, aliases, equals, sym;
-var table = document.createElement("table");
-// create the core symbol header
-row = table.insertRow(table.rows.length);
-th = document.createElement("th");
-th.appendChild(document.createTextNode("Symbol(s)"));
-row.appendChild(th);
-th = document.createElement("th");
-th.appendChild(document.createTextNode("Name"));
-row.appendChild(th);
-th = document.createElement("th");
-if (this.has_complement()) {
-th.appendChild(document.createTextNode("Complement"));
-}
-row.appendChild(th);
-// list the core symbols
-for (i = 0; i < this.ncore; i++) {
-row = table.insertRow(table.rows.length);
-td = document.createElement("td");
-if (this.symbols[i].colour != null) {
-td.style.color = '#' + this.symbols[i].colour;
-}
-td.appendChild(document.createTextNode(this.symbols[i].symbol));
-aliases = this.get_aliases(i);
-if (aliases.length > 0) {
-td.appendChild(document.createTextNode(' ' + aliases.split('').join(' ')));
-}
-row.appendChild(td);
-td = document.createElement("td");
-if (this.symbols[i].name != null) {
-td.appendChild(document.createTextNode(this.symbols[i].name));
-}
-row.appendChild(td);
-td = document.createElement("td");
-if (this.symbols[i].complement != null) {
-td.style.color = this.get_colour(this.get_index(this.symbols[i].complement));
-td.appendChild(document.createTextNode(this.symbols[i].complement));
-}
-row.appendChild(td);
-}
-// create the ambiguous symbol header
-row = table.insertRow(table.rows.length);
-th = document.createElement("th");
-th.appendChild(document.createTextNode("Symbol(s)"));
-row.appendChild(th);
-th = document.createElement("th");
-th.appendChild(document.createTextNode("Name"));
-row.appendChild(th);
-th = document.createElement("th");
-th.appendChild(document.createTextNode("Matches"));
-row.appendChild(th);
-// list the ambiguous symbols
-for (i = this.ncore; i < this.symbols.length; i++) {
-row = table.insertRow(table.rows.length);
-td = document.createElement("td");
-if (this.symbols[i].colour != null) {
-td.style.color = '#' + this.symbols[i].colour;
-}
-td.appendChild(document.createTextNode(this.symbols[i].symbol));
-aliases = this.get_aliases(i);
-if (aliases.length > 0) {
-td.appendChild(document.createTextNode(' ' + aliases.split('').join(' ')));
-}
-row.appendChild(td);
-td = document.createElement("td");
-if (this.symbols[i].name != null) {
-td.appendChild(document.createTextNode(this.symbols[i].name));
-}
-row.appendChild(td);
-td = document.createElement("td");
-equals = this.symbols[i].equals.split('');
-for (j = 0; j < equals.length; j++) {
-if (j != 0) td.appendChild(document.createTextNode(' '));
-sym = document.createElement("span");
-sym.style.color = this.get_colour(this.get_index(equals[j]));
-sym.appendChild(document.createTextNode(equals[j]));
-td.appendChild(sym);
-}
-row.appendChild(td);
-}
-return table;
-};
-// returns a dictionary of the colours for EPS
-Alphabet.prototype._as_eps_dict = function() {
-"use strict";
-var i, sym, rgb;
-var out = "/fullColourDict <<\n";
-for (i = 0; i < this.ncore; i++) {
-sym = this.get_symbol(i);
-sym = sym.replace(/\\/g, "\\\\");
-sym = sym.replace(/\(/g, "\\(");
-sym = sym.replace(/\)/g, "\\)");
-rgb = this.get_rgb(i);
-out += " (" + sym + ") [" + rgb.red.toFixed(4) + " " + rgb.green.toFixed(4) + " " + rgb.blue.toFixed(4) + "]\n";
-}
-out += ">> def\n";
-out += "/mutedColourDict <<\n";
-for (i = 0; i < this.ncore; i++) {
-sym = this.get_symbol(i);
-sym = sym.replace(/\\/g, "\\\\");
-sym = sym.replace(/\(/g, "\\(");
-sym = sym.replace(/\)/g, "\\)");
-rgb = Alphabet.lighten_colour(this.get_rgb(i));
-out += " (" + sym + ") [" + rgb.red.toFixed(4) + " " + rgb.green.toFixed(4) + " " + rgb.blue.toFixed(4) + "]\n";
-}
-out += ">> def\n";
-return out;
-};
-// return the alphabet name or a list of primary symbols
-Alphabet.prototype.toString = function() {
-"use strict";
-if (this.name != null) {
-return this.name;
-} else {
-return this.get_symbols();
-}
-};
-//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-// Helper functions
-//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-// Convert a colour specified in RGB colourspace values into LAB colourspace
-Alphabet.rgb2lab = function(rgb) {
-"use strict";
-var xyzHelper, labHelper;
-// XYZ helper
-xyzHelper = function(value) {
-if (value > 0.0445) {
-value = (value + 0.055) / 1.055;
-value = Math.pow(value, 2.4);
-} else {
-value /= 12.92;
-}
-value *= 100;
-return value;
-};
-// lab helper
-labHelper = function(value) {
-if (value > 0.008856) {
-value = Math.pow(value, 1.0 / 3.0);
-} else {
-value = (7.787 * value) + (16.0 / 116.0);
-}
-return value;
-};
-// convert into XYZ colourspace
-var c1, c2, c3;
-if (typeof rgb == "number") {
-c1 = xyzHelper(((rgb >> 16) & 0xFF) / 255.0);
-c2 = xyzHelper(((rgb >> 8) & 0xFF) / 255.0);
-c3 = xyzHelper((rgb & 0xFF) / 255.0);
-} else {
-c1 = xyzHelper(rgb.red);
-c2 = xyzHelper(rgb.green);
-c3 = xyzHelper(rgb.blue);
-}
-var x = (c1 * 0.4124) + (c2 * 0.3576) + (c3 * 0.1805);
-var y = (c1 * 0.2126) + (c2 * 0.7152) + (c3 * 0.0722);
-var z = (c1 * 0.0193) + (c2 * 0.1192) + (c3 * 0.9505);
-// convert into Lab colourspace
-c1 = labHelper(x / 95.047);
-c2 = labHelper(y / 100.0);
-c3 = labHelper(z / 108.883);
-var l = (116.0 * c2) - 16;
-var a = 500.0 * (c1 - c2);
-var b = 200.0 * (c2 - c3);
-return {"l": l, "a": a, "b": b};
-};
-// Convert a colour specified in HSV colourspace into RGB colourspace
-Alphabet.hsv2rgb = function(hue, sat, value, output_object) {
-// achromatic (grey)
-var r = value;
-var g = value;
-var b = value;
-if (sat != 0) {
-var h = hue / 60.0;
-var i = Math.floor(h);
-var f = h - i;
-var p = value * (1.0 - sat);
-var q = value * (1.0 - (sat * f));
-var t = value * (1.0 - (sat * (1.0 - f)));
-if (i == 0) {
-r = value;
-g = t;
-b = p;
-} else if (i == 1) {
-r = q;
-g = value;
-b = p;
-} else if (i == 2) {
-r = p;
-g = value;
-b = t;
-} else if (i == 3) {
-r = p;
-g = q;
-b = value;
-} else if (i == 4) {
-r = t;
-g = p;
-b = value;
-} else {
-r = value;
-g = p;
-b = q;
-}
-}
-if (output_object) {
-return {"red": r, "green": g, "blue": b};
-} else {
-return (Math.floor(r * 255) << 15) | (Math.floor(g * 255) << 8) | (Math.floor(b * 255));
-}
-};
-// Calculate a distance score between two colours in LAB colourspace
-Alphabet.lab_dist = function(lab1, lab2) {
-var c1 = Math.sqrt((lab1.l * lab1.l) + (lab1.a * lab1.a));
-var c2 = Math.sqrt((lab2.l * lab2.l) + (lab2.a * lab2.a));
-var dc = c1 - c2;
-var dl = lab1.l - lab2.l;
-var da = lab1.a - lab2.a;
-var db = lab1.b - lab2.b;
-// we don't want NaN due to rounding errors so fudge things a bit...
-var dh = 0;
-var dh_squared = (da * da) + (db * db) - (dc * dc);
-if (dh_squared > 0) {
-dh = Math.sqrt(dh_squared);
-}
-var first = dl;
-var second = dc / (1.0 + (0.045 * c1));
-var third = dh / (1.0 + (0.015 * c1));
-return Math.sqrt((first * first) + (second * second) + (third * third));
-};
-// convert an RGB value into a HSL value
-Alphabet.rgb2hsl = function(rgb) {
-"use strict";
-var min, max, delta, h, s, l, r, g, b;
-if (typeof rgb == "number") {
-r = ((rgb >> 16) & 0xFF) / 255.0;
-g = ((rgb >> 8) & 0xFF) / 255.0;
-b = (rgb & 0xFF) / 255.0;
-} else {
-r = rgb.red;
-g = rgb.green;
-b = rgb.blue;
-}
-min = Math.min(r, g, b);
-max = Math.max(r, g, b);
-delta = max - min;
-l = min + (delta / 2);
-if (max == min) {
-h = 0; // achromatic (grayscale)
-s = 0;
-} else {
-if (l > 0.5) {
-s = delta / (2 - max - min);
-} else {
-s = delta / (max + min);
-}
-if (max == r) {
-h = (g - b) / delta;
-if (g < b) h += 6;
-} else if (max == g) {
-h = ((b - r) / delta) + 2;
-} else {
-h = ((r - g) / delta) + 4;
-}
-h /= 6;
-}
-return {"h": h, "s": s, "l": l};
-};
-// convert a HSL value into an RGB value
-Alphabet.hsl2rgb = function(hsl, output_object) {
-"use strict";
-function _hue(p, q, t) {
-"use strict";
-if (t < 0) t += 1;
-else if (t > 1) t -= 1;
-if (t < (1.0 / 6.0)) {
-return p + ((q - p) * 6.0 * t);
-} else if (t < 0.5) {
-return q;
-} else if (t < (2.0 / 3.0)) {
-return p + ((q - p) * ((2.0 / 3.0) - t) * 6.0);
-} else {
-return p;
-}
-}
-var r, g, b, p, q;
-if (hsl.s == 0) {
-// achromatic (grayscale)
-r = hsl.l;
-g = hsl.l;
-b = hsl.l;
-} else {
-if (hsl.l < 0.5) {
-q = hsl.l * (1 + hsl.s);
-} else {
-q = hsl.l + hsl.s - (hsl.l * hsl.s);
-}
-p = (2 * hsl.l) - q;
-r = _hue(p, q, hsl.h + (1.0 / 3.0));
-g = _hue(p, q, hsl.h);
-b = _hue(p, q, hsl.h - (1.0 / 3.0));
-}
-if (output_object) {
-return {"red": r, "green": g, "blue": b};
-} else {
-return (Math.floor(r * 255) << 15) | (Math.floor(g * 255) << 8) | (Math.floor(b * 255));
-}
-};
-Alphabet.lighten_colour = function(rgb) {
-"use strict";
-var hsl = Alphabet.rgb2hsl(rgb);
-hsl.l += (1.0 - hsl.l) * 2 / 3;
-return Alphabet.hsl2rgb(hsl, typeof rgb != "number");
-};
-//======================================================================
-// end Alphabet object
-//======================================================================
-//======================================================================
-// start StandardAlphabet object
-//======================================================================
-// an extension of the alphabet object to support some additional fields
-// only present in standard alphabets.
-var StandardAlphabet = function(enum_code, enum_name, alphabet_data) {
-Alphabet.apply(this, [alphabet_data]);
-this.enum_code = enum_code;
-this.enum_name = enum_name;
-};
-StandardAlphabet.prototype = Alphabet.prototype;
-StandardAlphabet.prototype.constructor = StandardAlphabet;
-// A unique code for this standard alphabet.
-// This code will be a power of 2 to enable creation of bitsets for
-// a selection of standard alphabets.
-StandardAlphabet.prototype.get_code = function() {
-return this.enum_code;
-};
-// A unique name for this standard alphabet.
-// this name will be all upper case and the same as the property that
-// refers to this alphabet in the AlphStd collection.
-StandardAlphabet.prototype.get_enum = function() {
-return this.enum_name;
-};
-//======================================================================
-// end StandardAlphabet object
-//======================================================================
-// A collection of standard alphabets.
-var AlphStd = {
-RNA: new StandardAlphabet(1, "RNA", {
-"name": "RNA",
-"like": "RNA",
-"ncore": 4,
-"symbols": [
-{"symbol": "A", "name": "Adenine", "colour": "CC0000"},
-{"symbol": "C", "name": "Cytosine", "colour": "0000CC"},
-{"symbol": "G", "name": "Guanine", "colour": "FFB300"},
-{"symbol": "U", "name": "Uracil", "colour": "008000",
-"aliases": "T"},
-{"symbol": "N", "name": "Any base", "equals": "ACGU", "aliases": "X."},
-{"symbol": "V", "name": "Not U", "equals": "ACG"},
-{"symbol": "H", "name": "Not G", "equals": "ACU"},
-{"symbol": "D", "name": "Not C", "equals": "AGU"},
-{"symbol": "B", "name": "Not A", "equals": "CGU"},
-{"symbol": "M", "name": "Amino", "equals": "AC"},
-{"symbol": "R", "name": "Purine", "equals": "AG"},
-{"symbol": "W", "name": "Weak", "equals": "AU"},
-{"symbol": "S", "name": "Strong", "equals": "CG"},
-{"symbol": "Y", "name": "Pyrimidine", "equals": "CU"},
-{"symbol": "K", "name": "Keto", "equals": "GU"}
-]
-}),
-DNA: new StandardAlphabet(2, "DNA", {
-"name": "DNA",
-"like": "DNA",
-"ncore": 4,
-"symbols": [
-{"symbol": "A", "name": "Adenine", "colour": "CC0000", "complement": "T"},
-{"symbol": "C", "name": "Cytosine", "colour": "0000CC", "complement": "G"},
-{"symbol": "G", "name": "Guanine", "colour": "FFB300", "complement": "C"},
-{"symbol": "T", "name": "Thymine", "colour": "008000", "complement": "A",
-"aliases": "U"},
-{"symbol": "N", "name": "Any base", "equals": "ACGT", "aliases": "X."},
-{"symbol": "V", "name": "Not T", "equals": "ACG"},
-{"symbol": "H", "name": "Not G", "equals": "ACT"},
-{"symbol": "D", "name": "Not C", "equals": "AGT"},
-{"symbol": "B", "name": "Not A", "equals": "CGT"},
-{"symbol": "M", "name": "Amino", "equals": "AC"},
-{"symbol": "R", "name": "Purine", "equals": "AG"},
-{"symbol": "W", "name": "Weak", "equals": "AT"},
-{"symbol": "S", "name": "Strong", "equals": "CG"},
-{"symbol": "Y", "name": "Pyrimidine", "equals": "CT"},
-{"symbol": "K", "name": "Keto", "equals": "GT"}
-]
-}),
-PROTEIN: new StandardAlphabet(4, "PROTEIN", {
-"name": "Protein",
-"like": "PROTEIN",
-"ncore": 20,
-"symbols": [
-{"symbol": "A", "name": "Alanine", "colour": "0000CC"},
-{"symbol": "C", "name": "Cysteine", "colour": "0000CC"},
-{"symbol": "D", "name": "Aspartic acid", "colour": "FF00FF"},
-{"symbol": "E", "name": "Glutamic acid", "colour": "FF00FF"},
-{"symbol": "F", "name": "Phenylalanine", "colour": "0000CC"},
-{"symbol": "G", "name": "Glycine", "colour": "FFB300"},
-{"symbol": "H", "name": "Histidine", "colour": "FFCCCC"},
-{"symbol": "I", "name": "Isoleucine", "colour": "0000CC"},
-{"symbol": "K", "name": "Lysine", "colour": "CC0000"},
-{"symbol": "L", "name": "Leucine", "colour": "0000CC"},
-{"symbol": "M", "name": "Methionine", "colour": "0000CC"},
-{"symbol": "N", "name": "Asparagine", "colour": "008000"},
-{"symbol": "P", "name": "Proline", "colour": "FFFF00"},
-{"symbol": "Q", "name": "Glutamine", "colour": "008000"},
-{"symbol": "R", "name": "Arginine", "colour": "CC0000"},
-{"symbol": "S", "name": "Serine", "colour": "008000"},
-{"symbol": "T", "name": "Threonine", "colour": "008000"},
-{"symbol": "V", "name": "Valine", "colour": "0000CC"},
-{"symbol": "W", "name": "Tryptophan", "colour": "0000CC"},
-{"symbol": "Y", "name": "Tyrosine", "colour": "33E6CC"},
-{"symbol": "X", "name": "Any amino acid", "equals": "ACDEFGHIKLMNPQRSTVWY", "aliases": "*."},
-{"symbol": "B", "name": "Asparagine or Aspartic acid", "equals": "DN"},
-{"symbol": "Z", "name": "Glutamine or Glutamic acid", "equals": "EQ"},
-{"symbol": "J", "name": "Leucine or Isoleucine", "equals": "IL"}
-]
-})
-};
-//======================================================================
-// start Symbol object
-//======================================================================
-var Symbol = function(alph_index, scale, alphabet) {
-"use strict";
-//variable prototype
-this.symbol = alphabet.get_symbol(alph_index);
-this.scale = scale;
-this.colour = alphabet.get_colour(alph_index);
-};
-Symbol.prototype.get_symbol = function() {
-"use strict";
-return this.symbol;
-};
-Symbol.prototype.get_scale = function() {
-"use strict";
-return this.scale;
-};
-Symbol.prototype.get_colour = function() {
-"use strict";
-return this.colour;
-};
-Symbol.prototype.toString = function() {
-"use strict";
-return this.symbol + " " + (Math.round(this.scale*1000)/10) + "%";
-};
-function compare_symbol(sym1, sym2) {
-"use strict";
-if (sym1.get_scale() < sym2.get_scale()) {
-return -1;
-} else if (sym1.get_scale() > sym2.get_scale()) {
-return 1;
-} else {
-return 0;
-}
-}
-//======================================================================
-// end Symbol object
-//======================================================================
-//======================================================================
-// start Pspm object
-//======================================================================
-var Pspm = function(matrix, name, ltrim, rtrim, nsites, evalue, pssm, alt) {
-"use strict";
-var row, col, data, row_sum, delta, evalue_re;
-if (typeof name !== "string") {
-name = "";
-}
-this.name = name;
-//construct
-if (matrix instanceof Pspm) {
-// copy constructor
-this.alph_length = matrix.alph_length;
-this.motif_length = matrix.motif_length;
-this.name = matrix.name;
-this.alt = matrix.alt;
-this.nsites = matrix.nsites;
-this.evalue = matrix.evalue;
-this.ltrim = matrix.ltrim;
-this.rtrim = matrix.rtrim;
-this.pspm = [];
-for (row = 0; row < matrix.motif_length; row++) {
-this.pspm[row] = [];
-for (col = 0; col < matrix.alph_length; col++) {
-this.pspm[row][col] = matrix.pspm[row][col];
-}
-}
-if (matrix.pssm != null) {
-this.pssm = [];
-for (row = 0; row < matrix.motif_length; row++) {
-this.pspm[row] = [];
-for (col = 0; col < matrix.alph_length; col++) {
-this.pssm[row][col] = matrix.pssm[row][col];
-}
-}
-}
-} else {
-// check parameters
-if (ltrim == null) {
-ltrim = 0;
-} else if (typeof ltrim !== "number" || ltrim % 1 !== 0 || ltrim < 0) {
-throw new Error("ltrim must be a non-negative integer, got: " + ltrim);
-}
-if (rtrim == null) {
-rtrim = 0;
-} else if (typeof rtrim !== "number" || rtrim % 1 !== 0 || rtrim < 0) {
-throw new Error("rtrim must be a non-negative integer, got: " + rtrim);
-}
-if (nsites != null) {
-if (typeof nsites !== "number" || nsites < 0) {
-throw new Error("nsites must be a positive number, got: " + nsites);
-} else if (nsites == 0) {
-nsites = null;
-}
-}
-if (evalue != null) {
-if (typeof evalue === "number") {
-if (evalue < 0) {
-throw new Error("evalue must be a non-negative number, got: " + evalue);
-}
-} else if (typeof evalue === "string") {
-evalue_re = /^((?:[+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)|inf)$/;
-if (!evalue_re.test(evalue)) {
-throw new Error("evalue must be a non-negative number, got: " + evalue);
-}
-} else {
-throw new Error("evalue must be a non-negative number, got: " + evalue);
-}
-}
-// set properties
-this.name = name;
-this.alt = alt;
-this.nsites = nsites;
-this.evalue = evalue;
-this.ltrim = ltrim;
-this.rtrim = rtrim;
-if (typeof matrix === "string") {
-// string constructor
-data = parse_pspm_string(matrix);
-this.alph_length = data["alph_length"];
-this.motif_length = data["motif_length"];
-this.pspm = data["pspm"];
-if (this.evalue == null) {
-if (data["evalue"] != null) {
-this.evalue = data["evalue"];
-} else {
-this.evalue = 0;
-}
-}
-if (this.nsites == null) {
-if (typeof data["nsites"] === "number") {
-this.nsites = data["nsites"];
-} else {
-this.nsites = 20;
-}
-}
-} else {
-// assume pspm is a nested array
-this.motif_length = matrix.length;
-this.alph_length = (matrix.length > 0 ? matrix[0].length : 0);
-if (this.nsites == null) {
-this.nsites = 20;
-}
-if (this.evalue == null) {
-this.evalue = 0;
-}
-this.pspm = [];
-// copy pspm and check
-for (row = 0; row < this.motif_length; row++) {
-if (this.alph_length != matrix[row].length) {
-throw new Error("COLUMN_MISMATCH");
-}
-this.pspm[row] = [];
-row_sum = 0;
-for (col = 0; col < this.alph_length; col++) {
-this.pspm[row][col] = matrix[row][col];
-row_sum += this.pspm[row][col];
-}
-delta = 0.1;
-if (isNaN(row_sum) || (row_sum > 1 && (row_sum - 1) > delta) ||
-(row_sum < 1 && (1 - row_sum) > delta)) {
-throw new Error("INVALID_SUM");
-}
-}
-// copy pssm
-if (pssm != null) {
-this.pssm = [];
-for (row = 0; row < this.motif_length; row++) {
-this.pssm[row] = [];
-for (col = 0; col < this.alph_length; col++) {
-this.pssm[row][col] = pssm[row][col];
-}
-}
-}
-}
-}
-};
-Pspm.prototype.copy = function() {
-"use strict";
-return new Pspm(this);
-};
-Pspm.prototype.reverse = function() {
-"use strict";
-var x, y, temp, temp_trim;
-//reverse
-x = 0;
-y = this.motif_length-1;
-while (x < y) {
-temp = this.pspm[x];
-this.pspm[x] = this.pspm[y];
-this.pspm[y] = temp;
-x++;
-y--;
-}
-// reverse pssm (if defined)
-if (typeof this.pssm !== "undefined") {
-//reverse
-x = 0;
-y = this.motif_length-1;
-while (x < y) {
-temp = this.pssm[x];
-this.pspm[x] = this.pssm[y];
-this.pssm[y] = temp;
-x++;
-y--;
-}
-}
-//swap triming
-temp_trim = this.ltrim;
-this.ltrim = this.rtrim;
-this.rtrim = temp_trim;
-return this; //allow function chaining...
-};
-Pspm.prototype.reverse_complement = function(alphabet) {
-"use strict";
-var x, y, temp, i, row, c, temp_trim;
-if (this.alph_length != alphabet.get_size_core()) {
-throw new Error("The alphabet size does not match the size of the pspm.");
-}
-if (!alphabet.has_complement()) {
-throw new Error("The specified alphabet can not be complemented.");
-}
-// reverse motif
-this.reverse();
-//complement
-for (x = 0; x < this.motif_length; x++) {
-row = this.pspm[x];
-for (i = 0; i < row.length; i++) {
-c = alphabet.get_complement(i);
-if (c < i) continue;
-temp = row[i];
-row[i] = row[c];
-row[c] = temp;
-}
-}
-// complement pssm (if defined)
-if (typeof this.pssm !== "undefined") {
-//complement
-for (x = 0; x < this.motif_length; x++) {
-row = this.pssm[x];
-for (i = 0; i < row.length; i++) {
-c = alphabet.get_complement(i);
-if (c < i) continue;
-temp = row[i];
-row[i] = row[c];
-row[c] = temp;
-}
-}
-}
-return this; //allow function chaining...
-};
-Pspm.prototype.get_stack = function(position, alphabet, ssc) {
-"use strict";
-var row, stack_ic, alphabet_ic, stack, i, sym;
-if (this.alph_length != alphabet.get_size_core()) {
-throw new Error("The alphabet size does not match the size of the pspm.");
-}
-row = this.pspm[position];
-stack_ic = this.get_stack_ic(position, alphabet);
-if (ssc) stack_ic -= this.get_error(alphabet);
-alphabet_ic = alphabet.get_ic();
-stack = [];
-for (i = 0; i < this.alph_length; i++) {
-sym = new Symbol(i, row[i]*stack_ic/alphabet_ic, alphabet);
-if (sym.get_scale() <= 0) {
-continue;
-}
-stack.push(sym);
-}
-stack.sort(compare_symbol);
-return stack;
-};
-Pspm.prototype.get_stack_ic = function(position, alphabet) {
-"use strict";
-var row, H, i;
-if (this.alph_length != alphabet.get_size_core()) {
-throw new Error("The alphabet size does not match the size fo the pspm.");
-}
-row = this.pspm[position];
-H = 0;
-for (i = 0; i < this.alph_length; i++) {
-if (row[i] === 0) {
-continue;
-}
-H -= (row[i] * (Math.log(row[i]) / Math.LN2));
-}
-return alphabet.get_ic() - H;
-};
-Pspm.prototype.get_error = function(alphabet) {
-"use strict";
-if (this.nsites === 0) {
-return 0;
-}
-return (alphabet.get_size_core()-1) / (2 * Math.LN2 * this.nsites);
-};
-Pspm.prototype.get_motif_length = function() {
-"use strict";
-return this.motif_length;
-};
-Pspm.prototype.get_alph_length = function() {
-"use strict";
-return this.alph_length;
-};
-Pspm.prototype.get_left_trim = function() {
-"use strict";
-return this.ltrim;
-};
-Pspm.prototype.get_right_trim = function() {
-"use strict";
-return this.rtrim;
-};
-Pspm.prototype.as_best_match = function(alphabet) {
-"use strict";
-var match, odds, best_odds, best_index;
-var i, j;
-match = "";
-for (i = 0; i < this.motif_length; i++) {
-best_index = 0;
-best_odds = this.pspm[i][0] / alphabet.get_bg_freq(0);
-for (j = 1; j < this.alph_length; j++) {
-odds = this.pspm[i][j] / alphabet.get_bg_freq(j);
-if (odds > best_odds) {
-best_odds = odds;
-best_index = j;
-}
-}
-match += alphabet.get_symbol(best_index);
-}
-return match;
-};
-Pspm.prototype.as_count_matrix = function() {
-"use strict";
-var count, count_text, text;
-var i, j;
-text = "";
-for (i = 0; i < this.motif_length; i++) {
-if (i !== 0) {
-text += "\n";
-}
-for (j = 0; j < this.alph_length; j++) {
-if (j !== 0) {
-text += " ";
-}
-count = Math.round(this.nsites * this.pspm[i][j]);
-count_text = "" + count;
-// pad up to length of 4
-if (count_text.length < 4) {
-text += (new Array(5 - count_text.length)).join(" ") + count_text;
-} else {
-text += count_text;
-}
-}
-}
-return text;
-};
-Pspm.prototype.as_probability_matrix = function() {
-"use strict";
-var text;
-var i, j;
-text = "";
-for (i = 0; i < this.motif_length; i++) {
-if (i !== 0) {
-text += "\n";
-}
-for (j = 0; j < this.alph_length; j++) {
-if (j !== 0) {
-text += " ";
-}
-text += this.pspm[i][j].toFixed(6);
-}
-}
-return text;
-};
-Pspm.prototype.as_score_matrix = function(alphabet, pseudo) {
-"use strict";
-var me, score, out, row, col, score_text;
-me = this;
-if (typeof this.pssm === "undefined") {
-if (!(typeof alphabet === "object" && alphabet != null && alphabet instanceof Alphabet)) {
-throw new Error("The alphabet is required to generate the pssm.");
-}
-if (typeof pseudo === "undefined") {
-pseudo = 0.01;
-} else if (typeof pseudo !== "number" || pseudo < 0) {
-throw new Error("Expected positive number for pseudocount");
-}
-score = function(row, col) {
-"use strict";
-var p, bg, p2;
-p = me.pspm[row][col];
-bg = alphabet.get_bg_freq(col);
-p2 = (p * me.nsites + bg * pseudo) / (me.nsites + pseudo);
-return (p2 > 0 ? Math.round((Math.log(p2 / bg) / Math.LN2) * 100) : -10000);
-};
-} else {
-score = function(row, col) {
-"use strict";
-return me.pssm[row][col];
-};
-}
-out = "";
-for (row = 0; row < this.motif_length; row++) {
-for (col = 0; col < this.alph_length; col++) {
-if (col !== 0) {
-out += " ";
-}
-score_text = "" + score(row, col);
-// pad out to 6 characters
-if (score_text.length < 6) {
-out += (new Array(7 - score_text.length)).join(" ") + score_text;
-} else {
-out += score_text;
-}
-}
-out += "\n";
-}
-return out;
-}
-Pspm.prototype.as_pspm = function() {
-"use strict";
-return "letter-probability matrix: alength= " + this.alph_length +
-" w= " + this.motif_length + " nsites= " + this.nsites +
-" E= " + (typeof this.evalue === "number" ?
-this.evalue.toExponential() : this.evalue) + "\n" +
-this.as_probability_matrix();
-};
-Pspm.prototype.as_pssm = function(alphabet, pseudo) {
-"use strict";
-return "log-odds matrix: alength= " + this.alph_length +
-" w= " + this.motif_length +
-" E= " + (typeof this.evalue == "number" ?
-this.evalue.toExponential() : this.evalue) + "\n" +
-this.as_score_matrix(alphabet, pseudo);
-};
-Pspm.prototype.as_meme = function(options) {
-var with_header, with_pspm, with_pssm, version, alphabet, bg_source, pseudocount, strands;
-var out, alen, i;
-// get the options
-if (typeof options !== "object" || options === null) {
-options = {};
-}
-with_header = (typeof options["with_header"] === "boolean" ? options["with_header"] : false);
-with_pspm = (typeof options["with_pspm"] === "boolean" ? options["with_pspm"] : false);
-with_pssm = (typeof options["with_pssm"] === "boolean" ? options["with_pssm"] : false);
-if (!with_pspm && !with_pssm) with_pspm = true;
-if (with_header) {
-if (typeof options["version"] === "string" && /^\d+(?:\.\d+){0,2}$/.test(options["version"])) {
-version = options["version"];
-} else if (typeof options["version"] === "number") {
-version = options["version"].toFixed(0);
-} else {
-version = "4";
-}
-if (typeof options["strands"] === "number" && options["strands"] === 1) {
-strands = 1;
-} else {
-strands = 2;
-}
-if (typeof options["bg_source"] === "string") {
-bg_source = options["bg_source"];
-} else {
-bg_source = "unknown source";
-}
-if (typeof options["alphabet"] === "object" && options["alphabet"] != null
-&& options["alphabet"] instanceof Alphabet) {
-alphabet = options["alphabet"];
-} else {
-throw new Error("The alphabet is required to generate the header.");
-}
-}
-// now create the output
-out = "";
-if (with_header) {
-out = "MEME version " + version + "\n\n";
-out += alphabet.as_meme() + "\n";
-if (alphabet.has_complement()) { // assume DNA has both strands unless otherwise specified
-out += "strands: " + (strands === 1 ? "+" : "+ -") + "\n\n";
-}
-out += "Background letter frequencies (from " + bg_source + "):\n";
-alen = alphabet.get_size_core();
-for (i = 0; i < alen; i++) {
-if (i !== 0) {
-if (i % 9 === 0) { // maximum of nine entries per line
-out += "\n";
-} else {
-out += " ";
-}
-}
-out += alphabet.get_symbol(i) + " " + alphabet.get_bg_freq(i).toFixed(3);
-}
-}
-out += "\n\n";
-out += "MOTIF " + this.name + (this.alt == null ? "" : " " + this.alt);
-if (with_pssm) {
-out += "\n\n";
-out += this.as_pssm(options["alphabet"], options["pseudocount"]);
-}
-if (with_pspm) {
-out += "\n\n";
-out += this.as_pspm();
-}
-return out;
-}
-Pspm.prototype.toString = function() {
-"use strict";
-var str, i, row;
-str = "";
-for (i = 0; i < this.pspm.length; i++) {
-row = this.pspm[i];
-str += row.join("\t") + "\n";
-}
-return str;
-};
-function parse_pspm_properties(str) {
-"use strict";
-var parts, i, eqpos, before, after, properties, prop, num, num_re;
-num_re = /^((?:[+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)|inf)$/;
-parts = trim(str).split(/\s+/);
-// split up words containing =
-for (i = 0; i < parts.length;) {
-eqpos = parts[i].indexOf("=");
-if (eqpos != -1) {
-before = parts[i].substr(0, eqpos);
-after = parts[i].substr(eqpos+1);
-if (before.length > 0 && after.length > 0) {
-parts.splice(i, 1, before, "=", after);
-i += 3;
-} else if (before.length > 0) {
-parts.splice(i, 1, before, "=");
-i += 2;
-} else if (after.length > 0) {
-parts.splice(i, 1, "=", after);
-i += 2;
-} else {
-parts.splice(i, 1, "=");
-i++;
-}
-} else {
-i++;
-}
-}
-properties = {};
-for (i = 0; i < parts.length; i += 3) {
-if (parts.length - i < 3) {
-throw new Error("Expected PSPM property was incomplete. "+
-"Remaing parts are: " + parts.slice(i).join(" "));
-}
-if (parts[i+1] !== "=") {
-throw new Error("Expected '=' in PSPM property between key and " +
-"value but got " + parts[i+1]);
-}
-prop = parts[i].toLowerCase();
-num = parts[i+2];
-if (!num_re.test(num)) {
-throw new Error("Expected numeric value for PSPM property '" +
-prop + "' but got '" + num + "'");
-}
-properties[prop] = num;
-}
-return properties;
-}
-function parse_pspm_string(pspm_string) {
-"use strict";
-var header_re, lines, first_line, line_num, col_num, alph_length,
-motif_length, nsites, evalue, pspm, i, line, match, props, parts,
-j, prob;
-header_re = /^letter-probability\s+matrix:(.*)$/i;
-lines = pspm_string.split(/\n/);
-first_line = true;
-line_num = 0;
-col_num = 0;
-alph_length;
-motif_length;
-nsites;
-evalue;
-pspm = [];
-for (i = 0; i < lines.length; i++) {
-line = trim(lines[i]);
-if (line.length === 0) {
-continue;
-}
-// check the first line for a header though allow matrices without it
-if (first_line) {
-first_line = false;
-match = header_re.exec(line);
-if (match !== null) {
-props = parse_pspm_properties(match[1]);
-if (props.hasOwnProperty("alength")) {
-alph_length = parseFloat(props["alength"]);
-if (alph_length != 4 && alph_length != 20) {
-throw new Error("PSPM property alength should be 4 or 20" +
-" but got " + alph_length);
-}
-}
-if (props.hasOwnProperty("w")) {
-motif_length = parseFloat(props["w"]);
-if (motif_length % 1 !== 0 || motif_length < 1) {
-throw new Error("PSPM property w should be an integer larger " +
-"than zero but got " + motif_length);
-}
-}
-if (props.hasOwnProperty("nsites")) {
-nsites = parseFloat(props["nsites"]);
-if (nsites <= 0) {
-throw new Error("PSPM property nsites should be larger than " +
-"zero but got " + nsites);
-}
-}
-if (props.hasOwnProperty("e")) {
-evalue = props["e"];
-if (evalue < 0) {
-throw new Error("PSPM property evalue should be " +
-"non-negative but got " + evalue);
-}
-}
-continue;
-}
-}
-pspm[line_num] = [];
-col_num = 0;
-parts = line.split(/\s+/);
-for (j = 0; j < parts.length; j++) {
-prob = parseFloat(parts[j]);
-if (prob != parts[j] || prob < 0 || prob > 1) {
-throw new Error("Expected probability but got '" + parts[j] + "'");
-}
-pspm[line_num][col_num] = prob;
-col_num++;
-}
-line_num++;
-}
-if (typeof motif_length === "number") {
-if (pspm.length != motif_length) {
-throw new Error("Expected PSPM to have a motif length of " +
-motif_length + " but it was actually " + pspm.length);
-}
-} else {
-motif_length = pspm.length;
-}
-if (typeof alph_length !== "number") {
-alph_length = pspm[0].length;
-if (alph_length != 4 && alph_length != 20) {
-throw new Error("Expected length of first row in the PSPM to be " +
-"either 4 or 20 but got " + alph_length);
-}
-}
-for (i = 0; i < pspm.length; i++) {
-if (pspm[i].length != alph_length) {
-throw new Error("Expected PSPM row " + i + " to have a length of " +
-alph_length + " but the length was " + pspm[i].length);
-}
-}
-return {"pspm": pspm, "motif_length": motif_length,
-"alph_length": alph_length, "nsites": nsites, "evalue": evalue};
-}
-//======================================================================
-// end Pspm object
-//======================================================================
-//======================================================================
-// start Logo object
-//======================================================================
-var Logo = function(alphabet, options) {
-"use strict";
-this.alphabet = alphabet;
-this.fine_text = "";
-this.x_axis = 1;
-this.y_axis = true;
-this.xlate_nsyms = 1;
-this.xlate_start = null;
-this.xlate_end = null;
-this.pspm_list = [];
-this.pspm_column = [];
-this.rows = 0;
-this.columns = 0;
-if (typeof options === "string") {
-// the old method signature had fine_text here so we support that
-this.fine_text = options;
-} else if (typeof options === "object" && options != null) {
-this.fine_text = (typeof options.fine_text === "string" ? options.fine_text : "");
-this.x_axis = (typeof options.x_axis === "boolean" ? (options.x_axis ? 1 : 0) : 1);
-if (options.x_axis_hidden != null && options.x_axis_hidden) this.x_axis = -1;
-this.y_axis = (typeof options.y_axis === "boolean" ? options.y_axis : true);
-this.xlate_nsyms = (typeof options.xlate_nsyms === "number" ? options.xlate_nsyms : this.xlate_nsyms);
-this.xlate_start = (typeof options.xlate_start === "number" ? options.xlate_start : this.xlate_start);
-this.xlate_end = (typeof options.xlate_end === "number" ? options.xlate_end : this.xlate_end);
-}
-};
-Logo.prototype.add_pspm = function(pspm, column) {
-"use strict";
-var col;
-if (typeof column === "undefined") {
-column = 0;
-} else if (column < 0) {
-throw new Error("Column index out of bounds.");
-}
-this.pspm_list[this.rows] = pspm;
-this.pspm_column[this.rows] = column;
-this.rows++;
-col = column + pspm.get_motif_length();
-if (col > this.columns) {
-this.columns = col;
-}
-};
-Logo.prototype.get_columns = function() {
-"use strict";
-return this.columns;
-};
-Logo.prototype.get_xlate_nsyms = function() {
-"use strict";
-return this.xlate_nsyms;
-};
-Logo.prototype.get_xlate_start = function() {
-"use strict";
-return (this.xlate_start != null ? this.xlate_start : 0);
-};
-Logo.prototype.get_xlate_end = function() {
-"use strict";
-return (this.xlate_end != null ? this.xlate_end : this.columns * this.xlate_nsyms);
-};
-Logo.prototype.get_xlate_columns = function() {
-"use strict";
-return this.get_xlate_end() - this.get_xlate_start();
-};
-Logo.prototype.get_rows = function() {
-"use strict";
-return this.rows;
-};
-Logo.prototype.get_pspm = function(row_index) {
-"use strict";
-if (row_index < 0 || row_index >= this.rows) {
-throw new Error("INDEX_OUT_OF_BOUNDS");
-}
-return this.pspm_list[row_index];
-};
-Logo.prototype.get_offset = function(row_index) {
-"use strict";
-if (row_index < 0 || row_index >= this.rows) {
-throw new Error("INDEX_OUT_OF_BOUNDS");
-}
-return this.pspm_column[row_index];
-};
-Logo.prototype._as_eps_data = function(ssc, errbars) {
-var i, j, pos, stack_pos, pspm, stack, sym, out;
-out = "";
-for (i = 0; i < this.rows; i++) {
-out += "\nStartLine\n";
-// Indent
-for (j = 0; j < this.pspm_column[i]; j++) {
-out += "() startstack\nendstack\n\n";
-}
-pspm = this.pspm_list[i];
-if (pspm.get_left_trim() > 0) {
-out += "MuteColour\nDrawTrimEdge\n" + pspm.get_left_trim() + " DrawTrimBg\n";
-}
-for (pos = 0; pos < pspm.get_motif_length(); pos++) {
-if (pos != 0 && pos == pspm.get_left_trim()) { // enable full colour
-out += "DrawTrimEdge\nRestoreColour\n";
-} else if (pos == (pspm.get_motif_length() - pspm.get_right_trim())) {
-out += "MuteColour\n" + pspm.get_right_trim() + " DrawTrimBg\n";
-}
-out += "(" + (pos + 1) + ") startstack\n";
-stack = pspm.get_stack(pos, this.alphabet, ssc);
-for (stack_pos = 0; stack_pos < stack.length; stack_pos++) {
-sym = stack[stack_pos];
-out += " " + (sym.get_scale() * this.alphabet.get_ic()) + " (" + sym.get_symbol() + ") numchar\n";
-}
-if (errbars) {
-out += " " + pspm.get_error(this.alphabet) + " Ibeam\n";
-}
-out += "endstack\n\n";
-}
-if (pspm.get_right_trim() > 0 || pspm.get_left_trim() == pspm.get_motif_length()) {
-out += "RestoreColour\n";
-}
-out += "EndLine\n";
-}
-return out;
-};
-Logo.prototype.as_eps = function(options) {
-"use strict";
-if (this.xlate_nsyms != 1) throw new Error("Unsupported setting xlate_nsyms for EPS");
-if (this.xlate_start != null) throw new Error("Unsupported setting xlate_start for EPS");
-if (this.xlate_end != null) throw new Error("Unsupported setting xlate_end for EPS");
-var LOGOHEIGHT = 7.5; // default height of line in cm
-var cm2pts, height, width, now, ssc, errbars;
-if (typeof options === "undefined") {
-options = {};
-}
-cm2pts = 72 / 2.54;
-if (typeof options.logo_height == "number") {
-height = options.logo_height;
-} else {
-height = LOGOHEIGHT * this.rows;
-}
-if (typeof options.logo_width == "number") {
-width = options.logo_width;
-} else {
-width = this.columns + 2;
-}
-now = new Date();
-ssc = (typeof options.ssc == "boolean" ? options.ssc : false);
-errbars = (typeof options.show_error_bar == "boolean" ? options.show_error_bar : ssc);
-var values = {
-"LOGOHEIGHT": height,
-"LOGOWIDTH": width,
-"BOUNDINGHEIGHT": Math.round(height * cm2pts),
-"BOUNDINGWIDTH": Math.round(width * cm2pts),
-"LOGOLINEHEIGHT": (height / this.rows),
-"CHARSPERLINE": this.columns,
-"BARBITS": this.alphabet.get_ic(),
-"LOGOTYPE": (this.alphabet.has_complement() ? "NA" : "AA"),
-"CREATIONDATE": now.getDate() + "." + (now.getMonth() + 1) + "." + now.getFullYear() + " " + now.getHours() + ":" + now.getMinutes() + ":" + now.getSeconds(),
-"ERRORBARFRACTION": (typeof options.error_bar_fraction == "number" ? options.error_bar_fraction : 1.0),
-"TICBITS": (typeof options.ticbits == "number" ? options.ticbits : 1.0),
-"TITLE": (typeof options.title == "string" ? options.title : ""),
-"FINEPRINT": (typeof options.fineprint == "string" ? options.fineprint : this.fine_text),
-"XAXISLABEL": (typeof options.xaxislabel == "string" ? options.xaxislabel : ""),
-"YAXISLABEL": (typeof options.yaxislabel == "string" ? options.yaxislabel : "bits"),
-"SSC": ssc,
-"YAXIS": (typeof options.show_y_axis == "boolean" ? options.show_y_axis : this.y_axis),
-"SHOWENDS": (typeof options.show_ends == "boolean" ? options.show_ends : false),
-"ERRBAR": errbars,
-"OUTLINE": (typeof options.show_outline == "boolean" ? options.show_outline : false),
-"NUMBERING": (typeof options.show_numbering == "boolean" ? options.show_numbering : this.x_axis != 0),
-"SHOWINGBOX": (typeof options.show_box == "boolean" ? options.show_box : false),
-"CREATOR": (typeof options.creator == "string" ? options.creator : "motif_logo.js"),
-"FONTSIZE": (typeof options.label_font_size == "number" ? options.label_font_size : 12),
-"TITLEFONTSIZE": (typeof options.title_font_size == "number" ? options.title_font_size : 12),
-"SMALLFONTSIZE": (typeof options.small_font_size == "number" ? options.small_font_size : 6),
-"TOPMARGIN" : (typeof options.top_margin == "number" ? options.top_margin : 0.9),
-"BOTTOMMARGIN": (typeof options.bottom_margin == "number" ? options.bottom_margin : 0.9),
-"COLORDICT": this.alphabet._as_eps_dict(),
-"DATA": this._as_eps_data(ssc, errbars)
-};
-// now this requires that the script containing the template has been imported!
-return motif_logo_template(values);
-};
-//======================================================================
-// end Logo object
-//======================================================================
-// calculate the exact size (in pixels) of an object drawn on the
-// canvas assuming that the background of the canvas is transparent.
-function canvas_bounds(ctx, cwidth, cheight) {
-"use strict";
-var data, r, c, top_line, bottom_line, left_line, right_line,
-txt_width, txt_height;
-// extract the image data
-data = ctx.getImageData(0, 0, cwidth, cheight).data;
-// set initial values
-top_line = -1; bottom_line = -1; left_line = -1; right_line = -1;
-txt_width = 0; txt_height = 0;
-// Find the top-most line with a non-transparent pixel
-for (r = 0; r < cheight; r++) {
-for (c = 0; c < cwidth; c++) {
-if (data[r * cwidth * 4 + c * 4 + 3]) {
-top_line = r;
-break;
-}
-}
-if (top_line != -1) {
-break;
-}
-}
-// Only bother looking if we found at least one set pixel...
-if (top_line != -1) {
-//find the last line with a non-transparent pixel
-for (r = cheight-1; r >= top_line; r--) {
-for(c = 0; c < cwidth; c++) {
-if(data[r * cwidth * 4 + c * 4 + 3]) {
-bottom_line = r;
-break;
-}
-}
-if (bottom_line != -1) {
-break;
-}
-}
-// calculate height
-txt_height = bottom_line - top_line + 1;
-// Find the left-most line with a non-transparent pixel
-for (c = 0; c < cwidth; c++) {
-for (r = top_line; r <= bottom_line; r++) {
-if (data[r * cwidth * 4 + c * 4 + 3]) {
-left_line = c;
-break;
-}
-}
-if (left_line != -1) {
-break;
-}
-}
-//find the right most line with a non-transparent pixel
-for (c = cwidth-1; c >= left_line; c--) {
-for(r = top_line; r <= bottom_line; r++) {
-if(data[r * cwidth * 4 + c * 4 + 3]) {
-right_line = c;
-break;
-}
-}
-if (right_line != -1) {
-break;
-}
-}
-txt_width = right_line - left_line + 1;
-}
-//return the bounds
-return {bound_top: top_line, bound_bottom: bottom_line,
-bound_left: left_line, bound_right: right_line, width: txt_width,
-height: txt_height};
-}
-//======================================================================
-// start RasterizedAlphabet
-//======================================================================
-// Rasterize Alphabet
-// 1) Measure width of text at default font for all symbols in alphabet
-// 2) sort in width ascending
-// 3) Drop the top and bottom 10% (designed to ignore outliers like 'W' and 'I')
-// 4) Calculate the average as the maximum scaling factor (designed to stop I becoming a rectangular blob).
-// 5) Assume scale of zero would result in width of zero, interpolate scale required to make perfect width font
-// 6) Draw text onto temp canvas at calculated scale
-// 7) Find bounds of drawn text
-// 8) Paint on to another canvas at the desired height (but only scaling width to fit if larger).
-var RasterizedAlphabet = function(alphabet, logo_scale, font, width) {
-"use strict";
-var default_size, safety_pad, canvas, ctx, middle, baseline, widths, sizes,
-i, sym, size, tenpercent, avg_width, scale,
-target_width, target_height;
-//variable prototypes
-this.alphabet = alphabet;
-this.scale = logo_scale;
-this.sym_cache = {};
-this.stack_num_cache = [];
-this.scale_num_cache = [];
-// size of canvas
-default_size = 60; // size of measuring canvas
-safety_pad = 20; // pixels to pad around so we don't miss the edges
-// create a canvas to do our measuring
-canvas = document.createElement("canvas");
-if (!canvas.getContext) throw new Error("No canvas support");
-canvas.width = default_size + 2 * safety_pad;
-canvas.height = default_size + 2 * safety_pad;
-middle = Math.round(canvas.width / 2);
-baseline = Math.round(canvas.height - safety_pad);
-ctx = canvas.getContext('2d');
-if (!supports_text(ctx)) throw new Error("Canvas does not support text");
-ctx.font = font;
-ctx.textAlign = "center";
-ctx.translate(middle, baseline);
-// list of widths
-widths = [];
-sizes = [];
-//now measure each letter in the alphabet
-for (i = 0; i < alphabet.get_size_core(); ++i) {
-// reset the canvas
-ctx.clearRect(0, 0, canvas.width, canvas.height);
-ctx.fillStyle = alphabet.get_colour(i);
-// draw the test text
-ctx.fillText(alphabet.get_symbol(i), 0, 0);
-//measure
-size = canvas_bounds(ctx, canvas.width, canvas.height);
-if (size.width === 0) throw new Error("Invisible symbol!");
-widths.push(size.width);
-sizes[i] = size;
-}
-//sort the widths
-widths.sort(function(a,b) {return a - b;});
-//drop 10% of the items off each end
-tenpercent = Math.floor(widths.length / 10);
-for (i = 0; i < tenpercent; ++i) {
-widths.pop();
-widths.shift();
-}
-//calculate average width
-avg_width = 0;
-for (i = 0; i < widths.length; ++i) {
-avg_width += widths[i];
-}
-avg_width /= widths.length;
-// calculate the target width
-target_width = width * this.scale * 2;
-// calculate scales
-for (i = 0; i < alphabet.get_size_core(); ++i) {
-sym = alphabet.get_symbol(i);
-size = sizes[i];
-// calculate scale
-scale = target_width / Math.max(avg_width, size.width);
-// estimate scaled height
-target_height = size.height * scale;
-// create an appropriately sized canvas
-canvas = document.createElement("canvas");
-canvas.width = target_width;
-canvas.height = target_height + safety_pad * 2;
-// calculate the middle
-middle = Math.round(canvas.width / 2);
-// calculate the baseline
-baseline = Math.round(canvas.height - safety_pad);
-// get the context and prepare to draw the rasterized text
-ctx = canvas.getContext('2d');
-ctx.font = font;
-ctx.fillStyle = alphabet.get_colour(i);
-ctx.textAlign = "center";
-ctx.translate(middle, baseline);
-ctx.save();
-ctx.scale(scale, scale);
-// draw the text
-ctx.fillText(sym, 0, 0);
-ctx.restore();
-this.sym_cache[sym] = {"image": canvas, "size": canvas_bounds(ctx, canvas.width, canvas.height)};
-}
-};
-RasterizedAlphabet.prototype.get_alphabet = function() {
-return this.alphabet;
-};
-RasterizedAlphabet.prototype.get_scale = function() {
-return this.scale;
-};
-RasterizedAlphabet.prototype.draw_stack_sym = function(ctx, letter, dx, dy, dWidth, dHeight) {
-"use strict";
-var entry, image, size;
-entry = this.sym_cache[letter];
-image = entry.image;
-size = entry.size;
-ctx.drawImage(image, 0, size.bound_top -1, image.width, size.height+1, dx, dy, dWidth, dHeight);
-};
-RasterizedAlphabet.prototype.draw_stack_num = function(ctx, font, stack_width, index) {
-var image, image_ctx, text_length;
-if (index >= this.stack_num_cache.length) {
-image = document.createElement("canvas");
-// measure the text
-image_ctx = image.getContext('2d');
-image_ctx.save();
-image_ctx.font = font;
-text_length = image_ctx.measureText("" + (index + 1)).width;
-image_ctx.restore();
-// resize the canvas to fit
-image.width = Math.ceil(stack_width);
-image.height = Math.ceil(text_length);
-// draw the text
-image_ctx = image.getContext('2d');
-image_ctx.translate(Math.round(stack_width / 2), 0);
-image_ctx.font = font;
-image_ctx.textBaseline = "middle";
-image_ctx.textAlign = "right";
-image_ctx.rotate(-(Math.PI / 2));
-image_ctx.fillText("" + (index + 1), 0, 0);
-this.stack_num_cache[index] = image;
-} else {
-image = this.stack_num_cache[index];
-}
-ctx.drawImage(image, 0, 0);
-}
-RasterizedAlphabet.prototype.draw_scale_num = function(ctx, font, num) {
-var image, image_ctx, text_size, m_length;
-if (num >= this.scale_num_cache.length) {
-image = document.createElement("canvas");
-// measure the text
-image_ctx = image.getContext('2d');
-image_ctx.font = font;
-text_size = image_ctx.measureText("" + num);
-if (text_size.actualBoundingBoxAscent && text_size.actualBoundingBoxDesent) {
-// resize the canvas to fit
-image.width = Math.ceil(text_size.width);
-image.height = Math.ceil(text_size.actualBoundingBoxAscent + text_size.actualBoundingBoxDesent);
-// draw the text
-image_ctx = image.getContext('2d');
-image_ctx.font = font;
-image_ctx.textAlign = "right";
-image_ctx.fillText("" + num, image.width, text_size.actualBoundingBoxAscent);
-} else {
-// measure width of 'm' to approximate height, we double it later anyway
-m_length = image_ctx.measureText("m").width;
-// resize the canvas to fit
-image.width = Math.ceil(text_size.width);
-image.height = Math.ceil(2 * m_length);
-// draw the text
-image_ctx = image.getContext('2d');
-image_ctx.font = font;
-image_ctx.textAlign = "right";
-image_ctx.textBaseline = "middle";
-image_ctx.fillText("" + num, image.width, m_length);
-}
-this.scale_num_cache[num] = image;
-} else {
-image = this.scale_num_cache[num];
-}
-ctx.drawImage(image, -image.width, -Math.round(image.height / 2))
-}
 //======================================================================
 // end RasterizedAlphabet
 //======================================================================
 //======================================================================
 // start LogoMetrics object
 //======================================================================
-var LogoMetrics = function(ctx, logo_columns, logo_rows, has_names, has_finetext, x_axis, y_axis) {
-"use strict";
-var i, row_height;
-//variable prototypes
-this.pad_top = (has_names ? 5 : 0);
-this.pad_left = (y_axis ? 10 : 0);
-this.pad_right = (has_finetext ? 15 : 0);
-this.pad_bottom = 0;
-this.pad_middle = 20;
-this.name_height = 14;
-this.name_font = "bold " + this.name_height + "px Times, sans-serif";
-this.name_spacer = 0;
-this.y_axis = y_axis;
-this.y_label = "bits";
-this.y_label_height = 12;
-this.y_label_font = "bold " + this.y_label_height + "px Helvetica, sans-serif";
-this.y_label_spacer = 3;
-this.y_num_height = 12;
-this.y_num_width = 0;
-this.y_num_font = "bold " + this.y_num_height + "px Helvetica, sans-serif";
-this.y_tic_width = 5;
-this.stack_pad_left = 0;
-this.stack_font = "bold 25px Helvetica, sans-serif";
-this.stack_height = 90;
-this.stack_width = 26;
-this.stacks_pad_right = 5;
-this.x_axis = x_axis;
-this.x_num_above = 2;
-this.x_num_height = 12;
-this.x_num_width = 0;
-this.x_num_font = "bold " + this.x_num_height + "px Helvetica, sans-serif";
-this.fine_txt_height = 6;
-this.fine_txt_above = 2;
-this.fine_txt_font = "normal " + this.fine_txt_height + "px Helvetica, sans-serif";
-this.letter_metrics = new Array();
-this.summed_width = 0;
-this.summed_height = 0;
-//calculate the width of the y axis numbers
-ctx.font = this.y_num_font;
-for (i = 0; i <= 2; i++) {
-this.y_num_width = Math.max(this.y_num_width, ctx.measureText("" + i).width);
-}
-//calculate the width of the x axis numbers (but they are rotated so it becomes height)
-if (x_axis == 1) {
-ctx.font = this.x_num_font;
-for (i = 1; i <= logo_columns; i++) {
-this.x_num_width = Math.max(this.x_num_width, ctx.measureText("" + i).width);
-}
-} else if (x_axis == 0) {
-this.x_num_height = 4;
-this.x_num_width = 4;
-} else {
-this.x_num_height = 0;
-this.x_num_width = 0;
-}
-//calculate how much vertical space we want to draw this
-//first we add the padding at the top and bottom since that's always there
-this.summed_height += this.pad_top + this.pad_bottom;
-//all except the last row have the same amount of space allocated to them
-if (logo_rows > 1) {
-row_height = this.stack_height + this.pad_middle;
-if (has_names) {
-row_height += this.name_height;
-//the label is allowed to overlap into the spacer
-row_height += Math.max(this.y_num_height/2, this.name_spacer);
-//the label is allowed to overlap the space used by the other label
-row_height += Math.max(this.y_num_height/2, this.x_num_height + this.x_num_above);
-} else {
-row_height += this.y_num_height/2;
-//the label is allowed to overlap the space used by the other label
-row_height += Math.max(this.y_num_height/2, this.x_num_height + this.x_num_above);
-}
-this.summed_height += row_height * (logo_rows - 1);
-}
-//the last row has the name and fine text below it but no padding
-this.summed_height += this.stack_height + (this.y_axis ? this.y_num_height/2 : 0);
-var fine_txt_total = (has_finetext ? this.fine_txt_height + this.fine_txt_above : 0);
-if (has_names) {
-this.summed_height += fine_txt_total + this.name_height;
-this.summed_height += Math.max((this.y_axis ? this.y_num_height/2 : 0),
-this.x_num_height + this.x_num_above + this.name_spacer);
-} else {
-this.summed_height += Math.max((this.y_axis ? this.y_num_height/2 : 0),
-this.x_num_height + this.x_num_above + fine_txt_total);
-}
-//calculate how much horizontal space we want to draw this
-//first add the padding at the left and right since that's always there
-this.summed_width += this.pad_left + this.pad_right;
-if (this.y_axis) {
-//add on the space for the y-axis label
-this.summed_width += this.y_label_height + this.y_label_spacer;
-//add on the space for the y-axis
-this.summed_width += this.y_num_width + this.y_tic_width;
-}
-//add on the space for the stacks
-this.summed_width += (this.stack_pad_left + this.stack_width) * logo_columns;
-//add on the padding after the stacks (an offset from the fine text)
-this.summed_width += this.stacks_pad_right;
-};
-//======================================================================
-// end LogoMetrics object
-//======================================================================
-//found this trick at http://talideon.com/weblog/2005/02/detecting-broken-images-js.cfm
-function image_ok(img) {
-"use strict";
-// During the onload event, IE correctly identifies any images that
-// weren't downloaded as not complete. Others should too. Gecko-based
-// browsers act like NS4 in that they report this incorrectly.
-if (!img.complete) {
-return false;
-}
-// However, they do have two very useful properties: naturalWidth and
-// naturalHeight. These give the true size of the image. If it failed
-// to load, either of these should be zero.
-if (typeof img.naturalWidth !== "undefined" && img.naturalWidth === 0) {
-return false;
-}
-// No other way of checking: assume it's ok.
-return true;
-}
-function supports_text(ctx) {
-"use strict";
-if (!ctx.fillText) {
-return false;
-}
-if (!ctx.measureText) {
-return false;
-}
-return true;
-}
-//draws the scale, returns the width
-function draw_scale(ctx, metrics, alphabet_ic, raster) {
-"use strict";
-var tic_height, i;
-tic_height = metrics.stack_height / alphabet_ic;
-ctx.save();
-ctx.translate(metrics.y_label_height, metrics.y_num_height/2);
-//draw the axis label
-ctx.save();
-ctx.font = metrics.y_label_font;
-ctx.translate(0, metrics.stack_height/2);
-ctx.rotate(-(Math.PI / 2));
-ctx.textAlign = "center";
-ctx.fillText("bits", 0, 0);
-ctx.restore();
-ctx.translate(metrics.y_label_spacer + metrics.y_num_width, 0);
-//draw the axis tics
-ctx.save();
-ctx.translate(0, metrics.stack_height);
-for (i = 0; i <= alphabet_ic; i++) {
-//draw the number
-ctx.save();
-ctx.translate(-1, 0);
-raster.draw_scale_num(ctx, metrics.y_num_font, i);
-ctx.restore();
-//draw the tic
-ctx.fillRect(0, -1, metrics.y_tic_width, 2);
-//prepare for next tic
-ctx.translate(0, -tic_height);
-}
-ctx.restore();
-ctx.fillRect(metrics.y_tic_width - 2, 0, 2, metrics.stack_height)
-ctx.restore();
-}
-function draw_stack_num(ctx, metrics, row_index, raster) {
-"use strict";
-ctx.save();
-ctx.translate(0, Math.round(metrics.stack_height + metrics.x_num_above));
-if (metrics.x_axis == 1) {
-raster.draw_stack_num(ctx, metrics.x_num_font, metrics.stack_width, row_index);
-} else if (metrics.x_axis == 0) {
-// draw dots instead of the numbers (good for small logos)
-ctx.beginPath();
-var radius = Math.round(metrics.x_num_height / 2);
-ctx.arc(Math.round(metrics.stack_width / 2), radius, radius, 0, 2 * Math.PI, false);
-ctx.fill();
-}
-ctx.restore();
-}
-function draw_stack(ctx, metrics, symbols, raster) {
-"use strict";
-var preferred_pad, sym_min, i, sym, sym_height, pad;
-preferred_pad = 0;
-sym_min = 5;
-ctx.save();//1
-ctx.translate(0, metrics.stack_height);
-for (i = 0; i < symbols.length; i++) {
-sym = symbols[i];
-sym_height = metrics.stack_height * sym.get_scale();
-pad = preferred_pad;
-if (sym_height - pad < sym_min) {
-pad = Math.min(pad, Math.max(0, sym_height - sym_min));
-}
-sym_height -= pad;
-//translate to the correct position
-ctx.translate(0, -(pad/2 + sym_height));
-//draw
-raster.draw_stack_sym(ctx, sym.get_symbol(), 0, 0, metrics.stack_width, sym_height);
-//translate past the padding
-ctx.translate(0, -(pad/2));
-}
-ctx.restore();//1
-}
-function draw_dashed_line(ctx, pattern, start, x1, y1, x2, y2) {
-"use strict";
-var x, y, len, i, dx, dy, tlen, theta, mulx, muly, lx, ly;
-dx = x2 - x1;
-dy = y2 - y1;
-tlen = Math.pow(dx*dx + dy*dy, 0.5);
-theta = Math.atan2(dy,dx);
-mulx = Math.cos(theta);
-muly = Math.sin(theta);
-lx = [];
-ly = [];
-for (i = 0; i < pattern; ++i) {
-lx.push(pattern[i] * mulx);
-ly.push(pattern[i] * muly);
-}
-i = start;
-x = x1;
-y = y1;
-len = 0;
-ctx.beginPath();
-while (len + pattern[i] < tlen) {
-ctx.moveTo(x, y);
-x += lx[i];
-y += ly[i];
-ctx.lineTo(x, y);
-len += pattern[i];
-i = (i + 1) % pattern.length;
-x += lx[i];
-y += ly[i];
-len += pattern[i];
-i = (i + 1) % pattern.length;
-}
-if (len < tlen) {
-ctx.moveTo(x, y);
-x += mulx * (tlen - len);
-y += muly * (tlen - len);
-ctx.lineTo(x, y);
-}
-ctx.stroke();
-}
-function draw_trim_background(ctx, metrics, left_start, left_end, left_divider, right_start, right_end, right_divider) {
-"use strict";
-var left_size = left_end - left_start;
-var right_size = right_end - right_start;
-var line_x;
-ctx.save();//s8
-ctx.fillStyle = "rgb(240, 240, 240)";
-if (left_size > 0) {
-ctx.fillRect(left_start * metrics.stack_width, 0, left_size * metrics.stack_width, metrics.stack_height);
-}
-if (right_size > 0) {
-ctx.fillRect(right_start * metrics.stack_width, 0, right_size * metrics.stack_width, metrics.stack_height);
-}
-ctx.fillStyle = "rgb(51, 51, 51)";
-if (left_size > 0 && left_divider) {
-line_x = (left_end * metrics.stack_width) - 0.5;
-draw_dashed_line(ctx, [3], 0, line_x, 0, line_x, metrics.stack_height);
-}
-if (right_size > 0 && right_divider) {
-line_x = (right_start * metrics.stack_width) + 0.5;
-draw_dashed_line(ctx, [3], 0, line_x, 0, line_x, metrics.stack_height);
-}
-ctx.restore();//s8
-}
-function size_logo_on_canvas(logo, canvas, show_names, scale) {
-"use strict";
-var draw_name, draw_finetext, metrics;
-draw_name = (typeof show_names === "boolean" ? show_names : (logo.get_rows() > 1));
-draw_finetext = (logo.fine_text.length > 0);
-if (canvas.width !== 0 && canvas.height !== 0) {
-return;
-}
-metrics = new LogoMetrics(canvas.getContext('2d'),
-logo.get_xlate_columns(), logo.get_rows(), draw_name, draw_finetext, logo.x_axis, logo.y_axis);
-if (typeof scale == "number") {
-//resize the canvas to fit the scaled logo
-canvas.width = metrics.summed_width * scale;
-canvas.height = metrics.summed_height * scale;
-} else {
-if (canvas.width === 0 && canvas.height === 0) {
-canvas.width = metrics.summed_width;
-canvas.height = metrics.summed_height;
-} else if (canvas.width === 0) {
-canvas.width = metrics.summed_width * (canvas.height / metrics.summed_height);
-} else if (canvas.height === 0) {
-canvas.height = metrics.summed_height * (canvas.width / metrics.summed_width);
-}
-}
-}
-function draw_logo_on_canvas(logo, canvas, show_names, scale) {
-"use strict";
-var i, draw_name, draw_finetext, ctx, metrics, raster, pspm_i, pspm,
-offset, col_index, motif_position, ssc;
-ssc = false;
-draw_name = (typeof show_names === "boolean" ? show_names : (logo.get_rows() > 1));
-draw_finetext = (logo.fine_text.length > 0);
-ctx = canvas.getContext('2d');
-//assume that the user wants the canvas scaled equally so calculate what the best width for this image should be
-metrics = new LogoMetrics(ctx, logo.get_xlate_columns(), logo.get_rows(), draw_name, draw_finetext, logo.x_axis, logo.y_axis);
-if (typeof scale == "number") {
-//resize the canvas to fit the scaled logo
-canvas.width = metrics.summed_width * scale;
-canvas.height = metrics.summed_height * scale;
-} else {
-if (canvas.width === 0 && canvas.height === 0) {
-scale = 1;
-canvas.width = metrics.summed_width;
-canvas.height = metrics.summed_height;
-} else if (canvas.width === 0) {
-scale = canvas.height / metrics.summed_height;
-canvas.width = metrics.summed_width * scale;
-} else if (canvas.height === 0) {
-scale = canvas.width / metrics.summed_width;
-canvas.height = metrics.summed_height * scale;
-} else {
-scale = Math.min(canvas.width / metrics.summed_width, canvas.height / metrics.summed_height);
-}
-}
-// cache the raster based on the assumption that we will be drawing a lot
-// of logos the same size and alphabet
-if (typeof draw_logo_on_canvas.raster_cache === "undefined") {
-draw_logo_on_canvas.raster_cache = [];
-}
-for (i = 0; i < draw_logo_on_canvas.raster_cache.length; i++) {
-raster = draw_logo_on_canvas.raster_cache[i];
-if (raster.get_alphabet().equals(logo.alphabet) &&
-Math.abs(raster.get_scale() - scale) < 0.1) break;
-raster = null;
-}
-if (raster == null) {
-raster = new RasterizedAlphabet(logo.alphabet, scale, metrics.stack_font, metrics.stack_width);
-draw_logo_on_canvas.raster_cache.push(raster);
-}
-ctx = canvas.getContext('2d');
-ctx.save();//s1
-ctx.scale(scale, scale);
-ctx.save();//s2
-ctx.save();//s7
-//create margin
-ctx.translate(Math.round(metrics.pad_left), Math.round(metrics.pad_top));
-for (pspm_i = 0; pspm_i < logo.get_rows(); ++pspm_i) {
-pspm = logo.get_pspm(pspm_i);
-offset = logo.get_offset(pspm_i);
-//optionally draw name if this isn't the last row or is the only row
-if (draw_name && (logo.get_rows() == 1 || pspm_i != (logo.get_rows()-1))) {
-ctx.save();//s4
-ctx.translate(Math.round(metrics.summed_width/2), Math.round(metrics.name_height));
-ctx.font = metrics.name_font;
-ctx.textAlign = "center";
-ctx.fillText(pspm.name, 0, 0);
-ctx.restore();//s4
-ctx.translate(0, Math.round(metrics.name_height +
-Math.min(0, metrics.name_spacer - metrics.y_num_height/2)));
-}
-//draw scale
-if (logo.y_axis) draw_scale(ctx, metrics, logo.alphabet.get_ic(), raster);
-ctx.save();//s5
-//translate across past the scale
-if (logo.y_axis) {
-ctx.translate(Math.round(metrics.y_label_height + metrics.y_label_spacer +
-metrics.y_num_width + metrics.y_tic_width), Math.round(metrics.y_num_height / 2));
-}
-//draw the trimming background
-if (pspm.get_left_trim() > 0 || pspm.get_right_trim() > 0) {
-var left_start = offset * logo.get_xlate_nsyms();
-var left_end = (offset + pspm.get_left_trim()) * logo.get_xlate_nsyms();
-var left_divider = true;
-if (left_end < logo.get_xlate_start() || left_start > logo.get_xlate_end()) {
-// no overlap
-left_start = 0;
-left_end = 0;
-left_divider = false;
-} else {
-if (left_start < logo.get_xlate_start()) {
-left_start = logo.get_xlate_start();
-}
-if (left_end > logo.get_xlate_end()) {
-left_end = logo.get_xlate_end();
-left_divider = false;
-}
-left_start -= logo.get_xlate_start();
-left_end -= logo.get_xlate_start();
-if (left_end < left_start) {
-left_start = 0;
-left_end = 0;
-left_divider = false;
-}
-}
-var right_end = (offset + pspm.get_motif_length()) * logo.get_xlate_nsyms();
-//var right_start = right_end - (pspm.get_left_trim() * logo.get_xlate_nsyms());
-var right_start = right_end - (pspm.get_right_trim() * logo.get_xlate_nsyms());
-var right_divider = true;
-if (right_end < logo.get_xlate_start() || right_start > logo.get_xlate_end()) {
-// no overlap
-right_start = 0;
-right_end = 0;
-right_divider = false;
-} else {
-if (right_start < logo.get_xlate_start()) {
-right_start = logo.get_xlate_start();
-right_divider = false;
-}
-if (right_end > logo.get_xlate_end()) {
-right_end = logo.get_xlate_end();
-}
-right_start -= logo.get_xlate_start();
-right_end -= logo.get_xlate_start();
-if (right_end < right_start) {
-right_start = 0;
-right_end = 0;
-right_divider = false;
-}
-}
-draw_trim_background(ctx, metrics, left_start, left_end, left_divider, right_start, right_end, right_divider);
-}
-//draw letters
-var xlate_col;
-for (xlate_col = logo.get_xlate_start(); xlate_col < logo.get_xlate_end(); xlate_col++) {
-ctx.translate(metrics.stack_pad_left,0);
-col_index = Math.floor(xlate_col / logo.get_xlate_nsyms());
-if (xlate_col % logo.get_xlate_nsyms() == 0) {
-if (col_index >= offset && col_index < (offset + pspm.get_motif_length())) {
-motif_position = col_index - offset;
-draw_stack_num(ctx, metrics, motif_position, raster);
-draw_stack(ctx, metrics, pspm.get_stack(motif_position, logo.alphabet, ssc), raster);
-}
-} else {
-if (col_index >= offset && col_index < (offset + pspm.get_motif_length())) {
-ctx.save();// s5.1
-ctx.translate(0, Math.round(metrics.stack_height));
-// TODO draw a dot or dash or something to indicate continuity of the motif
-ctx.restore(); //s5.1
-}
-}
-ctx.translate(Math.round(metrics.stack_width), 0);
-}
-ctx.restore();//s5
-////optionally draw name if this is the last row but isn't the only row
-if (draw_name && (logo.get_rows() != 1 && pspm_i == (logo.get_rows()-1))) {
-//translate vertically past the stack and axis's
-ctx.translate(0, metrics.y_num_height/2 + metrics.stack_height +
-Math.max(metrics.y_num_height/2, metrics.x_num_above + metrics.x_num_width + metrics.name_spacer));
-ctx.save();//s6
-ctx.translate(metrics.summed_width/2, metrics.name_height);
-ctx.font = metrics.name_font;
-ctx.textAlign = "center";
-ctx.fillText(pspm.name, 0, 0);
-ctx.restore();//s6
-ctx.translate(0, metrics.name_height);
-} else {
-//translate vertically past the stack and axis's
-ctx.translate(0, metrics.y_num_height/2 + metrics.stack_height +
-Math.max(metrics.y_num_height/2, metrics.x_num_above + metrics.x_num_width));
-}
-//if not the last row then add middle padding
-if (pspm_i != (logo.get_rows() -1)) {
-ctx.translate(0, metrics.pad_middle);
-}
-}
-ctx.restore();//s7
-if (logo.fine_text.length > 0) {
-ctx.translate(metrics.summed_width - metrics.pad_right, metrics.summed_height - metrics.pad_bottom);
-ctx.font = metrics.fine_txt_font;
-ctx.textAlign = "right";
-ctx.fillText(logo.fine_text, 0,0);
-}
-ctx.restore();//s2
-ctx.restore();//s1
-}
-function create_canvas(c_width, c_height, c_id, c_title, c_display) {
-"use strict";
-var canvas = document.createElement("canvas");
-//check for canvas support before attempting anything
-if (!canvas.getContext) {
-return null;
-}
-var ctx = canvas.getContext('2d');
-//check for html5 text drawing support
-if (!supports_text(ctx)) {
-return null;
-}
-//size the canvas
-canvas.width = c_width;
-canvas.height = c_height;
-canvas.id = c_id;
-canvas.title = c_title;
-canvas.style.display = c_display;
-return canvas;
-}
-function logo_1(alphabet, fine_text, pspm) {
-"use strict";
-var logo = new Logo(alphabet, fine_text);
-logo.add_pspm(pspm);
-return logo;
-}
-function logo_2(alphabet, fine_text, target, query, query_offset) {
-"use strict";
-var logo = new Logo(alphabet, fine_text);
-if (query_offset < 0) {
-logo.add_pspm(target, -query_offset);
-logo.add_pspm(query);
-} else {
-logo.add_pspm(target);
-logo.add_pspm(query, query_offset);
-}
-return logo;
-}
-/*
-* Specifies an alternate source for an image.
-* If the image with the image_id specified has
-* not loaded then a generated logo will be used
-* to replace it.
-*
-* Note that the image must either have dimensions
-* or a scale must be set.
-*/
-function alternate_logo(logo, image_id, scale) {
-"use strict";
-var image = document.getElementById(image_id);
-if (!image) {
-alert("Can't find specified image id (" +  image_id + ")");
-return;
-}
-//if the image has loaded then there is no reason to use the canvas
-if (image_ok(image)) {
-return;
-}
-//the image has failed to load so replace it with a canvas if we can.
-var canvas = create_canvas(image.width, image.height, image_id, image.title, image.style.display);
-if (canvas === null) {
-return;
-}
-//draw the logo on the canvas
-draw_logo_on_canvas(logo, canvas, null, scale);
-//replace the image with the canvas
-image.parentNode.replaceChild(canvas, image);
-}
-/*
-* Specifes that the element with the specified id
-* should be replaced with a generated logo.
-*/
-function replace_logo(logo, replace_id, scale, title_txt, display_style) {
-"use strict";
-var element = document.getElementById(replace_id);
-if (!replace_id) {
-alert("Can't find specified id (" + replace_id + ")");
-return;
-}
-//found the element!
-var canvas = create_canvas(50, 120, replace_id, title_txt, display_style);
-if (canvas === null) {
-return;
-}
-//draw the logo on the canvas
-draw_logo_on_canvas(logo, canvas, null, scale);
-//replace the element with the canvas
-element.parentNode.replaceChild(canvas, element);
-}
-/*
-* Fast string trimming implementation found at
-* http://blog.stevenlevithan.com/archives/faster-trim-javascript
-*
-* Note that regex is good at removing leading space but
-* bad at removing trailing space as it has to first go through
-* the whole string.
-*/
-function trim (str) {
-"use strict";
-var ws, i;
-str = str.replace(/^\s\s*/, '');
-ws = /\s/; i = str.length;
-while (ws.test(str.charAt(--i)));
-return str.slice(0, i + 1);
-}
-</script>
-<script>
-var current_motif = 0;
-var dreme_alphabet = new Alphabet(data.alphabet, data.control_db.freqs);
-/*
-* Create a pspm for the given motif data
-*/
-function motif_pspm(m) {
-return new Pspm(m.pwm, m.id, 0, 0, m.nsites, m.evalue);
-}
-/*
-* Create a count matrix from the given motif data
-*/
-function motif_count_matrix(motif) {
-return motif_pspm(motif).as_count_matrix();
-}
-/*
-* Create a probablity matrix from the given motif data
-*/
-function motif_prob_matrix(motif) {
-return motif_pspm(motif).as_probability_matrix();
-}
-/*
-* Create a minimal meme format motif from the given motif data
-*/
-function motif_minimal_meme(motif) {
-return motif_pspm(motif).as_meme({
-"with_header": true,
-"with_pspm": true,
-"with_pssm": false,
-"version": data["version"],
-"alphabet": dreme_alphabet,
-"strands": (data.options.revcomp ? 2 : 1)
-});
-}
-/*
-* Fill in a template variable
-*/
-function set_tvar(template, tvar, value) {
-var node;
-node = find_child(template, tvar);
-if (node === null) {
-throw new Error("Template does not contain variable " + tvar);
-}
-node.innerHTML = "";
-if (typeof value !== "object") {
-node.appendChild(document.createTextNode(value));
-} else {
-node.appendChild(value);
-}
-}
-/*
-* Make a canvas with the motif logo drawn on it.
-*/
-function make_logo(motif, height, rc) {
-var pspm = new Pspm(motif["pwm"]);
-if (rc) pspm = pspm.copy().reverse_complement(dreme_alphabet);
-var logo = new Logo(dreme_alphabet);
-logo.add_pspm(pspm, 0);
-var canvas = document.createElement('canvas');
-canvas.height = height;
-canvas.width = 0;
-draw_logo_on_canvas(logo, canvas, false);
-return canvas;
-}
-/*
-* Create a button designed to contain a single symbol
-*/
-function make_sym_btn(symbol, title, action) {
-var box, sbox;
-box = document.createElement("div");
-box.tabIndex = 0;
-box.className = "sym_btn";
-sbox = document.createElement("span");
-if (typeof symbol == "string") {
-sbox.appendChild(document.createTextNode(symbol));
-} else {
-sbox.appendChild(symbol);
-}
-box.appendChild(sbox);
-box.title = title;
-box.addEventListener('click', action, false);
-box.addEventListener('keydown', action, false);
-return box;
-}
-/*
-* Create a pair of text spans with different classes.
-* This is useful when using CSS to only display one of them.
-*/
-function text_pair(txt1, cls1, txt2, cls2) {
-var container, part1, part2;
-container = document.createElement("span");
-part1 = document.createElement("span");
-part1.appendChild(document.createTextNode(txt1));
-part1.className = cls1;
-container.appendChild(part1);
-part2 = document.createElement("span");
-part2.appendChild(document.createTextNode(txt2));
-part2.className = cls2;
-container.appendChild(part2);
-return container;
-}
-/*
-* Make a colourised sequence.
-*/
-function make_seq(seq) {
-var i, j, letter, lbox, sbox;
-sbox = document.createElement("span");
-for (i = 0; i < seq.length; i = j) {
-letter = seq.charAt(i);
-for (j = i+1; j < seq.length; j++) {
-if (seq.charAt(j) !== letter) {
-break;
-}
-}
-lbox = document.createElement("span");
-lbox.style.color = dreme_alphabet.get_colour(dreme_alphabet.get_index(letter));
-lbox.appendChild(document.createTextNode(seq.substring(i, j)));
-sbox.appendChild(lbox);
-}
-return sbox;
-}
-/*
-* Create a description element taking into account the newlines in the source text.
-*/
-function make_description(text) {
-var i, j, lines, p;
-var container = document.createElement("div");
-var paragraphs = text.split(/\n\n+/);
-for (i = 0; i < paragraphs.length; i++) {
-lines = paragraphs[i].split(/\n/);
-p = document.createElement("p");
-p.appendChild(document.createTextNode(lines[0]));
-for (j = 1; j < lines.length; j++) {
-p.appendChild(document.createElement("br"));
-p.appendChild(document.createTextNode(lines[j]));
-}
-container.appendChild(p);
-}
-return container;
-}
-/*
-* Make the table header for the discovered motifs.
-*/
-function make_motif_header() {
-var row = document.createElement("tr");
-add_text_header_cell(row, "", "", "motif_ordinal");
-add_text_header_cell(row, "Motif", "pop_motifs_word", "motif_word");
-add_text_header_cell(row, "Logo", "pop_motifs_logo", "motif_logo");
-if (data.options.revcomp) {
-add_text_header_cell(row, "RC Logo", "pop_motifs_rc_logo", "motif_logo");
-}
-add_text_header_cell(row, "E-value", "pop_motifs_evalue", "motif_evalue");
-add_text_header_cell(row, "Unerased E-value", "pop_motifs_uevalue", "motif_evalue");
-add_text_header_cell(row, "More", "pop_more", "motif_more");
-add_text_header_cell(row, "Submit/Download", "pop_submit_dl", "motif_submit");
-row.className = "more";
-return row;
-}
-/*
-* Make a compact motif summary row for the discovered motifs.
-*/
-function make_motif_row(tbody, ordinal, motif) {
-var row = document.createElement("tr");
-add_text_cell(row, "" + ordinal + ".", "motif_ordinal");
-add_text_cell(row, motif["id"], "motif_word");
-add_cell(row, make_logo(motif, 50, false), "motif_logo");
-if (data.options.revcomp) {
-add_cell(row, make_logo(motif, 50, true), "motif_logo");
-}
-add_text_cell(row, motif["evalue"], "motif_evalue");
-add_text_cell(row, motif["unerased_evalue"], "motif_evalue");
-add_cell(row, make_sym_btn(text_pair("\u21A7", "less", "\u21A5", "more"), "Show more information.", function(e) { toggle_class(tbody, "collapsed"); }, "\u21A5", ""), "motif_more");
-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");
-return row;
-}
-/*
-* Make a sortable table of enriched matching rows.
-*/
-function make_motif_words(motif) {
-var row, i, match;
-var table = document.createElement("table");
-var thead = document.createElement("thead");
-row = document.createElement("tr");
-add_text_header_cell(row, "Word", "pop_match_word", "match_word", function(e) {sort_table(this, compare_words);});
-add_text_header_cell(row, "Positives", "pop_match_pos", "match_count", function(e) {sort_table(this, compare_counts);});
-add_text_header_cell(row, "Negatives", "pop_match_neg", "match_count", function(e) {sort_table(this, compare_counts);});
-add_text_header_cell(row, "P-value", "pop_match_pval", "match_evalue", function(e) {sort_table(this, compare_evalues);});
-add_text_header_cell(row, "E-value", "pop_match_eval", "match_evalue", function(e) {sort_table(this, compare_evalues);});
-thead.appendChild(row);
-table.appendChild(thead);
-var tbody = document.createElement("tbody");
-for (i = 0; i < motif.matches.length; i++) {
-match = motif.matches[i];
-row = document.createElement("tr");
-add_cell(row, make_seq(match.seq), "match_word");
-add_text_cell(row, match.p + " / " + data.sequence_db.count, "match_count");
-add_text_cell(row, match.n + " / " + data.control_db.count, "match_count");
-add_text_cell(row, match.pvalue, "match_evalue");
-add_text_cell(row, match.evalue, "match_evalue");
-tbody.appendChild(row);
-}
-table.appendChild(tbody);
-return table;
-}
-/*
-* Make an expanded view of a discovered motif.
-*/
-function make_motif_exp(tbody, ordinal, motif) {
-"use strict";
-var box, pspm, logo_box;
-box = $("tmpl_motif_expanded").cloneNode(true);
-toggle_class(box, "template", false);
-box.id = "";
-find_child(box, "tvar_logo").appendChild(make_logo(motif, 150, false));
-if (data.options.revcomp) {
-find_child(box, "tvar_rclogo").appendChild(make_logo(motif, 150, true));
-}
-set_tvar(box, "tvar_p", motif["p"]);
-set_tvar(box, "tvar_p_total", data.sequence_db.count);
-set_tvar(box, "tvar_n", motif["n"]);
-set_tvar(box, "tvar_n_total", data.control_db.count);
-set_tvar(box, "tvar_pvalue", motif["pvalue"]);
-set_tvar(box, "tvar_evalue", motif["evalue"]);
-set_tvar(box, "tvar_uevalue", motif["unerased_evalue"]);
-set_tvar(box, "tvar_words", make_motif_words(motif));
-var cell = document.createElement("td");
-cell.colSpan = 8;
-cell.appendChild(box);
-var row = document.createElement("tr");
-row.className = "more";
-row.appendChild(cell);
-return row;
-}
-/*
-* Convert a string containing a scientific number into the log of that number
-* without having an intermediate representation of the number.
-* This is intended to avoid underflow problems with the tiny evalues that
-* MEME and DREME can create.
-*/
-function sci2log(scinum) {
-"use strict";
-var ev_re, match, sig, exp;
-ev_re = /^(.*)e(.*)$/;
-if (match = ev_re.exec(scinum)) {
-sig = parseFloat(match[1]);
-exp = parseInt(match[2]);
-return Math.log(sig) + (exp * Math.log(10));
-}
-return 0;
-}
-/*
-* Create a table of discovered motifs. A fresh table body is used for each
-* motif to make hiding/showing rows with css easier.
-*/
-function make_motifs() {
-"use strict";
-var i, row, tbody, motif, ordinal;
-// make the motifs table
-var container = $("motifs");
-container.innerHTML = ""; // clear content
-var table = document.createElement("table");
-// add a header that is always shown
-var thead = document.createElement("thead");
-thead.appendChild(make_motif_header());
-table.appendChild(thead);
-for (i = 0; i < data.motifs.length; i++) {
-ordinal = i + 1;
-motif = data.motifs[i];
-tbody = document.createElement("tbody");
-tbody.className = "collapsed";
-tbody.appendChild(make_motif_row(tbody, ordinal, motif));
-tbody.appendChild(make_motif_exp(tbody, ordinal, motif));
-// create a following header for every row except the last one
-if ((i + 1) < data.motifs.length) tbody.appendChild(make_motif_header());
-table.appendChild(tbody);
-}
-container.appendChild(table);
-}
-/*
-* Create a table showing all the alphabet symbols, their names and frequencies.
-*/
-function make_alpha_bg(alph, freqs) {
-function colour_symbol(index) {
-var span = document.createElement("span");
-span.appendChild(document.createTextNode(alph.get_symbol(index)));
-span.style.color = alph.get_colour(index);
-span.className = "alpha_symbol";
-return span;
-}
-var table, thead, tbody, row, th, span, i;
-// create table
-table = document.createElement("table");
-table.className = "inputs";
-// create header
-thead = document.createElement("thead");
-table.appendChild(thead);
-row = thead.insertRow(thead.rows.length);
-if (alph.has_complement()) {
-add_text_header_cell(row, "Name", "pop_alph_name");
-add_text_header_cell(row, "Bg.", "pop_alph_control");
-add_text_header_cell(row, "");
-add_text_header_cell(row, "");
-add_text_header_cell(row, "");
-add_text_header_cell(row, "Bg.", "pop_alph_control");
-add_text_header_cell(row, "Name", "pop_alph_name");
-} else {
-add_text_header_cell(row, "");
-add_text_header_cell(row, "Name", "pop_alph_name");
-add_text_header_cell(row, "Bg.", "pop_alph_control");
-}
-// add alphabet entries
-tbody = document.createElement("tbody");
-table.appendChild(tbody);
-if (alph.has_complement()) {
-for (i = 0; i < alph.get_size_core(); i++) {
-var c = alph.get_complement(i);
-if (i > c) continue;
-row = tbody.insertRow(tbody.rows.length);
-add_text_cell(row, alph.get_name(i));
-add_text_cell(row, "" + freqs[i].toFixed(3));
-add_cell(row, colour_symbol(i));
-add_text_cell(row, "~");
-add_cell(row, colour_symbol(c));
-add_text_cell(row, "" + freqs[c].toFixed(3));
-add_text_cell(row, alph.get_name(c));
-}
-} else {
-for (i = 0; i < alph.get_size_core(); i++) {
-row = tbody.insertRow(tbody.rows.length);
-add_cell(row, colour_symbol(i));
-add_text_cell(row, alph.get_name(i));
-add_text_cell(row, "" + freqs[i].toFixed(3));
-}
-}
-return table;
-}
-/*
-* Updates the format download text in the popup.
-* This is called when either the format or current motif changes.
-*/
-function update_outpop_format(index) {
-var motif = data.motifs[index];
-var fn = [motif_count_matrix, motif_prob_matrix, motif_minimal_meme];
-var suffix = ["_counts.txt", "_freqs.txt", ".meme"];
-var format = parseInt($("text_format").value);
-var text = fn[format](motif);
-prepare_download(text, "text/plain", motif.id + suffix[format], $("outpop_text_dl"));
-$("outpop_text").value = text;
-}
-/*
-* Updates the motif logos and format download text in the popup.
-* This is called whenever the current motif changes.
-*/
-function update_outpop_motif(index) {
-"use strict";
-var motifs, motif, pspm, logo, canvas, num;
-motifs = data["motifs"];
-if (index < 0 || index >= motifs.length) {return;}
-current_motif = index;
-motif = motifs[index];
-pspm = new Pspm(motif["pwm"]);
-logo = new Logo(dreme_alphabet, "");
-logo.add_pspm(pspm, 0);
-canvas = $("outpop_logo");
-canvas.width = canvas.width; // clear canvas
-draw_logo_on_canvas(logo, canvas, false);
-canvas = $("outpop_logo_rc");
-canvas.width = canvas.width; // clear rc canvas
-if (data.options.revcomp) {
-pspm.reverse_complement(dreme_alphabet);
-logo = new Logo(dreme_alphabet, "");
-logo.add_pspm(pspm, 0);
-draw_logo_on_canvas(logo, canvas, false);
-}
-num = $("outpop_num");
-num.innerHTML = "";
-num.appendChild(document.createTextNode("" + (index + 1)));
-update_outpop_format(index);
-}
-/*
 * Initialise and display the download popup.
-*/
-function action_show_outpop(e, ordinal) {
-"use strict";
-function init() {
-"use strict";
-var close_btn, next_btn, prev_btn, cancel_btn, do_btn;
-var tab1, tab2, tab3;
-var pnl1, pnl2, pnl3;
-var format_list;
-var tbl_submit, inputs, i, default_prog;
-close_btn = $("outpop_close");
-close_btn.addEventListener("click", action_hide_outpop, false);
-close_btn.addEventListener("keydown", action_hide_outpop, false);
-next_btn = $("outpop_next");
-next_btn.addEventListener("click", action_outpop_next, false);
-next_btn.addEventListener("keydown", action_outpop_next, false);
-prev_btn = $("outpop_prev");
-prev_btn.addEventListener("click", action_outpop_prev, false);
-prev_btn.addEventListener("keydown", action_outpop_prev, false);
-cancel_btn = $("outpop_cancel");
-cancel_btn.addEventListener("click", action_hide_outpop, false);
-do_btn = $("outpop_do");
-do_btn.addEventListener("click", action_outpop_submit, false);
-tab1 = $("outpop_tab_1");
-tab1.tabIndex = 0;
-tab1.addEventListener("click", action_outpop_tab, false);
-tab1.addEventListener("keydown", action_outpop_tab, false);
-tab2 = $("outpop_tab_2");
-tab2.tabIndex = 0;
-tab2.addEventListener("click", action_outpop_tab, false);
-tab2.addEventListener("keydown", action_outpop_tab, false);
-tab3 = $("outpop_tab_3");
-tab3.tabIndex = 0;
-tab3.addEventListener("click", action_outpop_tab, false);
-tab3.addEventListener("keydown", action_outpop_tab, false);
-pnl1 = $("outpop_pnl_1");
-pnl2 = $("outpop_pnl_2");
-pnl3 = $("outpop_pnl_3");
-toggle_class(tab1, "activeTab", true);
-toggle_class(tab2, "activeTab", false);
-toggle_class(tab3, "activeTab", false);
-pnl1.style.display = "block";
-pnl2.style.display = "none";
-pnl3.style.display = "none";
-format_list = $("text_format");
-format_list.addEventListener("change", action_outpop_format, false);
-// setup program selection
-tbl_submit = $("programs");
-// when not dna, hide the inputs for programs that require dna motifs
-toggle_class(tbl_submit, "alphabet_dna", dreme_alphabet.has_complement());//TODO FIXME alphabet_dna is a bad name for a field when allowing custom alphabets
-// add a click listener for the radio buttons
-inputs = tbl_submit.querySelectorAll("input[type='radio']");
-for (i = 0; i < inputs.length; i++) {
-inputs[i].addEventListener("click", action_outpop_program, false);
-}
-// ensure that a default program option is selected for DNA and Protein
-default_prog = document.getElementById(dreme_alphabet.has_complement() ? "submit_tomtom" : "submit_fimo");
-default_prog.checked = true;
-action_outpop_program.call(default_prog);
-// disable reverse-complement when not DNA
-$("logo_rc_option").disabled = !dreme_alphabet.has_complement();
-// set errorbars on when ssc is on
-$("logo_ssc").addEventListener("change", action_outpop_ssc, false);
-}
-// store the focused element
-action_hide_outpop.last_active = document.activeElement;
-if (!e) e = window.event;
-if (e.type === "keydown") {
-if (e.keyCode !== 13 && e.keyCode !== 32) {
-return;
-}
-// stop a submit or something like that
-e.preventDefault();
-}
-// hide the help popup
-help_popup();
-// on first load initilize the popup
-if (!action_show_outpop.ready) {
-init();
-action_show_outpop.ready = true;
-}
-update_outpop_motif(ordinal - 1);
-// display the download popup
-$("grey_out_page").style.display = "block";
-$("download").style.display = "block";
-$("outpop_close").focus();
-}
-/*
-* Hide the download popup.
-*/
-function action_hide_outpop(e) {
-if (!e) e = window.event;
-if (e.type === "keydown") {
-if (e.keyCode !== 13 && e.keyCode !== 32) {
-return;
-}
-// stop a submit or something like that
-e.preventDefault();
-}
-$("download").style.display = "none";
-$("grey_out_page").style.display = "none";
-if (typeof action_hide_outpop.last_active !== "undefined") {
-action_hide_outpop.last_active.focus();
-}
-}
-/*
-* Show the next motif in the download popup.
-*/
-function action_outpop_next(e) {
-if (!e) e = window.event;
-if (e.type === "keydown") {
-if (e.keyCode !== 13 && e.keyCode !== 32) {
-return;
-}
-// stop a submit or something like that
-e.preventDefault();
-}
-update_outpop_motif(current_motif + 1);
-}
-/*
-* Show the previous motif in the download popup.
-*/
-function action_outpop_prev(e) {
-if (!e) e = window.event;
-if (e.type === "keydown") {
-if (e.keyCode !== 13 && e.keyCode !== 32) {
-return;
-}
-// stop a submit or something like that
-e.preventDefault();
-}
-update_outpop_motif(current_motif - 1);
-}
-/*
-* Highlight the selected row in the program list.
-*/
-function action_outpop_program() {
-"use strict";
-var table, tr, rows, i;
-tr = find_parent_tag(this, "TR");
-table = find_parent_tag(tr, "TABLE");
-rows = table.querySelectorAll("tr");
-for (i = 0; i < rows.length; i++) {
-toggle_class(rows[i], "selected", rows[i] === tr);
-}
-}
-/*
-* Enable error bars when small sample correction is enabled.
-*/
-function action_outpop_ssc() {
-"use strict";
-$("logo_err").value = $("logo_ssc").value;
-}
-/*
-* Submit the motif to the selected program.
-*/
-function action_outpop_submit(e) {
-"use strict";
-var form, input, program, motifs;
-// find out which program is selected
-var radios, i;
-radios = document.getElementsByName("program");
-program = "fimo"; // default to fimo, since it works with all alphabet types
-for (i = 0; i < radios.length; i++) {
-if (radios[i].checked) program = radios[i].value;
-}
-motifs = motif_minimal_meme(data.motifs[current_motif]);
-form = document.createElement("form");
-form.setAttribute("method", "post");
-form.setAttribute("action", site_url + "/tools/" + program);
-input = document.createElement("input");
-input.setAttribute("type", "hidden");
-input.setAttribute("name", "motifs_embed");
-input.setAttribute("value", motifs);
-form.appendChild(input);
-document.body.appendChild(form);
-form.submit();
-document.body.removeChild(form);
-}
-/*
-* Download the format text.
-* Wire the link containing the data URI text to a download button so it looks
-* the same as the server submit stuff.
-*/
-function action_outpop_download_motif(e) {
-$("outpop_text_dl").click();
-}
-/*
-* Download the motif logo.
-* The EPS format can be calculated locally in Javascript
-*/
-function action_outpop_download_logo(e) {
-"use strict";
-var pspm, logo, eps;
-var logo_rc, logo_ssc, logo_width, logo_height;
-var motif = data.motifs[current_motif];
-if ($("logo_format").value == "0") { // EPS
-logo_rc = ($("logo_rc").value == "1");
-logo_ssc = ($("logo_ssc").value == "1");
-logo_width = parseFloat($("logo_width").value);
-if (isNaN(logo_width) || !isFinite(logo_width) || logo_width <= 0) logo_width = null;
-logo_height = parseFloat($("logo_height").value);
-if (isNaN(logo_height) || !isFinite(logo_height) || logo_height <= 0) logo_height = null;
-// create a PSPM from the motif
-pspm = motif_pspm(motif);
-if (logo_rc) pspm.reverse_complement(dreme_alphabet);
-logo = new Logo(dreme_alphabet);
-logo.add_pspm(pspm, 0);
-eps = logo.as_eps({"ssc": logo_ssc, "logo_width": logo_width, "logo_height": logo_height});
-prepare_download(eps, "application/postscript", motif.id + ".eps");
-} else {
-$("logo_motifs").value = motif_minimal_meme(motif);
-$("logo_form").submit();
-}
-}
-/*
-* Change the selected tab in the download popup.
-*/
-function action_outpop_tab(e) {
-"use strict";
-var tab1, tab2, tab3, pnl1, pnl2, pnl3, do_btn;
-if (!e) e = window.event;
-if (e.type === "keydown") {
-if (e.keyCode !== 13 && e.keyCode !== 32) {
-return;
-}
-// stop a submit or something like that
-e.preventDefault();
-}
-tab1 = $("outpop_tab_1");
-tab2 = $("outpop_tab_2");
-tab3 = $("outpop_tab_3");
-pnl1 = $("outpop_pnl_1");
-pnl2 = $("outpop_pnl_2");
-pnl3 = $("outpop_pnl_3");
-do_btn = $("outpop_do");
-toggle_class(tab1, "activeTab", (this === tab1));
-toggle_class(tab2, "activeTab", (this === tab2));
-toggle_class(tab3, "activeTab", (this === tab3));
-pnl1.style.display = ((this === tab1) ? "block" : "none");
-pnl2.style.display = ((this === tab2) ? "block" : "none");
-pnl3.style.display = ((this === tab3) ? "block" : "none");
-do_btn.value = ((this === tab1) ? "Submit" : "Download");
-do_btn.removeEventListener("click", action_outpop_submit, false);
-do_btn.removeEventListener("click", action_outpop_download_logo, false);
-do_btn.removeEventListener("click", action_outpop_download_motif, false);
-if (this === tab1) {
-do_btn.addEventListener("click", action_outpop_submit, false);
-} else if (this === tab2) {
-do_btn.addEventListener("click", action_outpop_download_motif, false);
-} else {
-do_btn.addEventListener("click", action_outpop_download_logo, false);
-}
-}
-/*
-* Update the text in the download format popup.
-*/
-function action_outpop_format() {
-update_outpop_format(current_motif);
-}
-/*
-* Find all text nodes in the given container.
-*/
-function text_nodes(container) {
-var textNodes = [];
-var stack = [container];
-// depth first search to maintain ordering when flattened
-while (stack.length > 0) {
-var node = stack.pop();
-if (node.nodeType == Node.TEXT_NODE) {
-textNodes.push(node);
-} else {
-for (var i = node.childNodes.length-1; i >= 0; i--) {
-stack.push(node.childNodes[i]);
-}
-}
-}
-return textNodes;
-}
-/*
-* Get the text out of a specific text node.
-*/
-function node_text(node) {
-if (node === undefined) {
-return '';
-} else if (node.textContent) {
-return node.textContent;
-} else if (node.innerText) {
-return node.innerText;
-} else {
-return '';
-}
-}
-/*
-* Get the text contained within the element.
-*/
-function elem_text(elem, separator) {
-if (separator === undefined) separator = '';
-return text_nodes(elem).map(node_text).join(separator);
-}
-/*
-* Sort all rows in the first table body based on the column of the given element and the comparison function.
-* The sort is not very fast and is intended for small tables only.
-*/
-function sort_table(colEle, compare_function) {
-//find the parent of colEle that is either a td or th
-var i, j;
-var cell = colEle;
-while (true) {
-if (cell == null) return;
-if (cell.nodeType == Node.ELEMENT_NODE &&
-(cell.tagName.toLowerCase() == "td" || cell.tagName.toLowerCase() == "th")) {
-break;
-}
-cell = cell.parentNode;
-}
-//find the parent of cell that is a tr
-var row = cell;
-while (true) {
-if (row == null) return;
-if (row.nodeType == Node.ELEMENT_NODE && row.tagName.toLowerCase() == "tr") {
-break;
-}
-row = row.parentNode;
-}
-//find the parent of row that is a table
-var table = row;
-while (true) {
-if (table == null) return;
-if (table.nodeType == Node.ELEMENT_NODE && table.tagName.toLowerCase() == "table") {
-break;
-}
-table = table.parentNode;
-}
-var column_index = cell.cellIndex;
-// do a bubble sort, because the tables are so small it doesn't matter
-var change;
-var trs = table.tBodies[0].getElementsByTagName('tr');
-var already_sorted = true;
-var reverse = false;
-while (true) {
-do {
-change = false;
-for (i = 0; i < trs.length -1; i++) {
-var v1 = elem_text(trs[i].cells[column_index]);
-var v2 = elem_text(trs[i+1].cells[column_index]);
-if (reverse) {
-var tmp = v1;
-v1 = v2;
-v2 = tmp;
-}
-if (compare_function(v1, v2) > 0) {
-exchange(trs[i], trs[i+1], table);
-change = true;
-already_sorted = false;
-trs = table.tBodies[0].getElementsByTagName('tr');
-}
-}
-} while (change);
-if (reverse) break;// we've sorted twice so exit
-if (!already_sorted) break;// sort did something so exit
-// when it's sorted one way already then sort the opposite way
-reverse = true;
-}
-// put arrows on the headers
-var headers = table.tHead.getElementsByTagName('tr');
-for (i = 0; i < headers.length; i++) {
-for (j = 0; j < headers[i].cells.length; j++) {
-var cell = headers[i].cells[j];
-var arrows = cell.getElementsByClassName("sort_arrow");
-var arrow;
-if (arrows.length == 0) {
-arrow = document.createElement("span");
-arrow.className = "sort_arrow";
-cell.insertBefore(arrow, cell.firstChild);
-} else {
-arrow = arrows[0];
-}
-arrow.innerHTML = "";
-if (j == column_index) {
-arrow.appendChild(document.createTextNode(reverse ? "\u25B2" : "\u25BC"));
-}
-}
-}
-}
-/*
-* Swap two rows in a table.
-*/
-function exchange(oRowI, oRowJ, oTable) {
-var i = oRowI.rowIndex;
-var j = oRowJ.rowIndex;
-if (i == j+1) {
-oTable.tBodies[0].insertBefore(oRowI, oRowJ);
-} if (j == i+1) {
-oTable.tBodies[0].insertBefore(oRowJ, oRowI);
-} else {
-var tmpNode = oTable.tBodies[0].replaceChild(oRowI, oRowJ);
-if(typeof(oRowI) != "undefined") {
-oTable.tBodies[0].insertBefore(tmpNode, oRowI);
-} else {
-oTable.appendChild(tmpNode);
-}
-}
-}
-/*
-* Compare two E-values which may be very small.
-*/
-function compare_evalues(v1, v2) {
-var e1 = sci2log(v1);
-var e2 = sci2log(v2);
-if (e1 < e2) return -1;
-else if (e1 > e2) return 1;
-return 0;
-}
-/*
-* Compare two counts.
-*/
-function compare_counts(v1, v2) {
-var re = /(\d+)\s*\/\s*\d+/;
-var m1 = re.exec(v1);
-var m2 = re.exec(v2);
-if (m1 == null && m2 == null) return 0;
-if (m1 == null) return -1;
-if (m2 == null) return 1;
-return parseInt(m2[1]) - parseInt(m1[1]);
-}
-/*
-* Compare two sequence words.
-*/
-function compare_words(v1, v2) {
-return v1.localeCompare(v2);
-}
-</script>
-<style>
-/* The following is the content of meme.css */
-body { background-color:white; font-size: 12px; font-family: Verdana, Arial, Helvetica, sans-serif;}
-div.help {
-display: inline-block;
-margin: 0px;
-padding: 0px;
-width: 12px;
-height: 13px;
-cursor: pointer;
-background-image: url(data:image/gif;base64,R0lGODlhDAANAIABANR0AP///yH5BAEAAAEALAAAAAAMAA0AAAIdhI8Xy22MIFgv1DttrrJ7mlGNNo4c+aFg6SQuUAAAOw==);
-}
-div.help:hover {
-background-image: url(data:image/gif;base64,R0lGODlhDAANAKEAANR0AP///9R0ANR0ACH+EUNyZWF0ZWQgd2l0aCBHSU1QACH5BAEAAAIALAAAAAAMAA0AAAIdDGynCe3PgoxONntvwqz2/z2K2ImjR0KhmSIZUgAAOw==);
-}
-p.spaced { line-height: 1.8em;}
-span.citation { font-family: "Book Antiqua", "Palatino Linotype", serif; color: #004a4d;}
-p.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;}
-td.jump { font-size: 13px; color: #ffffff; background-color: #00666a;
-font-family: Georgia, "Times New Roman", Times, serif;}
-a.jump { margin: 15px 0 0; font-style: normal; font-variant: small-caps;
-font-weight: bolder; font-family: Georgia, "Times New Roman", Times, serif;}
-h2.mainh {font-size: 1.5em; font-style: normal; margin: 15px 0 0;
-font-variant: small-caps; font-family: Georgia, "Times New Roman", Times, serif;}
-h2.line {border-bottom: 1px solid #CCCCCC; font-size: 1.5em; font-style: normal;
-margin: 15px 0 0; padding-bottom: 3px; font-variant: small-caps;
-font-family: Georgia, "Times New Roman", Times, serif;}
-h4 {border-bottom: 1px solid #CCCCCC; font-size: 1.2em; font-style: normal;
-margin: 10px 0 0; padding-bottom: 3px; font-family: Georgia, "Times New Roman", Times, serif;}
-h5 {margin: 0px}
-a.help { font-size: 9px; font-style: normal; text-transform: uppercase;
-font-family: Georgia, "Times New Roman", Times, serif;}
-div.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;}
-div.pad1 { margin: 10px 5px;}
-div.pad2 { margin: 25px 5px 5px;}
-h2.pad2 { padding: 25px 5px 5px;}
-div.pad3 { padding: 5px 0px 10px 30px;}
-div.box { border: 2px solid #CCCCCC; padding:10px; overflow: hidden;}
-div.bar { border-left: 7px solid #00666a; padding:5px; margin-top:25px; }
-div.subsection {margin:25px 0px;}
-img {border:0px none;}
-th.majorth {text-align:left;}
-th.minorth {font-weight:normal; text-align:left; width:8em; padding: 3px 0px;}
-th.actionth {font-weight:normal; text-align:left;}
-.explain h5 {font-size:1em; margin-left: 1em;}
-div.doc {margin-left: 2em; margin-bottom: 3em;}
-th.trainingset {
-border-bottom: thin dashed black;
-font-weight:normal;
-padding:0px 10px;
-}
-div.pop_content {
-position:absolute;
-z-index:50;
-width:300px;
-padding: 5px;
-background: #E4ECEC;
-font-size: 12px;
-font-family: Arial;
-border-style: double;
-border-width: 3px;
-border-color: #AA2244;
-display:none;
-}
-div.pop_content > *:first-child {
-margin-top: 0px;
-}
-div.pop_content h1, div.pop_content h2, div.pop_content h3, div.pop_content h4,
-div.pop_content h5, div.pop_content h6, div.pop_content p {
-margin: 0px;
-}
-div.pop_content p + h1, div.pop_content p + h2, div.pop_content p + h3,
-div.pop_content p + h4, div.pop_content p + h5, div.pop_content p + h6 {
-margin-top: 5px;
-}
-div.pop_content p + p {
-margin-top: 5px;
-}
-div.pop_content > *:last-child {
-margin-bottom: 0px;
-}
-div.pop_content div.pop_close {
-/* old definition */
-float:right;
-bottom: 0;
-}
-div.pop_content span.pop_close, div.pop_content span.pop_back {
-display: inline-block;
-border: 2px outset #661429;
-background-color: #CCC;
-padding-left: 1px;
-padding-right: 1px;
-padding-top: 0px;
-padding-bottom: 0px;
-cursor: pointer;
-color: #AA2244; /*#661429;*/
-font-weight: bold;
-}
-div.pop_content span.pop_close:active, div.pop_content span.pop_back:active {
-border-style: inset;
-}
-div.pop_content span.pop_close {
-float:right;
-/*border: 2px outset #AA002B;*/
-/*color: #AA2244;*/
-}
-div.pop_content:not(.nested) .nested_only {
-display: none;
-}
-div.pop_back_sec {
-margin-bottom: 5px;
-}
-div.pop_close_sec {
-margin-top: 5px;
-}
-table.hide_advanced tr.advanced {
-display: none;
-}
-span.show_more {
-display: none;
-}
-table.hide_advanced span.show_more {
-display: inline;
-}
-table.hide_advanced span.show_less {
-display: none;
-}
-/*****************************************************************************
-* Program logo styling
-****************************************************************************/
-div.prog_logo {
-border-bottom: 0.25em solid #0f5f60;
-height: 4.5em;
-width: 24em;
-display:inline-block;
-}
-div.prog_logo img {
-float:left;
-width: 4em;
-border-style: none;
-margin-right: 0.2em;
-}
-div.prog_logo h1, div.prog_logo h1:hover, div.prog_logo h1:active, div.prog_logo h1:visited {
-margin:0;
-padding:0;
-font-family: Arial, Helvetica,  sans-serif;
-font-size: 3.2em;
-line-height: 1em;
-vertical-align: top;
-display: block;
-color: #026666;
-letter-spacing: -0.06em;
-text-shadow: 0.04em 0.06em 0.05em #666;
-}
-div.prog_logo h2, div.prog_logo h2:hover, div.prog_logo h2:active, div.prog_logo h2:visited {
-display: block;
-margin:0;
-padding:0;
-font-family: Helvetica, sans-serif;
-font-size: 0.9em;
-line-height: 1em;
-letter-spacing: -0.06em;
-color: black;
-}
-div.big.prog_logo {
-font-size: 18px;
-}
-</style>
-<style>
-/* dreme output specific css */
-div.header {
-position: relative;
-overflow: hidden;
-margin-top: 15px;
-margin-bottom: 5px;
-margin-right: 3px;
-margin-left: 3px;
-}
-div.header > h2 {
-font-size: 1.5em;
-font-style: normal;
-margin: 0;
-font-variant: small-caps;
-font-family: Georgia, "Times New Roman", Times, serif;
-}
-div.header > span {
-position: absolute;
-right: 0;
-bottom: 0;
-}
-div.template {
-position: absolute;
-z-index: 1;
-left: 0;
-top: 0;
-visibility: hidden;
-}
-div.sym_btn {
-display:inline-block;
-text-decoration: underline;
-cursor: pointer;
-font-size: 20px;
-line-height:20px;
-text-align: center;
-width: 20px;
-height: 20px;
-color: blue;
-}
-div.sym_btn:hover {
-color: white;
-background-color: blue;
-}
-div.sym_btn.positioned {
-position: absolute;
-top: 0px;
-}
-div.box + div.box {
-margin-top: 5px;
-}
-th.motif_ordinal {
-}
-td.motif_ordinal {
-text-align: right;
-padding-right: 10px;
-font-weight: bold;
-font-size: large;
-}
-th.motif_word {
-padding-right: 10px;
-}
-td.motif_word {
-font-size:15px;
-font-family: 'Courier New', Courier, monospace;
-padding-right: 10px;
-}
-th.motif_logo {
-padding-right: 10px;
-}
-td.motif_logo {
-padding-right: 10px;
-}
-th.motif_evalue {
-text-align:right;
-padding-right: 10px;
-}
-td.motif_evalue {
-text-align: right;
-white-space: nowrap;
-padding-right: 20px;
-}
-th.motif_more {
-padding: 0 5px;
-}
-td.motif_more {
-text-align: center;
-padding: 0 5px;
-}
-th.motif_submit {
-padding: 0 5px;
-}
-td.motif_submit {
-text-align: center;
-padding: 0 5px;
-}
-th.match_word {
-padding-right: 10px;
-}
-td.match_word {
-padding-right: 10px;
-font-weight: bold;
-font-size: large;
-font-family: 'Courier New', Courier, monospace;
-}
-th.match_evalue, th.match_count {
-text-align: right;
-padding-right: 10px;
-}
-td.match_evalue, td.match_count {
-text-align: right;
-white-space: nowrap;
-padding-right: 20px;
-}
-div.tabArea {
-font-size: 80%;
-font-weight: bold;
-}
-.norc div.tabArea {
-display: none;
-}
-span.tab, span.tab:visited {
-cursor: pointer;
-color: #888;
-background-color: #ddd;
-border: 2px solid #ccc;
-padding: 2px 1em;
-text-decoration: none;
-}
-span.tab.middle {
-border-left-width: 0px;
-}
-div.tabArea.base span.tab {
-border-top-width: 0px;
-}
-div.tabArea.top span.tab {
-border-bottom-width: 0px;
-}
-span.tab:hover {
-background-color: #bbb;
-border-color: #bbb;
-color: #666;
-}
-span.tab.activeTab, span.tab.activeTab:hover, span.tab.activeTab:visited {
-background-color: white;
-color: black;
-cursor: default;
-}
-div.tabMain {
-border: 2px solid #ccc;
-background-color: white;
-padding: 10px;
-}
-div.tabMain.base {
-margin-top: 5px;
-display: inline-block;
-max-width: 98%;
-}
-div.tabMain.top {
-margin-bottom: 5px;
-}
-div.grey_background {
-position:fixed;
-z-index: 8;
-background-color: #000;
--ms-filter: "progid:DXImageTransform.Microsoft.Alpha(Opacity=50)";
-opacity: 0.5;
-left: 0;
-top: 0;
-width: 100%;
-height: 100%;
-}
-div.popup_wrapper {
-position:fixed;
-z-index:9;
-width:100%;
-height:0;
-top:50%;
-left:0;
-}
-div.popup {
-width: 600px;
-z-index:9;
-margin-left: auto;
-margin-right: auto;
-padding: 5px;
-background-color: #FFF;
-border-style: double;
-border-width: 5px;
-border-color: #00666a;
-position:relative;
-}
-div.close {
-cursor: pointer;
-border: 1px solid black;
-width:15px;
-height:15px;
-line-height:15px; /* this causes vertical centering */
-text-align:center;
-background-color:#FFF;
-color:#000;
-font-size:15px;
-font-family:monospace;
-}
-div.close:hover {
-color:#FFF;
-background-color:#000;
-}
-div.navnum {
-width:100%;
-height:20px;
-line-height:20px;
-text-align:center;
-font-size:medium;
-}
-div.navarrow {
-font-size: 30px;
-text-decoration:none;
-cursor: pointer;
--moz-user-select: none;
--webkit-user-select: none;
--ms-user-select: none;
-}
-div.navarrow > span.inactive {
-display: inline;
-}
-div.navarrow > span.active {
-display: none;
-}
-div.navarrow:hover > span.active {
-display: inline;
-}
-div.navarrow:hover > span.inactive {
-display: none;
-}
-table.programs {
-width: 100%;
-}
-table.programs tr {
-background-color: #EFE;
-}
-table.programs tr.selected {
-background-color: #262;
-color: #FFF;
-}
-table.programs tr.dna_only {
-display: none;
-}
-table.programs.alphabet_dna tr.dna_only {
-display: table-row;
-}
-table.inputs {
-margin-top: 20px;
-border-collapse:collapse;
-}
-table.inputs * td, table.inputs * th {
-padding-left: 15px;
-padding-right: 15px;
-padding-top: 1px;
-padding-bottom: 1px;
-}
-/* program settings */
-span.strand_none, span.strand_given, span.strand_both {
-display: none;
-}
-td.none span.strand_none, td.given span.strand_given, td.both span.strand_both {
-display: inline;
-}
-/* show the expanded motif only when the collapsed one is hidden */
-tbody *.less, tbody.collapsed *.more {
-display: none;
-}
-tbody.collapsed *.less {
-display: inline;
-}
 </style>
 </head>
 <body data-scrollpad="true">
 <!--  -->
 <div id="grey_out_page" class="grey_background" style="display:none;">
-</div>
-<!-- Help popups -->
-<div class="pop_content" id="pop_">
-<p>Help poup.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motifs_word">
-<p>
 The name of the motif uses the IUPAC codes for nucleotides which has
 a different letter to represent each of the 15 possible combinations.
-</p>
-<p>
 The name is itself a representation of the motif though the position
-weight matrix is not directly equalivant as it is generated from the
+weight matrix is not directly equivalent as it is generated from the
 sites found that matched the letters given in the name.
-</p>
-<p>
-<a id="doc_alphabets_url" href="#">
-Read more about the MEME suite's use of the IUPAC alphabets.
-</a>
-<script>$("doc_alphabets_url").href = site_url + "/doc/alphabets.html";</script>
-</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motifs_logo">
 <p>The logo of the motif.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motifs_rc_logo">
 <p>The logo of the reverse complement motif.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motifs_evalue">
 <p>The E-value is the enrichment p-value times the number of candidate
 motifs tested.</p>
 <p>The enrichment p-value is calculated using Fisher's Exact Test for
 enrichment of the motif in the positive sequences.</p>
 <p>Note that the counts used in Fisher's Exact Test are made after
 erasing sites that match previously found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motifs_uevalue">
 <p>The E-value of the motif calculated without erasing the sites of
 previously found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_more">
 <p>Show more information on the motif.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_submit_dl">
 <p>Submit your motif to another MEME Suite program or download your motif.</p>
 <h5>Supported Programs</h5>
-<dl>
 <dt>Tomtom</dt>
 <dd>Tomtom is a tool for searching for similar known motifs.
-</dd>
 <dt>MAST</dt>
 <dd>MAST is a tool for searching biological sequence databases for
 sequences that contain one or more of a group of known motifs.
-</dd>
 <dt>FIMO</dt>
 <dd>FIMO is a tool for searching biological sequence databases for
 sequences that contain one or more known motifs.
-</dd>
+<dt>GOMo</dt>
-<dt>GOMO</dt>
+<dd>GOMo is a tool for identifying possible roles (Gene Ontology
-<dd>GOMO is a tool for identifying possible roles (Gene Ontology
 terms) for DNA binding motifs.
-</dd>
 <dt>SpaMo</dt>
 <dd>SpaMo is a tool for inferring possible transcription factor
 complexes by finding motifs with enriched spacings.
-</dd>
-</dl>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motif_positives">
-<p># positive sequences matching the motif / # positive sequences.</p>
-<p>Note these counts are made after erasing sites that match previously
-found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motif_negatives">
-<p># negative sequences matching the motif / # negative sequences.</p>
-<p>Note these counts are made after erasing sites that match previously
-found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motif_pvalue">
-<p>The p-value of Fisher's Exact Test for enrichment of the motif in
-the positive sequences.</p>
-<p>Note that the counts used in Fisher's Exact Test are made after
-erasing sites that match previously found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motif_evalue">
-<p>The E-value is the motif p-value times the number of candidate motifs
-tested.</p>
-<p>Note that the p-value was calculated with counts made after
-erasing sites that match previously found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_motif_uevalue">
-<p>The E-value of the motif calculated without erasing the sites of
-previously found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_match_word">
-<p>All words matching the motif whose uncorrected p-value is less than
-<span id="help_add_pv_thresh"></span>.</p>
-<script>$("help_add_pv_thresh").innerHTML = data.options.add_pv_thresh;</script>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_match_pos">
-<p># positive sequences with matches to the word / # positive sequences.</p>
-<p>Note these counts are made after erasing sites that match previously
-found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_match_neg">
-<p># negative sequences with matches to the word / # negative sequences.</p>
-<p>Note these counts are made after erasing sites that match previously
-found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_match_pval">
-<p>The p-value of Fisher's Exact Test for enrichment of the word in
-the positive sequences.</p>
-<p>Note that the counts used in Fisher's Exact Test are made after
-erasing sites that match previously found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_match_eval">
-<p>The word p-value times the number of candidates tested.</p>
-<p>Note that the p-value was calculated with counts made after
-erasing sites that match previously found motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_seq_source">
-<p>The sequence file used by DREME to find the motifs.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_seq_alph">
-<p>The alphabet of the sequences.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_seq_count">
-<p>The count of the sequences.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_alph_name">
-<p>The name of the alphabet symbol.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<div class="pop_content" id="pop_alph_control">
-<p>The frequency of the alphabet symbol in the control dataset.</p>
-<div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
-</div>
-<!-- templates -->
-<div class="template box expanded_motif" id="tmpl_motif_expanded">
-<div>
-<span class="tvar_logo"></span>
-<span class="tvar_rclogo"></span>
-</div>
-<h4>Details</h4>
-<table class="details">
-<thead>
-<tr>
-<th class="match_count">Positives <div class="help" data-topic="pop_motif_positives"></div></th>
-<th class="match_count">Negatives <div class="help" data-topic="pop_motif_negatives"></div></th>
-<th class="match_evalue">P-value <div class="help" data-topic="pop_motif_pvalue"></div></th>
-<th class="match_evalue">E-value <div class="help" data-topic="pop_motif_evalue"></div></th>
-<th class="match_evalue">Unerased E-value <div class="help" data-topic="pop_motif_uevalue"></div></th>
-</tr>
-</thead>
-<tbody>
-<tr>
-<td class="match_count">
-<span class="tvar_p"></span> / <span class="tvar_p_total"></span>
-</td>
-<td class="match_count">
-<span class="tvar_n"></span> / <span class="tvar_n_total"></span>
-</td>
-<td class="tvar_pvalue match_evalue"></td>
-<td class="tvar_evalue match_evalue"></td>
-<td class="tvar_uevalue match_evalue"></td>
-</tr>
-</tbody>
-</table>
-<h4>Enriched Matching Words</h4>
-<div class="tvar_words"></div>
-</div>
-<div class="popup_wrapper">
-<div class="popup" style="display:none; top: -150px;" id="download">
-<div>
-<div style="float:right; ">
-<div id="outpop_close" class="close" tabindex="0">x</div>
-</div>
-<h2 class="mainh" style="margin:0; padding:0;">Submit or Download</h2>
-<div style="clear:both"></div>
-</div>
-<div style="height:100px">
-<div style="float:right; width: 30px;">
-<div id="outpop_prev" class="navarrow" tabindex="0">
-<span class="inactive">&#8679;</span><span class="active">&#11014;</span>
-</div>
-<div id="outpop_num" class="navnum"></div>
-<div id="outpop_next" class="navarrow" tabindex="0">
-<span class="inactive">&#8681;</span><span class="active">&#11015;</span>
-</div>
-</div>
-<div id="logo_box" style="height: 100px; margin-right: 40px;">
-<canvas id="outpop_logo" height="100" width="250"></canvas>
-<canvas id="outpop_logo_rc" height="100" width="250"></canvas>
-</div>
-</div>
-<div>
-<!-- tabs start -->
-<div class="tabArea top">
-<span id="outpop_tab_1" class="tab">Submit Motif</span><span
-id="outpop_tab_2" class="tab middle">Download Motif</span><span
-id="outpop_tab_3" class="tab middle">Download Logo</span>
-</div>
-<div class="tabMain top">
-<!-- Submit to another program -->
-<div id="outpop_pnl_1">
-<h4 class="compact">Submit to program</h4>
-<table id="programs" class="programs">
-<tr class="dna_only">
-<td><input type="radio" name="program" value="tomtom" id="submit_tomtom"></td>
-<td><label for="submit_tomtom">Tomtom</label></td>
-<td><label for="submit_tomtom">Find similar motifs in
-published libraries or a library you supply.</label></td>
-</tr>
-<tr>
-<td><input type="radio" name="program" value="fimo" id="submit_fimo"></td>
-<td><label for="submit_fimo">FIMO</label></td>
-<td><label for="submit_fimo">Find motif occurrences in
-sequence data.</label></td>
-</tr>
-<tr>
-<td><input type="radio" name="program" value="mast" id="submit_mast"></td>
-<td><label for="submit_mast">MAST</label></td>
-<td><label for="submit_mast">Rank sequences by affinity to
-groups of motifs.</label></td>
-</tr>
-<tr class="dna_only">
-<td><input type="radio" name="program" value="gomo" id="submit_gomo"></td>
-<td><label for="submit_gomo">GOMo</label></td>
-<td><label for="submit_gomo">Identify possible roles (Gene
-Ontology terms) for motifs.</label></td>
-</tr>
-<tr class="dna_only">
-<td><input type="radio" name="program" value="spamo" id="submit_spamo"></td>
-<td><label for="submit_spamo">SpaMo</label></td>
-<td><label for="submit_spamo">Find other motifs that are
-enriched at specific close spacings which might imply the existance of a complex.</label></td>
-</tr>
-</table>
-</div>
-<!-- download text format  -->
-<div id="outpop_pnl_2">
-<div>
-<label for="text_format">Format:</label>
-<select id="text_format">
-<option value="0">Count Matrix</option>
-<option value="1">Probability Matrix</option>
-<option value="2">Minimal MEME</option>
-</select>
-</div>
-<textarea id="outpop_text" name="content"
-style="width:99%; white-space: pre; word-wrap: normal; overflow-x: scroll;"
-rows="8" readonly="readonly" wrap="off"></textarea>
-<a id="outpop_text_dl" download="meme.txt" href=""></a>
-</div>
-<!-- download logo format -->
-<div id="outpop_pnl_3">
-<form id="logo_form" method="post" action="">
-<script>$("logo_form").action = site_url + "/utilities/generate_logo";</script>
-<input type="hidden" name="program" value="DREME"/>
-<input type="hidden" id="logo_motifs" name="motifs" value=""/>
-<table>
-<tr>
-<td><label for="logo_format">Format:</label></td>
-<td>
-<select id="logo_format" name="png">
-<option value="1">PNG (for web)</option>
-<option value="0">EPS (for publication)</option>
-</select>
-</td>
-</tr>
-<tr>
-<td><label for="logo_rc">Orientation:</label></td>
-<td>
-<select id="logo_rc" name="rc1">
-<option value="0">Normal</option>
-<option value="1" id="logo_rc_option">Reverse Complement</option>
-</select>
-</td>
-</tr>
-<tr>
-<td><label for="logo_ssc">Small Sample Correction:</label></td>
-<td>
-<input type="hidden" id="logo_err" name="errbars" value="0"/>
-<select id="logo_ssc" name="ssc">
-<option value="0">Off</option>
-<option value="1">On</option>
-</select>
-</td>
-</tr>
-<tr>
-<td><label for="logo_width">Width:</label></td>
-<td>
-<input type="text" id="logo_width" size="4" placeholder="default" name="width"/>&nbsp;cm
-</td>
-</tr>
-<tr>
-<td><label for="logo_height">Height:</label></td>
-<td>
-<input type="text" id="logo_height" size="4" placeholder="default" name="height"/>&nbsp;cm
-</td>
-</tr>
-</table>
-</form>
-</div>
-<!-- Buttons -->
-<div>
-<div style="float:left;">
-<input type="button" id="outpop_do" value="Submit" />
-</div>
-<div style="float:right;">
-<input id="outpop_cancel" type="button" value="Cancel" />
-</div>
-<div style="clear:both;"></div>
-</div>
-</div>
-</div>
-</div>
-</div>
 <!-- Page starts here -->
-<div id="top" class="pad1">
-<div class="prog_logo big">
-<img 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" alt="DREME Logo"/>
 <h1>DREME</h1>
 <h2>Discriminative Regular Expression Motif Elicitation</h2>
-</div>
+For further information on how to interpret these results please access
-<p class="spaced">
+To get a copy of the MEME software please access
-For further information on how to interpret these results or to get a
-copy of the MEME software please access
-<a href="http://meme.nbcr.net/">http://meme.nbcr.net</a>.
-</p>
-<p>
 If you use DREME in your research please cite the following paper:<br />
-<span class="citation">
 Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.
-<a href="http://bioinformatics.oxfordjournals.org/content/27/12/1653">[full text]</a>
-</span>
-</p>
-</div>
-<!-- navigation -->
-<div class="pad2">
-<a class="jump" href="#motifs_sec">Discovered Motifs</a>
-&nbsp;&nbsp;|&nbsp;&nbsp;
-<a class="jump" href="#inputs_sec">Inputs &amp; Settings</a>
-&nbsp;&nbsp;|&nbsp;&nbsp;
-<a class="jump" href="#info_sec">Program information</a>
-</div>
-<!-- alert the user when their browser is not up to the task -->
-<noscript><h1 style="color:red">Javascript is required to view these results!</h1></noscript>
-<h1 id="html5_warning" style="color:red; display:none;">Your browser does not support canvas!</h1>
-<script>
-if (!window.HTMLCanvasElement) $("html5_warning").style.display = "block";
-</script>
-<!-- description -->
-<div id="description_section" style="display:none">
-<div id="description" class="header">
-<h2>Description</h2>
-</div>
-<div id="description_text" class="box">
-</div>
-</div>
-<script>
-if (data.description) {
-$("description_text").innerHTML = "";
-$("description_text").appendChild(make_description(data.description));
-$("description_section").style.display = "block";
-}
-</script>
-<!-- motifs -->
-<div id="motifs_sec" class="header">
-<h2>Discovered Motifs</h2>
-<span><a href="#inputs_sec">Next</a>&nbsp;<a href="#">Top</a></span>
-</div>
-<div id="motifs" class="box">
-<p>No motifs were discovered!</p>
-</div>
-<script>make_motifs();</script>
-<!-- inputs and settings -->
-<div id="inputs_sec" class="header">
-<h2>Inputs &amp; Settings</h2>
-<span><a href="#motifs_sec">Previous</a>&nbsp;<a href="#info_sec">Next</a>&nbsp;<a href="#">Top</a></span>
-</div>
-<div class="box">
-<h4>Sequences</h4>
-<table id="seq_info" class="inputs">
-<tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>
-<th>Alphabet <div class="help" data-topic="pop_seq_alph"></div></th>
-<th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>
-</tr>
-<tr>
-<td id="ins_seq_source"></td>
-<td id="ins_seq_alphabet"></td>
-<td id="ins_seq_count"></td>
-</tr>
-</table>
-<script>
-{
-var db = data.sequence_db;
-$("ins_seq_source").innerHTML = db.file;
-$("ins_seq_alphabet").innerHTML = dreme_alphabet.get_alphabet_name();
-$("ins_seq_count").innerHTML = db.count;
-}
-</script>
-<h4>Control Sequences</h4>
-<table id="seq_info" class="inputs">
-<tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>
-<th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>
-</tr>
-<tr>
-<td id="ins_cseq_source"></td>
-<td id="ins_cseq_count"></td>
-</tr>
-</table>
-<script>
-{
-var db = data.control_db;
-if (db.from == "shuffled") {
-$("ins_cseq_source").innerHTML = "Shuffled Sequences";
-} else {
-$("ins_cseq_source").innerHTML = db.file;
-}
-$("ins_cseq_count").innerHTML = db.count;
-}
-</script>
-<h4>Background</h4>
-<span id="alpha_bg"></span>
-<script>
-{
-$("alpha_bg").appendChild(make_alpha_bg(dreme_alphabet, data.control_db.freqs));
-}
-</script>
-<h4>Other Settings</h4>
-<table id="tbl_settings" class="inputs hide_advanced">
-<tr>
-<th>Strand Handling</th>
-<td id="opt_strand">
-<span class="strand_none">This alphabet only has one strand</span>
-<span class="strand_given">Only the given strand is processed</span>
-<span class="strand_both">Both the given and reverse complement strands are processed</span>
-</td>
-</tr>
-<tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>
-<tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>
-<tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>
-<tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>
-<tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>
-</table>
-<script>
-{
-$("opt_strand").className = (dreme_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
-$("opt_ngen").innerHTML = data.options.ngen;
-$("opt_seed").innerHTML = data.options.seed;
-$("opt_stop_evalue").innerHTML = data.options.stop.evalue;
-$("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");
-$("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");
-}
-</script>
-</div>
-<!-- list information on this program -->
-<div id="info_sec" class="bar" style="position:relative">
-<div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>
-<div class="subsection">
-<h5 id="version">DREME version</h5>
-<span id="ins_version"></span>
-(Release date: <span id="ins_release"></span>)<br>
-</div>
-<script>
-$("ins_version").innerHTML = data["version"];
-$("ins_release").innerHTML = data["release"];
-</script>
-<div class="subsection">
-<h5 id="reference">Reference</h5>
-<span class="citation">
-Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.
-<a href="http://bioinformatics.oxfordjournals.org/content/27/12/1653">[full text]</a>
-</span>
-</div>
-<div class="subsection">
-<h5 id="command">Command line</h5>
-<textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">
-</textarea>
-<script>$("cmd").value = data["cmd"].join(" ");</script>
-</div>
-</div>
 </body>
 </html>

Mercurial > repos > iuc > meme_psp_gen

comparison test-data/dreme_output_test2.html @ 3:ff2f53a32d0e draft