Mercurial > repos > iuc > meme_fimo
diff test-data/meme_output_test2.html @ 15:0c5239d1aa65 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
| author | iuc |
|---|---|
| date | Wed, 11 Dec 2019 18:05:35 -0500 |
| parents | 4eb02864e5df |
| children | c5209f38700d |
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--- a/test-data/meme_output_test2.html Wed Dec 12 02:50:48 2018 -0500 +++ b/test-data/meme_output_test2.html Wed Dec 11 18:05:35 2019 -0500 @@ -7,7931 +7,21 @@ // @JSON_VAR data var data = { "program": "MEME", - "version": "4.12.0", - "release": "Tue Jun 27 16:22:50 2017 -0700", + "version": "5.0.5", + "release": "Mon Mar 18 20:12:19 2019 -0700", "stop_reason": "Stopped because requested number of motifs (1) found.", "cmd": [ - "meme", "meme_input_1.fasta", "-o", "meme_test2_out", "-nostatus", - "-maxsize", "1000000", "-sf", "Galaxy_FASTA_Input", "-dna", "-mod", - "zoops", "-nmotifs", "1", "-wnsites", "0.8", "-minw", "8", "-maxw", - "50", "-wg", "11", "-ws", "1", "-maxiter", "50", "-distance", - "0.001", "-prior", "dirichlet", "-b", "0.01", "-plib", - "prior30.plib", "-spmap", "uni", "-spfuzz", "0.5" + "meme", + "-o", + "-nostatus", "-maxsize", "1000000", "-sf", "Galaxy_FASTA_Input", + "-dna", "-mod", "zoops", "-nmotifs", "1", "-wnsites", "0.8", + "-minw", "8", "-maxw", "50", "-wg", "11", "-ws", "1", "-maxiter", + "50", "-distance", "0.001", "-prior", "dirichlet", "-b", "0.01", + "-plib", + "-spmap", "uni", "-spfuzz", "0.5" ], - "options": { - "mod": "zoops", - "revcomp": false, - "nmotifs": 1, - "minw": 8, - "maxw": 50, - "minsites": 2, - "maxsites": 30, - "wnsites": 0.8, - "spmap": "uni", - "spfuzz": 0.5, - "maxwords": -1, - "prior": "dirichlet", - "b": 0.01, - "maxiter": 50, - "distance": 0.001, - "wg": 11, - "ws": 1, - "noendgaps": false, - "substring": true - }, - "alphabet": { - "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", - "aliases": "U", - "name": "Thymine", - "colour": "008000", - "complement": "A" - }, { - "symbol": "N", - "aliases": "X.", - "name": "Any base", - "equals": "ACGT" - }, { - "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" - } - ] - }, - "background": { - "freqs": [0.294, 0.231, 0.257, 0.217] - }, - "sequence_db": { - "source": "Galaxy_FASTA_Input", - "psp_source": "prior30.plib", - "freqs": [0.294, 0.231, 0.257, 0.217], - "sequences": [ - { - "name": "chr21_19617074_19617124_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_26934381_26934431_+", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_28217753_28217803_-", - "length": 50, - "weight": 1.000000 - }, { - "name": "chr21_31710037_31710087_-", - "length": 50, - 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// 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> - // - // return true if any part of the passed element is visible in the viewport - // - function element_in_viewport(elem) { - var rect; - try { - rect = elem.getBoundingClientRect(); - } catch (e) { - return false; - } - return ( - rect.top < (window.innerHeight || document.body.clientHeight) && - rect.bottom > 0 && - rect.left < (window.innerWidth || document.body.clientWidth) && - rect.right > 0 - ); - } - - // - // Functions to delay a drawing task until it is required or it would not lag the display to do so - // - - // a list of items still to be drawn - var drawable_list = []; - // the delay between drawing objects that are not currently visible - var draw_delay = 1; - // the delay after a user interaction - var user_delay = 300; - // the delay after a user has stopped scrolling and is viewing the stuff drawn on the current page - var stop_delay = 300; - // the timer handle; allows resetting of the timer after user interactions - var draw_timer = null; - - // - // Drawable - // - // elem - a page element which defines the position on the page that drawing is to be done - // task - an object with the method run which takes care of painting the object - // - var Drawable = function(elem, task) { - this.elem = elem; - this.task = task; - } - - // - // Drawable.is_visible - // - // Determines if the element is visible in the viewport - // - Drawable.prototype.is_visible = function() { - return element_in_viewport(this.elem); - } - - // - // Drawable.run - // - // Run the task held by the drawable - Drawable.prototype.run = function() { - if (this.task) this.task.run(); - this.task = null; - } - - // - // Drawable.run - // - // Run the task iff visible - // returns true if the task ran or has already run - Drawable.prototype.run_visible = function() { - if (this.task) { - if (element_in_viewport(this.elem)) { - this.task.run(); - this.task = null; - return true; - } - return false; - } else { - return true; - } - } - - // - // draw_on_screen - // - // Checks each drawable object and draws those on screen. - // - function draw_on_screen() { - var found = false; - for (var i = 0; i < drawable_list.length; i++) { - if (drawable_list[i].run_visible()) { - drawable_list.splice(i--, 1); - found = true; - } - } - return found; - } - - // - // process_draw_tasks - // - // Called on a delay to process the next avaliable - // draw task. - // - function process_draw_tasks() { - var delay = draw_delay; - draw_timer = null; - if (drawable_list.length == 0) return; //no more tasks - if (draw_on_screen()) { - delay = stop_delay; //give the user a chance to scroll - } else { - //get next task - var drawable = drawable_list.shift(); - drawable.task.run(); - } - //allow UI updates between tasks - draw_timer = window.setTimeout("process_draw_tasks()", delay); - } - - // - // delayed_process_draw_tasks - // - // Call process_draw_tasks after a short delay. - // The delay serves to group multiple redundant events. - // Should be set as event handler for onscroll and onresize. - // - function delayed_process_draw_tasks() { - //reset the timer - if (drawable_list.length > 0) { - if (draw_timer != null) clearTimeout(draw_timer); - draw_timer = window.setTimeout("process_draw_tasks()", user_delay); - } - } - - // - // add_draw_task - // - // Add a drawing task to be called immediately if it is - // visible, or to be called on a delay to reduce stuttering - // effect on the web browser. - function add_draw_task(elem, task) { - drawable = new Drawable(elem, task); - if (drawable.is_visible()) { - task.run(); - } else { - drawable_list.push(drawable); - //reset timer - if (draw_timer != null) clearTimeout(draw_timer); - draw_timer = window.setTimeout("process_draw_tasks()", user_delay); - } - } - -</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> - -// PRIVATE GLOBAL (uhoh) -var _block_colour_lookup = {}; - -function block_colour(index) { - function hsl2rgb(hue, saturation, lightness) { - "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; - } - } - function _pad_hex(value) { - var hex = Math.round(value * 255).toString(16); - if (hex.length < 2) hex = "0" + hex; - return hex; - } - var r, g, b, p, q; - if (saturation == 0) { - // achromatic (grayscale) - r = lightness; - g = lightness; - b = lightness; - } else { - if (lightness < 0.5) { - q = lightness * (1 + saturation); - } else { - q = lightness + saturation - (lightness * saturation); - } - p = (2 * lightness) - q; - r = _hue(p, q, hue + (1.0 / 3.0)); - g = _hue(p, q, hue); - b = _hue(p, q, hue - (1.0 / 3.0)); - } - return "#" + _pad_hex(r) + _pad_hex(g) + _pad_hex(b); - } - if (typeof index !== "number" || index % 1 !== 0 || index < 0) return "#000000"; - // check for override - if (_block_colour_lookup[index] == null) { - var start = 0; //red - var sat = 100; - var light = 50; - var divisions = 1 << Math.ceil(Math.log(index + 1) / Math.LN2); - hue = start + (360 / divisions) * ((index - (divisions >> 1)) * 2 + 1); - // colour input fields only support values in the form #RRGGBB - _block_colour_lookup[index] = hsl2rgb(hue / 360, sat / 100, light / 100); - } - return _block_colour_lookup[index]; -} - -function set_block_colour(index, new_colour) { - _block_colour_lookup[index] = new_colour; - var blocks = document.querySelectorAll("div.block_motif[data-colour-index=\"" + index + "\"]"); - var i; - for (i = 0; i < blocks.length; i++) { - blocks[i].style.backgroundColor = new_colour; - } - var swatches = document.querySelectorAll("div.legend_swatch[data-colour-index=\"" + index + "\"]"); - var picker; - for (i = 0; i < swatches.length; i++) { - swatches[i].style.backgroundColor = new_colour; - picker = swatches[i].querySelector("input[type=\"color\"]"); - if (picker != null) picker.value = new_colour; - } -} - -function make_block_legend_entry(motif_name, motif_colour_index) { - if (typeof make_block_legend_entry.has_colour_picker !== "boolean") { - // test if colour picker is supported, based off Modernizer - // see http://stackoverflow.com/a/7787648/66387 - make_block_legend_entry.has_colour_picker = (function() { - var doc_ele = document.documentElement; - // We first check to see if the type we give it sticks.. - var input_ele = document.createElement('input'); - input_ele.setAttribute('type', 'color'); - var value_ok = input_ele.type !== 'text'; - if (value_ok) { - // If the type does, we feed it a textual value, which shouldn't be valid. - // If the value doesn't stick, we know there's input sanitization which infers a custom UI - var smile = ':)'; - input_ele.value = smile; - input_ele.style.cssText = 'position:absolute;visibility:hidden;'; - // chuck into DOM and force reflow for Opera bug in 11.00 - // github.com/Modernizr/Modernizr/issues#issue/159 - doc_ele.appendChild(input_ele); - doc_ele.offsetWidth; - value_ok = input_ele.value != smile; - doc_ele.removeChild(input_ele); - } - return value_ok; - })(); - } - var entry = document.createElement("div"); - entry.className = "legend_entry"; - var swatch; - swatch = document.createElement("div"); - swatch.className = "legend_swatch"; - swatch.setAttribute("data-colour-index", motif_colour_index); - swatch.style.backgroundColor = block_colour(motif_colour_index); - if (make_block_legend_entry.has_colour_picker) { - var picker = document.createElement("input"); - picker.type = "color"; - picker.value = block_colour(motif_colour_index); - picker.addEventListener("change", function(e) { - set_block_colour(motif_colour_index, picker.value); - }, false); - swatch.addEventListener("click", function(e) { - picker.click(); - }, false); - swatch.appendChild(picker); - } - entry.appendChild(swatch); - var name = document.createElement("div"); - name.className = "legend_text"; - name.appendChild(document.createTextNode(motif_name)); - entry.appendChild(name); - return entry; -} - -function make_block_ruler(max_len) { - var container = document.createElement("div"); - container.className = "block_container"; - var step; - if (max_len < 50) { - step = 1; - } else if (max_len < 100) { - step = 2; - } else if (max_len < 200) { - step = 4; - } else if (max_len < 500) { - step = 10; - } else if (max_len < 1000) { - step = 20; - } else if (max_len < 2000) { - step = 40; - } else if (max_len < 5000) { - step = 100; - } else if (max_len < 10000) { - step = 200; - } else if (max_len < 20000) { - step = 400; - } else { - step = Math.floor(max_len / 20000) * 400; - } - var peroid; - if (max_len < 10) { - peroid = 1; - } else if (max_len < 20) { - peroid = 2; - } else { - peroid = 5; - } - var i, cycle, offset, tic, label; - for (i = 0, cycle = 0; i < max_len; i += step, cycle = (cycle + 1) % peroid) { - offset = "" + ((i / max_len) * 100) + "%"; - tic = document.createElement("div"); - tic.style.left = offset; - tic.className = (cycle == 0 ? "tic_major" : "tic_minor"); - container.appendChild(tic); - if (cycle == 0) { - label = document.createElement("div"); - label.className = "tic_label"; - label.style.left = offset; - label.appendChild(document.createTextNode(i)); - container.appendChild(label); - } - } - return container; -} - -function _calculate_block_needle_drag_pos(e, data) { - var mouse; - e = e || window.event; - if (e.pageX || ev.pageY) { - mouse = {"x": e.pageX, "y": e.pageY}; - } else { - mouse = { - x:e.clientX + document.body.scrollLeft - document.body.clientLeft, - y:e.clientY + document.body.scrollTop - document.body.clientTop - }; - } - var cont = data.container; - var dragable_length = cont.clientWidth - - (cont.style.paddingLeft ? cont.style.paddingLeft : 0) - - (cont.style.paddingRight ? cont.style.paddingRight : 0); - //I believe that the offset parent is the body - //otherwise I would need to make this recursive - //maybe clientLeft would work, but the explanation of - //it is hard to understand and it apparently doesn't work - //in firefox 2. - var diff = mouse.x - cont.offsetLeft; - if (diff < 0) diff = 0; - if (diff > dragable_length) diff = dragable_length; - var pos = Math.round(diff / dragable_length * data.max); - if (pos > data.len) pos = data.len; - return pos; -} - -function _update_block_needle_drag(e, data, done) { - "use strict"; - var pos = _calculate_block_needle_drag_pos(e, data); - // read the needle positions - var left = parseInt(data.llabel.textContent, 10) - data.off - 1; - var right = parseInt(data.rlabel.textContent, 10) - data.off; - // validate needle positions - if (left >= data.len) left = data.len - 1; - if (left < 0) left = 0; - if (right > data.len) right = data.len; - if (right <= left) right = left + 1; - // calculate the new needle positions - if (data.moveboth) { - var size = right - left; - if (data.isleft) { - if ((pos + size) > data.len) pos = data.len - size; - left = pos; - right = pos + size; - } else { - if ((pos - size) < 0) pos = size; - left = pos - size; - right = pos; - } - } else { - if (data.isleft) { - if (pos >= right) pos = right - 1; - left = pos; - } else { - if (pos <= left) pos = left + 1; - right = pos; - } - } - // update the needle positions - data.lneedle.style.left = "" + (left / data.max * 100) + "%"; - data.llabel.textContent = "" + (left + data.off + 1); - data.rneedle.style.left = "" + (right / data.max * 100) + "%"; - data.rlabel.textContent = "" + (right + data.off); - data.handler(left, right, done); -} - -function _make_block_needle_drag_start_handler(isleft, data) { - return function (e) { - data.isleft = isleft; - data.moveboth = !(e.shiftKey); - document.addEventListener("mousemove", data.drag_during, false); - document.addEventListener("mouseup", data.drag_end, false); - }; -} - -function _make_block_needle_drag_end_handler(data) { - return function (e) { - document.removeEventListener("mousemove", data.drag_during, false); - document.removeEventListener("mouseup", data.drag_end, false); - _update_block_needle_drag(e, data, true); - }; -} - -function _make_block_needle_drag_during_handler(data) { - return function (e) { - _update_block_needle_drag(e, data, false); - }; -} - -// private function used by make_block_container -function _make_block_needle(isleft, value, data) { - var vbar = document.createElement('div'); - vbar.className = "block_needle " + (isleft ? "left" : "right"); - vbar.style.left = "" + (value / data.max * 100)+ "%"; - var label = document.createElement('div'); - label.className = "block_handle " + (isleft ? "left" : "right"); - // The needles sit between the sequence positions, so the left one sits at the - // start and the right at the end. This is why 1 is added to the displayed - // value for a left handle as the user doesn't need to know about this detail - label.textContent = "" + (isleft ? value + data.off + 1 : value + data.off); - label.unselectable = "on"; // so IE and Opera don't select the text, others are done in css - label.title = "Drag to move the displayed range. Hold shift and drag to change " + (isleft ? "lower" : "upper") + " bound of the range."; - vbar.appendChild(label); - if (isleft) { - data.lneedle = vbar; - data.llabel = label; - } else { - data.rneedle = vbar; - data.rlabel = label; - } - label.addEventListener("mousedown", _make_block_needle_drag_start_handler(isleft, data), false); - return vbar; -} - -function make_block_container(is_stranded, has_both_strands, max_len, show_len, offset, range_handler) { - offset = (offset != null ? offset : 0); - // make the container for the block diagram - var container = document.createElement("div"); - container.className = "block_container"; - container.setAttribute("data-max", max_len); - container.setAttribute("data-off", offset); - if (is_stranded) { - var plus = document.createElement("div"); - plus.appendChild(document.createTextNode("+")); - plus.className = "block_plus_sym"; - container.appendChild(plus); - if (has_both_strands) { - var minus = document.createElement("div"); - minus.appendChild(document.createTextNode("-")); - minus.className = "block_minus_sym"; - container.appendChild(minus); - } - } - var rule = document.createElement("div"); - rule.className = "block_rule"; - rule.style.width = ((show_len / max_len) * 100) + "%"; - container.appendChild(rule); - if (range_handler != null) { - var range_data = { - "max": max_len, - "len": show_len, - "off": offset, - "handler": range_handler, - "container": container, - "lneedle": null, "llabel": null, - "rneedle": null, "rlabel": null, - "isleft": false, "moveboth" : false - }; - range_data.drag_during = _make_block_needle_drag_during_handler(range_data); - range_data.drag_end = _make_block_needle_drag_end_handler(range_data); - container.appendChild(_make_block_needle(false, 1, range_data)); // add right first so z-index works - container.appendChild(_make_block_needle(true, 0, range_data)); - } - return container; -} - -function make_block_label(container, max_len, pos, length, message) { - "use strict"; - var label = document.createElement("div"); - label.className = "block_label"; - label.style.left = (((pos + (length / 2)) / max_len) * 100) + "%"; - label.appendChild(document.createTextNode(message)); - container.appendChild(label); -} - -function make_block(container, max_len, - site_pos, site_len, site_pvalue, site_rc, site_colour_index, site_secondary) { - "use strict"; - var block_height, block, block_region1, block_region2; - var max_block_height = 12; - var max_pvalue = 1e-10; - // calculate the height of the block - block_height = (site_pvalue < max_pvalue ? max_block_height : - (Math.log(site_pvalue) / Math.log(max_pvalue)) * max_block_height); - if (block_height < 1) block_height = 1; - // create a block to represent the motif - block = document.createElement("div"); - block.className = "block_motif" + (site_secondary ? " scanned_site" : "") + (site_rc ? " bottom" : " top"); - block.style.left = ((site_pos / max_len) * 100) + "%"; - block.style.top = (!site_rc ? max_block_height - block_height : - max_block_height + 1) + "px"; - block.style.width = ((site_len / max_len) * 100) + "%"; - block.style.height = block_height + "px"; - block.style.backgroundColor = block_colour(site_colour_index); - block.setAttribute("data-colour-index", site_colour_index); - // add to container - container.appendChild(block); - var activator = function (e) { - toggle_class(block, "active", true); - var new_e = new e.constructor(e.type, e); - block.dispatchEvent(new_e); - }; - var deactivator = function (e) { - toggle_class(block, "active", false); - var new_e = new e.constructor(e.type, e); - block.dispatchEvent(new_e); - } - // create a larger region to detect mouseover for the block - block_region1 = document.createElement("div"); - block_region1.className = "block_region top" + - (site_secondary ? " scanned_site" : "") + (site_rc ? "" : " main"); - block_region1.style.left = block.style.left; - block_region1.style.width = block.style.width; - block_region1.addEventListener('mouseover', activator, false); - block_region1.addEventListener('mouseout', deactivator, false); - container.appendChild(block_region1); - block_region2 = document.createElement("div"); - block_region2.className = "block_region bottom" + - (site_secondary ? " scanned_site" : "") + (site_rc ? " main" : ""); - block_region2.style.left = block.style.left; - block_region2.style.width = block.style.width; - block_region2.addEventListener('mouseover', activator, false); - block_region2.addEventListener('mouseout', deactivator, false); - container.appendChild(block_region2); - return block; -} - -function set_block_needle_positions(containingNode, start, end) { - var container, lneedle, llabel, rneedle, rlabel, max, off, left, right; - container = (/\bblock_container\b/.test(containingNode.className) ? containingNode : containingNode.querySelector(".block_container")); - max = parseInt(container.getAttribute("data-max"), 10); - off = parseInt(container.getAttribute("data-off"), 10); - left = start - off; - right = end - off; - lneedle = containingNode.querySelector(".block_needle.left"); - llabel = lneedle.querySelector(".block_handle.left"); - rneedle = containingNode.querySelector(".block_needle.right"); - rlabel = rneedle.querySelector(".block_handle.right"); - // update the needle positions - lneedle.style.left = "" + (left / max * 100) + "%"; - llabel.textContent = "" + (left + off + 1); - rneedle.style.left = "" + (right / max * 100) + "%"; - rlabel.textContent = "" + (right + off); -} - -function get_block_needle_positions(containingNode) { - var container, llabel, rlabel, max, off, left, right; - container = (/\bblock_container\b/.test(containingNode.className) ? containingNode : containingNode.querySelector(".block_container")); - max = parseInt(container.getAttribute("data-max"), 10); - off = parseInt(container.getAttribute("data-off"), 10); - llabel = containingNode.querySelector(".block_needle.left > .block_handle.left"); - rlabel = containingNode.querySelector(".block_needle.right > .block_handle.right"); - left = parseInt(llabel.textContent, 10) - off - 1; - right = parseInt(rlabel.textContent, 10) - off; - return {"start": left + off, "end": right + off}; -} -</script> - <script> -function make_alpha_bg_table(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 = "alpha_bg_table"; - // 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"); - if (freqs != null) add_text_header_cell(row, "Freq.", "pop_alph_freq"); - if (alph.has_bg()) add_text_header_cell(row, "Bg.", "pop_alph_bg"); - add_text_header_cell(row, ""); - add_text_header_cell(row, ""); - add_text_header_cell(row, ""); - if (alph.has_bg()) add_text_header_cell(row, "Bg.", "pop_alph_bg"); - if (freqs != null) add_text_header_cell(row, "Freq.", "pop_alph_freq"); - add_text_header_cell(row, "Name", "pop_alph_name"); - } else { - add_text_header_cell(row, ""); - add_text_header_cell(row, "Name", "pop_alph_name"); - if (freqs != null) add_text_header_cell(row, "Freq.", "pop_alph_freq"); - if (alph.has_bg()) add_text_header_cell(row, "Bg.", "pop_alph_bg"); - } - // 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)); - if (freqs != null) add_text_cell(row, "" + freqs[i].toFixed(3)); - if (alph.has_bg()) add_text_cell(row, "" + alph.get_bg_freq(i).toFixed(3)); - add_cell(row, colour_symbol(i)); - add_text_cell(row, "~"); - add_cell(row, colour_symbol(c)); - if (alph.has_bg()) add_text_cell(row, "" + alph.get_bg_freq(c).toFixed(3)); - if (freqs != null) 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)); - if (freqs != null) add_text_cell(row, "" + freqs[i].toFixed(3)); - if (alph.has_bg()) add_text_cell(row, "" + alph.get_bg_freq(i).toFixed(3)); - } - } - return table; -} - -</script> - <script> -var current_motif = 0; -var meme_alphabet = new Alphabet(data.alphabet, data.background.freqs); - -var DelayLogoTask = function(logo, canvas) { - this.logo = logo; - this.canvas = canvas; -}; - -DelayLogoTask.prototype.run = function () { - draw_logo_on_canvas(this.logo, this.canvas, false); -}; - -function motif_pspm(index) { - var motif, pwm, psm, name, ltrim, rtrim, nsites, evalue; - // get motif - motif = data["motifs"][index]; - // get motif paramters - pwm = motif["pwm"]; - psm = motif["psm"]; - name = "" + (index + 1); ltrim = 0; rtrim = 0; - nsites = motif["nsites"]; evalue = motif["evalue"]; - // make pspm - return new Pspm(pwm, name, ltrim, rtrim, nsites, evalue, psm); -} - -function motif_count_matrix(index) { - return motif_pspm(index).as_count_matrix(); -} - -function motif_prob_matrix(index) { - return motif_pspm(index).as_probability_matrix(); -} - -function motif_minimal_meme(index) { - return motif_pspm(index).as_meme({ - "with_header": true, - "with_pspm": true, - "with_pssm": true, - "version": data["version"], - "alphabet": meme_alphabet, - "strands": (meme_alphabet.has_complement() && data.options.revcomp ? 2 : 1) - }); -} - -function motif_fasta(index) { - "use strict"; - var motif, sites, site, seq, sequences, sequence, i, num, counter, out; - counter = {}; - sequences = data["sequence_db"]["sequences"]; - motif = data["motifs"][index]; - sites = motif["sites"]; - out = ""; - for (i = 0; i < sites.length; i++) { - site = sites[i]; - seq = site["seq"]; - sequence = sequences[seq]; - counter[seq] = (num = counter[seq]) ? (++num) : (num = 1); // inc counter - if (i !== 0) {out += "\n";} - out += ">" + sequence["name"] + "_site_" + num + " offset= " + site["pos"] + - (site["rc"] ? " RC\n" : "\n"); - out += site["match"]; - } - return out; -} - -function motif_raw(index) { - "use strict"; - var sites, i, out; - sites = data["motifs"][index]["sites"]; - out = ""; - for (i = 0; i < sites.length; i++) { - if (i !== 0) {out += "\n";} - out += sites[i]["match"]; - } - return out; -} - -function clone_template(template) { - "use strict"; - var node, help_btns, i, button; - node = $(template).cloneNode(true); - toggle_class(node, "template", false); - node.id = ""; - help_btns = node.querySelectorAll(".help"); - for (i = 0; i < help_btns.length; i++) { - button = help_btns[i]; - if (button.hasAttribute("data-topic")) { - button.tabIndex = "0"; - button.addEventListener("click", __toggle_help, false); - button.addEventListener("keydown", __toggle_help, false); - } - } - return node; -} - -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); - } -} - -function make_logo(alphabet, pspm, rc, offset, className) { - if (rc) pspm = pspm.copy().reverse_complement(alphabet); - var logo = new Logo(alphabet, ""); - logo.add_pspm(pspm, offset); - var canvas = document.createElement('canvas'); - canvas.height = 50; - canvas.width = 0; - canvas.className = className; - size_logo_on_canvas(logo, canvas, false); - add_draw_task(canvas, new DelayLogoTask(logo, canvas)); - return canvas; -} - -function make_small_logo(alphabet, pspm, options) { - if (typeof options === "undefined") options = {}; - if (options.rc) pspm = pspm.copy().reverse_complement(alphabet); - var logo = new Logo(alphabet, {x_axis: false, y_axis: false}); - logo.add_pspm(pspm, (typeof options.offset === "number" ? options.offset : 0)); - var canvas = document.createElement('canvas'); - if (typeof options.className === "string") canvas.className = options.className; - if (typeof options.width === "number" && options.width > 0) { - canvas.height = 0; - canvas.width = options.width; - draw_logo_on_canvas(logo, canvas, false); - } else { - draw_logo_on_canvas(logo, canvas, false, 1/3); - } - return canvas; -} - -function make_large_logo(alphabet, pspm, rc, offset, className) { - if (rc) pspm = pspm.copy().reverse_complement(alphabet); - var logo = new Logo(alphabet, ""); - logo.add_pspm(pspm, offset); - var canvas = document.createElement('canvas'); - canvas.height = 200; - canvas.width = 0; - canvas.className = className; - size_logo_on_canvas(logo, canvas, false); - add_draw_task(canvas, new DelayLogoTask(logo, canvas)); - return canvas; -} - -function make_sym_btn(symbol, title, action) { - var box; - box = document.createElement("div"); - box.tabIndex = 0; - box.className = "sym_btn"; - box.appendChild(document.createTextNode(symbol)); - box.title = title; - box.addEventListener('click', action, false); - box.addEventListener('keydown', action, false); - return box; -} - -function make_seq(alphabet, 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 = alphabet.get_colour(alphabet.get_index(letter)); - lbox.appendChild(document.createTextNode(seq.substring(i, j))); - sbox.appendChild(lbox); - } - return sbox; -} - -// -// make_pv_text -// -// Returns the string p-value, with the p italicised. -/// -function make_pv_text() { - var pv_text = document.createElement("span"); - var pv_italic_text = document.createElement("span"); - pv_italic_text.appendChild(document.createTextNode("p")); - pv_italic_text.style.fontStyle = "italic"; - pv_text.appendChild(pv_italic_text); - pv_text.appendChild(document.createTextNode("-value")); - return pv_text; -} - -function append_site_entries(tbody, motif, site_index, count) { - "use strict"; - var i, end; - var sites, site, sequences, sequence; - var rbody; - if (typeof count !== "number") { - count = 20; - } - sequences = data["sequence_db"]["sequences"]; - sites = motif["sites"]; - end = Math.min(site_index + count, sites.length); - for (i = site_index; i < end; i++) { - site = sites[i]; - sequence = sequences[site["seq"]]; - - rbody = tbody.insertRow(tbody.rows.length); - add_text_cell(rbody, "" + (site["seq"] + 1) + ".", "site_num"); - add_text_cell(rbody, sequence["name"], "site_name"); - add_text_cell(rbody, site["rc"] ? "-" : "+", "site_strand"); - add_text_cell(rbody, site["pos"] + 1, "site_start"); - add_text_cell(rbody, site["pvalue"].toExponential(2), "site_pvalue"); - add_text_cell(rbody, site["lflank"], "site lflank"); - add_cell(rbody, make_seq(meme_alphabet, site["match"]), "site match"); - add_text_cell(rbody, site["rflank"], "site rflank"); - } - return i; -} - -function make_site_entries() { - "use strict"; - var region; - region = this; - if (region.data_site_index >= region.data_motif["sites"].length) { - // all sites created - region.removeEventListener('scroll', make_site_entries, false); - return; - } - // if there's still 100 pixels to scroll than don't do anything yet - if (region.scrollHeight - (region.scrollTop + region.offsetHeight) > 100) { - return; - } - - region.data_site_index = append_site_entries( - find_child(region, "sites_tbl").tBodies[0], - region.data_motif, region.data_site_index, 20 - ); -} - -function make_sites(motif) { - "use strict"; - function add_site_header(row, title, nopad, help_topic, tag_class) { - var div, divcp, th; - th = document.createElement("th"); - div = document.createElement("div"); - div.className = "sites_th_inner"; - if (typeof title !== "object") { - title = document.createTextNode("" + title); - } - div.appendChild(title); - if (help_topic) { - div.appendChild(document.createTextNode("\xA0")); - div.appendChild(help_button(help_topic)); - } - divcp = div.cloneNode(true); - divcp.className = "sites_th_hidden"; - th.appendChild(div); - th.appendChild(divcp); - if (nopad) { - th.className = "nopad"; - } - if (tag_class) { - th.className += " " + tag_class; - } - row.appendChild(th); - } - var outer_tbl, inner_tbl, tbl, thead, tbody, rhead; - - outer_tbl = document.createElement("div"); - outer_tbl.className = "sites_outer"; - - inner_tbl = document.createElement("div"); - inner_tbl.className = "sites_inner"; - outer_tbl.appendChild(inner_tbl); - - tbl = document.createElement("table"); - tbl.className = "sites_tbl"; - inner_tbl.appendChild(tbl); - - thead = document.createElement("thead"); - tbl.appendChild(thead); - tbody = document.createElement("tbody"); - tbl.appendChild(tbody); - - rhead = thead.insertRow(thead.rows.length); - add_site_header(rhead, "", true); - add_site_header(rhead, "Name", false, "pop_seq_name"); - add_site_header(rhead, "Strand", false, "pop_site_strand", "site_strand_title"); - add_site_header(rhead, "Start", false, "pop_site_start"); - add_site_header(rhead, make_pv_text(), false, "pop_site_pvalue"); - add_site_header(rhead, "", false); - add_site_header(rhead, "Sites", true, "pop_site_match"); - add_site_header(rhead, "", false); - - inner_tbl.data_motif = motif; - inner_tbl.data_site_index = append_site_entries(tbody, motif, 0, 20); - if (inner_tbl.data_site_index < motif["sites"].length) { - inner_tbl.addEventListener('scroll', make_site_entries, false); - } - return outer_tbl; -} - -function make_motif_table_entry(row, alphabet, ordinal, motif, colw) { - "use strict"; - function ev_sig(evalue_str) { - "use strict"; - var ev_re, match, sig, exp, num; - ev_re = /^(.*)e(.*)$/; - if (match = ev_re.exec(evalue_str)) { - sig = parseFloat(match[1]); - exp = parseInt(match[2]); - if (exp >= 0) { - return false; - } else if (exp <= -3) { - return true; - } else { - return sig * Math.pow(10, exp) <= 0.05; - } - } - return true; - } - function make_preview(alphabet, motif) { - "use strict"; - var pspm, preview, preview_rc; - var box, btn_box, logo_box, btn_plus, btn_minus; - if (motif["preview_logo"]) { - preview = motif["preview_logo"]; - preview_rc = motif["preview_logo_rc"]; - } else { - pspm = new Pspm(motif["pwm"]); - preview = make_logo(alphabet, pspm); - motif["preview_logo"] = preview; - if (alphabet.has_complement()) { - preview_rc = make_logo(alphabet, pspm, true, 0, "logo_rc"); - motif["preview_logo_rc"] = preview_rc; - } - } - if (preview_rc) { - btn_plus = document.createElement("div"); - btn_plus.appendChild(document.createTextNode("+")); - btn_plus.className = "preview_btn plus"; - btn_plus.tabIndex = "0"; - btn_plus.addEventListener("click", action_btn_rc, false); - btn_plus.addEventListener("keydown", action_btn_rc, false); - btn_minus = document.createElement("div"); - btn_minus.appendChild(document.createTextNode("-")); - btn_minus.className = "preview_btn minus"; - btn_minus.tabIndex = "0"; - btn_minus.addEventListener("click", action_btn_rc, false); - btn_minus.addEventListener("keydown", action_btn_rc, false); - btn_box = document.createElement("div"); - btn_box.className = "preview_btn_box"; - btn_box.appendChild(btn_plus); - btn_box.appendChild(btn_minus); - } - logo_box = document.createElement("div"); - logo_box.className = "preview_logo_box"; - logo_box.appendChild(preview); - if (preview_rc) logo_box.appendChild(preview_rc); - box = document.createElement("div"); - box.className = "preview_box"; - if (preview_rc) box.appendChild(btn_box); - box.appendChild(logo_box); - if (preview_rc) { - if (motif["rc"]) { - btn_minus.className += " active"; - logo_box.className += " show_rc_logo"; - } else { - btn_plus.className += " active"; - } - } - return box; - } - var pspm, preview, preview_rc, c; - row.data_motif = motif; - row.data_ordinal = ordinal; - if (!ev_sig(motif["evalue"])) { - row.style.opacity = 0.4; - } - add_text_cell(row, "" + ordinal + ".", "motif_ordinal"); - add_cell(row, make_preview(alphabet, motif), "motif_logo"); - add_text_cell(row, motif["evalue"], "motif_evalue"); - add_text_cell(row, motif["nsites"], "motif_nsites"); - add_text_cell(row, motif["len"], "motif_width"); - add_cell(row, make_sym_btn("\u21A7", "Show more information.", - action_show_more), "motif_more"); - add_cell(row, - make_sym_btn("\u21E2", - "Submit the motif to another MEME Suite program or download it.", - action_show_outpop), - "motif_submit"); - if (colw) { - for (c = 0; c < row.cells.length; c++) { - row.cells[c].style.minWidth = colw[c] + "px"; - } - } -} - -function make_motifs_table(alphabet, start_ordinal, motifs, colw, stop_reason) { - var i, j; - var tbl, thead, tbody, tfoot, row, preview; - var motif, pspm; - - tbl = document.createElement("table"); - - thead = document.createElement("thead"); - tbl.appendChild(thead); - tbody = document.createElement("tbody"); - tbl.appendChild(tbody); - tfoot = document.createElement("tfoot"); - tbl.appendChild(tfoot); - - row = thead.insertRow(thead.rows.length); - add_text_header_cell(row, "", "", "motif_ordinal"); - add_text_header_cell(row, "Logo", "", "motif_logo"); - add_text_header_cell(row, "E-value", "pop_ev", "motif_evalue"); - add_text_header_cell(row, "Sites", "pop_sites", "motif_nsites"); - add_text_header_cell(row, "Width", "pop_width", "motif_width"); - add_text_header_cell(row, "More", "pop_more", "motif_more"); - add_text_header_cell(row, "Submit/Download", "pop_submit_dl", "motif_submit"); - - for (i = 0; i < motifs.length; i++) { - row = tbody.insertRow(tbody.rows.length); - make_motif_table_entry(row, alphabet, start_ordinal + i, motifs[i], colw); - } - - row = tfoot.insertRow(tfoot.rows.length); - add_text_header_cell(row, stop_reason, "", "stop_reason", "", 6); - - return tbl; -} - -function make_expanded_motif(alphabet, ordinal, motif, less_x, submit_x) { - "use strict"; - var box, pspm, logo_box, large_logo, large_logo_rc, tab_logo, tab_logo_rc; - var btn, offset, norc; - - box = clone_template("tmpl_motif_expanded"); - box.data_motif = motif; - box.data_ordinal = ordinal; - - pspm = new Pspm(motif["pwm"]); - if (typeof motif["rc"] !== "boolean") { - motif["rc"] = false; - } - if (motif["large_logo"]) { - large_logo = motif["large_logo"]; - large_logo_rc = motif["large_logo_rc"]; - } else { - large_logo = make_large_logo(alphabet, pspm, false, 0); - motif["large_logo"] = large_logo; - if (alphabet.has_complement()) { - large_logo_rc = make_large_logo(alphabet, pspm, true, 0, "logo_rc"); - motif["large_logo_rc"] = large_logo_rc; - } - } - norc = (large_logo_rc == null); - toggle_class(box, "norc", norc); - - logo_box = find_child(box, "tvar_logo"); - logo_box.appendChild(large_logo); - if (large_logo_rc) logo_box.appendChild(large_logo_rc); - toggle_class(logo_box, "show_rc_logo", motif["rc"]); - - tab_logo = find_child(box, "tvar_tab"); - tab_logo_rc = find_child(box, "tvar_tab_rc"); - - toggle_class(tab_logo, "activeTab", !motif["rc"]); - toggle_class(tab_logo_rc, "activeTab", motif["rc"]); - - tab_logo.addEventListener('click', action_rc_tab, false); - tab_logo.addEventListener('keydown', action_rc_tab, false); - tab_logo_rc.addEventListener('click', action_rc_tab, false); - tab_logo_rc.addEventListener('keydown', action_rc_tab, false); - - set_tvar(box, "tvar_ordinal", ordinal); - set_tvar(box, "tvar_evalue", motif["evalue"]); - set_tvar(box, "tvar_width", motif["len"]); - set_tvar(box, "tvar_site_count", motif["nsites"]); - set_tvar(box, "tvar_llr", motif["llr"]); - set_tvar(box, "tvar_ic", motif["ic"]); - set_tvar(box, "tvar_re", motif["re"]); - set_tvar(box, "tvar_bt", motif["bt"]); - set_tvar(box, "tvar_sites", make_sites(motif)); - - offset = 32; // 1* 5px padding + 2 * 10px padding + 2 * 2px border + 3px ?? - - btn = find_child(box, "tvar_less"); - btn.style.left = (less_x - offset) + "px"; - btn.addEventListener('click', action_show_less, false); - btn.addEventListener('keydown', action_show_less, false); - btn = find_child(box, "tvar_submit"); - btn.style.left = (submit_x - offset) + "px"; - btn.addEventListener('click', action_show_outpop, false); - btn.addEventListener('keydown', action_show_outpop, false); - return box; -} - - -// -// -/// -function make_motifs() { - "use strict"; - function pixel_value(str_in) { - "use strict"; - var px_re, match; - px_re = /^(\d+)px$/; - if (match = px_re.exec(str_in)) { - return parseInt(match[1], 10); - } - return 0; - } - var container, tbl; - var colw, r, row, c, cell, cell_style, pad_left, pad_right; - - // make the motifs table - container = $("motifs"); - container.innerHTML = ""; // clear content - - tbl = make_motifs_table(meme_alphabet, 1, data["motifs"], colw, data["stop_reason"]); - container.appendChild(tbl); - - // measure table column widths - colw = []; - row = tbl.tBodies[0].rows[0]; - for (c = 0; c < row.cells.length; c++) { - var padLeft, padRight; - cell = row.cells[c]; - cell_style = window.getComputedStyle(cell, null); - pad_left = pixel_value(cell_style.getPropertyValue("padding-left")); - pad_right = pixel_value(cell_style.getPropertyValue("padding-right")); - colw[c] = cell.clientWidth - pad_left - pad_right; - if (typeof colw[c] !== "number" || colw[c] < 0) { - colw[c] = 1; - } - } - - // set minimum table column widths on each row so later when we remove rows it still aligns - for (r = 0; r < tbl.tBodies[0].rows.length; r++) { - row = tbl.tBodies[0].rows[r]; - for (c = 0; c < row.cells.length; c++) { - row.cells[c].style.minWidth = colw[c] + "px"; - } - } - - // store the table column widths so we can create rows latter with the same minimums - container.data_colw = colw; - - // calculate the x offset for the buttons - row = tbl.tBodies[0].rows[0]; - container.data_more_x = coords(find_child(find_child(row, "motif_more"), "sym_btn"))[0]; - container.data_submit_x = coords(find_child(find_child(row, "motif_submit"), "sym_btn"))[0]; - - draw_on_screen(); -} - -function make_meme_block(container, max_seq_len, is_scan, site) { - "use strict"; - var motif = data.motifs[site.motif]; - var block = make_block(container, max_seq_len, site.pos, motif.len, - site.pvalue, site.rc, site.motif, is_scan); - var handler = (is_scan ? - make_scan_popup(site, motif, block) : - make_block_popup(site, motif, block)); - block.addEventListener("mouseover", handler, false); - block.addEventListener("mouseout", handler, false); -} - -function append_blocks_entries(tbody, seq_index, count) { - "use strict"; - var i, end, j; - var max_pvalue, max_block_height, max_seq_len, sequences; - var sequence, sites, scans, scan; - var container, plus, minus, rule, row; - // define some constants - max_seq_len = data.sequence_db.max_length; - // determine how many to load - end = Math.min(seq_index + count, data.sequence_db.sequences.length); - for (i = seq_index; i < end; i++) { - // get the sequence - sequence = data.sequence_db.sequences[i]; - // make the containers for the block diagram - container = make_block_container(meme_alphabet.has_complement(), - data.options.revcomp, max_seq_len, sequence.length); - // create blocks for the motif sites - sites = sequence["sites"]; - for (j = 0; j < sites.length; j++) - make_meme_block(container, max_seq_len, false, sites[j]); - // create blocks for the scanned sites - scan = data.scan[i]; - for (j = 0; j < scan.sites.length; j++) - make_meme_block(container, max_seq_len, true, scan.sites[j]); - // create a row for the sequence - row = tbody.insertRow(tbody.rows.length); - toggle_class(row, "empty_seq", sites.length == 0 && scan.sites.length == 0); - toggle_class(row, "only_scan", sites.length == 0 && scan.sites.length > 0); - add_text_cell(row, (i + 1) + ".", "blockdiag_num"); - add_text_cell(row, sequence["name"], "blockdiag_name"); - add_text_cell(row, scan["pvalue"].toExponential(2), "blockdiag_pvalue"); - add_cell(row, container, "block_td"); - } - return end; -} - -function make_blocks_entries() { - "use strict"; - var region; - region = this; - if (region.data_blocks_index >= data["sequence_db"]["sequences"].length) { - // all sites created - region.removeEventListener('scroll', make_blocks_entries, false); - return; - } - // if there's still 100 pixels to scroll than don't do anything yet - if (region.scrollHeight - (region.scrollTop + region.offsetHeight) > 100) { - return; - } - - region.data_blocks_index = append_blocks_entries( - find_child(region, "blocks_tbl").tBodies[0], - region.data_blocks_index, 20 - ); -} - -function make_blocks() { - "use strict"; - function add_seqs_filter(container, id, checked, label_text, help_topic) { - "use strict"; - var label, radio; - radio = document.createElement("input"); - radio.type = "radio"; - radio.name = "seqs_display"; - radio.id = id; - radio.checked = checked; - radio.addEventListener('click', action_seqs_filter, false); - label = document.createElement("label"); - label.appendChild(document.createTextNode(label_text)); - label.htmlFor = id; - container.appendChild(radio); - container.appendChild(label); - if (help_topic) { - container.appendChild(document.createTextNode("\xA0")); - container.appendChild(help_button(help_topic)); - } - } - function add_blocks_header(row, title, nopad, help_topic) { - "use strict"; - var div, divcp, th; - th = document.createElement("th"); - div = document.createElement("div"); - div.className = "blocks_th_inner"; - if (typeof title !== "object") { - title = document.createTextNode("" + title); - } - div.appendChild(title); - if (help_topic) { - div.appendChild(document.createTextNode("\xA0")); - div.appendChild(help_button(help_topic)); - } - divcp = div.cloneNode(true); - divcp.className = "blocks_th_hidden"; - th.appendChild(div); - th.appendChild(divcp); - if (nopad) { - th.className = "nopad"; - } - row.appendChild(th); - } - var container; - var page, view_height, outer_tbl, inner_tbl, tbl, thead, tbody, rhead; - var in_view, i, seq_count; - - page = (document.compatMode === "CSS1Compat") ? document.documentElement : document.body; - view_height = Math.max(page.clientHeight - 300, 300); - - container = $("blocks"); - toggle_class(container, "hide_empty_seqs", true); - toggle_class(container, "hide_only_scan", true); - container.innerHTML = ""; - add_seqs_filter(container, "rdo_sites_only", true, "Only Motif Sites", "pop_motif_sites"); - add_seqs_filter(container, "rdo_sites_and_scan", false, "Motif Sites+Scanned Sites", "pop_scanned_sites"); - add_seqs_filter(container, "rdo_all_seqs", false, "All Sequences", "pop_all_sequences"); - - outer_tbl = document.createElement("div"); - outer_tbl.className = "blocks_outer"; - - inner_tbl = document.createElement("div"); - inner_tbl.id = "blocks_scroll"; - inner_tbl.className = "blocks_inner"; - inner_tbl.style.maxHeight = view_height + "px"; - outer_tbl.appendChild(inner_tbl); - - tbl = document.createElement("table"); - tbl.className = "blocks_tbl"; - inner_tbl.appendChild(tbl); - - thead = document.createElement("thead"); - tbl.appendChild(thead); - tbody = document.createElement("tbody"); - tbl.appendChild(tbody); - - rhead = thead.insertRow(thead.rows.length); - add_blocks_header(rhead, "", true); - add_blocks_header(rhead, "Name", false, "pop_seq_name"); - add_blocks_header(rhead, make_pv_text(), false, "pop_seq_pvalue"); - add_blocks_header(rhead, "Motif Location", false, "pop_motif_location"); - - container.appendChild(outer_tbl); - - - seq_count = data["sequence_db"]["sequences"].length; - in_view = Math.max(Math.ceil(view_height / 25), 1); - i = append_blocks_entries(tbody, 0, in_view); - - while (i < seq_count && inner_tbl.scrollHeight - (inner_tbl.scrollTop + inner_tbl.offsetHeight) < 400) { - i = append_blocks_entries(tbody, i, 20); - } - inner_tbl.data_blocks_index = i; - if (i < seq_count) { - inner_tbl.addEventListener('scroll', make_blocks_entries, false); - } -} - -function make_scan_popup(site, motif) { - return function (e) { - "use strict"; - var pop, xy, padding, edge_padding, pop_left, pop_top, page_width; - var lflank, match, rflank, pspm; - if (!e) var e = window.event; - pop = make_scan_popup.pop; - if (e.type === "mouseover") { - if (pop) return; - pop = clone_template("tmpl_scan_info"); - pspm = new Pspm(motif.pwm); - if (site.rc) pspm.reverse_complement(meme_alphabet); - set_tvar(pop, "tvar_logo", make_small_logo(meme_alphabet, pspm, {"className": "scan_logo"})); - set_tvar(pop, "tvar_motif", motif.id); - set_tvar(pop, "tvar_pvalue", site.pvalue.toExponential(2)); - set_tvar(pop, "tvar_start", site.pos + 1); - set_tvar(pop, "tvar_end", site.pos + motif.len); - - document.body.appendChild(pop); - position_popup(this, pop); - make_scan_popup.pop = pop; - } else if (e.type === "mouseout") { - if (pop) { - pop.parentNode.removeChild(pop); - make_scan_popup.pop = null; - } - } - }; -} - -function make_block_popup(site, motif, block) { - return function (e) { - "use strict"; - var pop; - var lflank, match, rflank, pspm, ruler, match_seq, match_width; - if (!e) var e = window.event; - pop = make_block_popup.pop; - if (e.type === "mouseover") { - if (pop) return; - pop = clone_template("tmpl_block_info"); - pspm = new Pspm(motif.pwm); - if (site.rc) { // must be dna - pspm.reverse_complement(meme_alphabet); - lflank = meme_alphabet.invcomp_seq(site.rflank); - match = meme_alphabet.invcomp_seq(site.match); - rflank = meme_alphabet.invcomp_seq(site.lflank); - } else { - lflank = site.lflank; - match = site.match; - rflank = site.rflank; - } - ruler = document.getElementById("measure_match"); - match_seq = make_seq(meme_alphabet, match); - ruler.innerHTML = ""; - ruler.appendChild(match_seq); - match_width = ruler.clientWidth; - ruler.removeChild(match_seq); - set_tvar(pop, "tvar_lflank", lflank); - set_tvar(pop, "tvar_match", match_seq); - set_tvar(pop, "tvar_rflank", rflank); - set_tvar(pop, "tvar_logo_pad", lflank); - set_tvar(pop, "tvar_logo", make_small_logo(meme_alphabet, pspm, {"width": match_width})); - set_tvar(pop, "tvar_motif", motif.id); - set_tvar(pop, "tvar_pvalue", site.pvalue.toExponential(2)); - set_tvar(pop, "tvar_start", site.pos + 1); - set_tvar(pop, "tvar_end", site.pos + motif.len); - - document.body.appendChild(pop); - position_popup(block, pop); - make_block_popup.pop = pop; - } else if (e.type === "mouseout") { - if (pop) { - pop.parentNode.removeChild(pop); - make_block_popup.pop = null; - } - } - }; -} - -function update_outpop_format(index) { - switch(parseInt($("text_format").value)) { - case 0: // count matrix - $("outpop_text").value = motif_count_matrix(index); - $("text_name").value = "motif_" + (index + 1) + "_counts.txt"; - break; - case 1: // prob matrix - $("outpop_text").value = motif_prob_matrix(index); - $("text_name").value = "motif_" + (index + 1) + "_freqs.txt"; - break; - case 2: // minimal meme - $("outpop_text").value = motif_minimal_meme(index); - $("text_name").value = "motif_" + (index + 1) + ".txt"; - break; - case 3: // fasta - $("outpop_text").value = motif_fasta(index); - $("text_name").value = "motif_" + (index + 1) + "_fasta.txt"; - break; - case 4: // raw - $("outpop_text").value = motif_raw(index); - $("text_name").value = "motif_" + (index + 1) + "_raw.txt"; - break; - default: - throw new Error("Unknown motif format"); - } -} - -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(meme_alphabet, ""); - logo.add_pspm(pspm, 0); - canvas = $("outpop_logo"); - canvas.width = canvas.width; // clear canvas - draw_logo_on_canvas(logo, canvas, false); - if (meme_alphabet.has_complement()) { - pspm.reverse_complement(meme_alphabet); - logo = new Logo(meme_alphabet, ""); - canvas = $("outpop_logo_rc"); - canvas.width = canvas.width; // clear canvas - draw_logo_on_canvas(logo, canvas, false); - } - num = $("outpop_num"); - num.innerHTML = ""; - num.appendChild(document.createTextNode("" + (index + 1))); - update_outpop_format(index); -} - -// -// action_show_more -// -// Show more information on the motif. -/// -function action_show_more(e) { - var node, tr, tbody, table, container, motif, ordinal; - var expanded_motif; - 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(); - } - // find the row that contains the cell - node = this; - do { - if (node.tagName === "TR") break; - } while (node = node.parentNode); - if (!node) throw new Error("Expected to find row!?"); - tr = node; - // get info - motif = tr.data_motif; - ordinal = tr.data_ordinal; - // find tbody - do { - if (node.tagName === "TBODY") break; - } while (node = node.parentNode); - if (!node) throw new Error("Expected to find tbody!?"); - tbody = node; - // find table - do { - if (node.tagName === "TABLE") break; - } while (node = node.parentNode); - if (!node) throw new Error("Expected to find table!?"); - table = node; - // find container - container = node.parentNode; - // make a expanded motif - motif["expanded"] = true; - expanded_motif = make_expanded_motif(meme_alphabet, ordinal, motif, - container.data_more_x, container.data_submit_x); - // now determine how to place it - if (tbody.rows.length === 1) { - // only us in the table so the table can be replaced - container.replaceChild(expanded_motif, table); - } else if (tbody.rows[0] === tr) { - // first row, so remove and insert an expanded motif before - table.deleteRow(tr.rowIndex); - container.insertBefore(expanded_motif, table); - } else if (tbody.rows[tbody.rows.length -1] === tr) { - // last row, so remove and insert an expanded motif after - table.deleteRow(tr.rowIndex); - container.insertBefore(expanded_motif, table.nextSibling); - } else { - var table2, tbody2; - table2 = table.cloneNode(false); - table2.appendChild(table.tHead.cloneNode(true)); - tbody2 = table.tBodies[0].cloneNode(false); - table2.appendChild(tbody2); - container.insertBefore(table2, table.nextSibling); - for (i = tbody.rows.length - 1; i >= 0; i--) { - row = tbody.rows[i]; - row.parentNode.removeChild(row); - if (row === tr) { - break; - } - tbody2.insertBefore(row, tbody2.rows[0]); - } - container.insertBefore(expanded_motif, table2); - } - find_child(expanded_motif, "tvar_less").focus(); -} - -// -// action_show_less -// -// Show less information on the motif. -/// -function action_show_less(e) { - var btn; - var expanded_motif, container, motif, ordinal, colw, focus_target; - var table, tbody, tbody2, row, table_before, table_after; - 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(); - } - btn = this; - // find expanded motif - expanded_motif = find_parent(btn, "expanded_motif"); - if (!expanded_motif) throw new Error("Expected expanded motif."); - // find the container - container = expanded_motif.parentNode; - // get data - motif = expanded_motif.data_motif; - ordinal = expanded_motif.data_ordinal; - colw = container.data_colw; - // get the table before - table_before = expanded_motif.previousSibling; - if (table_before && table_before.tagName !== "TABLE") { - table_before = null; - } - // get the table after - table_after = expanded_motif.nextSibling; - if (table_after && table_after.tagName !== "TABLE") { - table_after = null; - } - // see if there is a table below or above that we can put this in. - // if there is a table both below and above then add this motif and - // all ones below to the above table - motif["expanded"] = false; - if (table_before && table_after) { - tbody = table_before.tBodies[0]; - row = tbody.insertRow(tbody.rows.length); - make_motif_table_entry(row, meme_alphabet, ordinal, motif, colw); - focus_target = find_child(row.cells[5], "sym_btn"); - container.removeChild(expanded_motif); - tbody2 = table_after.tBodies[0]; - while (tbody2.rows.length > 0) { - row = tbody2.rows[0]; - row.parentNode.removeChild(row); - tbody.appendChild(row); - } - container.removeChild(table_after); - } else if (table_before) { - tbody = table_before.tBodies[0]; - row = tbody.insertRow(tbody.rows.length); - make_motif_table_entry(row, meme_alphabet, ordinal, motif, colw); - focus_target = find_child(row.cells[5], "sym_btn"); - container.removeChild(expanded_motif); - } else if (table_after) { - tbody = table_after.tBodies[0]; - row = tbody.insertRow(0); - make_motif_table_entry(row, meme_alphabet, ordinal, motif, colw); - focus_target = find_child(row.cells[5], "sym_btn"); - container.removeChild(expanded_motif); - } else { - //no table above or below! - // make a new table - table = make_motifs_table(meme_alphabet, ordinal, [motif], colw, data["stop_reason"]); - focus_target = find_child(table.tBodies[0].rows[0].cells[5], "sym_btn"); - container.replaceChild(table, expanded_motif); - } - focus_target.focus(); -} - -function action_show_outpop(e) { - "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", meme_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(meme_alphabet.has_complement() ? "submit_tomtom" : "submit_fimo"); //TODO FIXME Tomtom might require a more strict definition of DNA - default_prog.checked = true; - action_outpop_program.call(default_prog); - // disable reverse-complement when not DNA - $("logo_rc_option").disabled = !meme_alphabet.has_complement(); - // set errorbars on when ssc is on - $("logo_ssc").addEventListener("change", action_outpop_ssc, false); - } - var node; - // 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; - } - // load the motif logo - node = this; - do { - if (/\bexpanded_motif\b/.test(node.className) || node.tagName === "TR") break; - } while (node = node.parentNode); - if (node === null) throw new Error("Expected node!"); - update_outpop_motif(node.data_ordinal - 1); - // display the download popup - $("grey_out_page").style.display = "block"; - $("download").style.display = "block"; - $("outpop_close").focus(); -} - -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(); - } -} - -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); -} - -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); -} - -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); - } -} - -function action_outpop_ssc() { - "use strict"; - $("logo_err").value = $("logo_ssc").value; -} - -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(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); -} - -function action_outpop_download_motif(e) { - $("text_form").submit(); -} - -function action_outpop_download_logo(e) { - "use strict"; - $("logo_motifs").value = motif_minimal_meme(current_motif); - $("logo_form").submit(); -} - -function action_btn_rc(e) { - "use strict"; - var node, tr, motif, box, logo_box, tab_st, tab_rc, rc; - 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(); - } - node = this; - do { - if (node.tagName === "TR") break; - } while (node = node.parentNode); - if (!node) throw new Error("Expected to find row!?"); - tr = node; - // get info - motif = tr.data_motif; - box = find_parent(this, "preview_box"); - logo_box = find_child(box, "preview_logo_box"); - tab_st = find_child(box, "plus"); - tab_rc = find_child(box, "minus"); - rc = (this === tab_rc); - motif["rc"] = rc; - toggle_class(logo_box, "show_rc_logo", rc); - toggle_class(tab_st, "active", !rc); - toggle_class(tab_rc, "active", rc); -} - -function action_rc_tab(e) { - "use strict"; - var box, logo_box, tab_st, tab_rc, rc; - 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(); - } - box = find_parent(this, "expanded_motif"); - logo_box = find_child(box, "tvar_logo"); - tab_st = find_child(box, "tvar_tab"); - tab_rc = find_child(box, "tvar_tab_rc"); - rc = (this === tab_rc); - box.data_motif["rc"] = rc; - toggle_class(logo_box, "show_rc_logo", rc); - toggle_class(tab_st, "activeTab", !rc); - toggle_class(tab_rc, "activeTab", rc); -} - -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); - } -} - -function action_seqs_filter() { - "use strict"; - var block_container; - block_container = $("blocks"); - if ($("rdo_all_seqs").checked) { - toggle_class(block_container, "hide_empty_seqs", false); - toggle_class(block_container, "hide_only_scan", false); - } else if ($("rdo_sites_and_scan").checked) { - toggle_class(block_container, "hide_empty_seqs", true); - toggle_class(block_container, "hide_only_scan", false); - } else if ($("rdo_sites_only").checked) { - toggle_class(block_container, "hide_empty_seqs", true); - toggle_class(block_container, "hide_only_scan", true); - } -} - -function action_outpop_format() { - update_outpop_format(current_motif); -} - -// -// page_loaded -// -// Called when the page has loaded for the first time. -/// -function page_loaded() { - post_load_setup(); -} - -// -// page_loaded -// -// Called when a cached page is reshown. -/// -function page_shown(e) { - if (e.persisted) post_load_setup(); -} - -// -// page_loaded -// -// Called when the page is resized -/// -function page_resized() { - var page, blocks_scroll; - update_scroll_pad(); - page = (document.compatMode === "CSS1Compat") ? document.documentElement : document.body; - blocks_scroll = $("blocks_scroll"); - if (blocks_scroll) { - blocks_scroll.style.maxHeight = Math.max(page.clientHeight - 300, 300) + "px"; - } -} - -// -// pre_load_setup -// -// Run before the page is displayed -/// -function pre_load_setup() { - var start, hue, sat, light, divisions; - var i, j, motifs, motif, sites, site, sequences, sequence; - var max_seq_len; - motifs = data["motifs"]; - sequences = data["sequence_db"]["sequences"]; - max_seq_len = 1; - for (i = 0; i < sequences.length; i++) { - sequence = sequences[i]; - sequence["sites"] = []; - if (sequence["length"] > max_seq_len) { - max_seq_len = sequence["length"]; - } - } - data["sequence_db"]["max_length"] = max_seq_len; - // use hsl colours - start = 0; //red - sat = 100; - light = 50; - for (i = 0; i < motifs.length; i++) { - motif = motifs[i]; - // give the motif a colour - divisions = 1 << Math.ceil(Math.log(i + 1) / Math.LN2); - hue = start + (360 / divisions) * ((i - (divisions >> 1)) * 2 + 1); - motif["colour"] = "hsl(" + hue + ", " + sat + "%, " + light + "%)"; - // associate sites with sequences as well - // to make generating the block diagram easier - sites = motif["sites"]; - for (j = 0; j < sites.length; j++) { - site = sites[j]; - sequence = sequences[site["seq"]]; - // record the motif index - site["motif"] = i; - // add the site to the sequence - sequence["sites"].push(site); - } - } -} - -// -// post_load_setup -// -// Run when the page has loaded, or been reloaded. -// -function post_load_setup() { - update_scroll_pad(); - if (data["motifs"].length > 0) { - make_motifs(); - make_blocks(); - } else { - $("motifs").innerHTML = "<p>No significant motifs found!</p>"; // clear content - $("motifs").innerHTML += "<p><b>" + data["stop_reason"] + "</b></p>"; - $("blocks").innerHTML = "<p>No significant motifs found!</p>"; - } -} - -pre_load_setup(); -</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> -.block_td { - height:25px; -} -.block_container { - position:relative; - box-sizing: border-box; - height: 25px; - padding: 0px; - margin: 0px; - margin-left: 1em; -} -.block_label { - position: absolute; - display: inline-block; - padding: 3px; - z-index: 4; - top: 6px; - height: 12px; - line-height: 12px; - font-size: 12px; - background-color: white; - border: 1px solid black; - -moz-border-radius: 12px; - -webkit-border-radius: 12px; - border-radius: 12px; - transform: translateX(-50%); -} -.block_motif { - position: absolute; - z-index: 3; - top: 0px; - box-sizing: border-box; - border: 1px solid black; - height: 12px; - background-color: cyan; -} -.block_motif.top { - border-bottom-width: 0; -} -.block_motif.bottom { - border-top-width: 0; -} -.block_motif.scanned_site { - opacity: 0.3; -} -.block_motif.scanned_site.active { - opacity: 0.9; -} -.block_region { - position:absolute; - z-index:6; - height:25px; - top:0px; -} -.block_region.main { - z-index:8; -} -.block_region.scanned_site { - z-index:5; -} -.block_region.scanned_site.main { - z-index:7; -} -.block_region.top { - height:13px; -} -.block_region.bottom { - height:13px; - top:12px; -} -.block_rule { - position:absolute; - z-index:2; - width:100%; - height:1px; - top:12px; - left:0px; - background-color:gray; -} -.block_plus_sym { - position:absolute; - z-index:4; - line-height:12px; - top:0px; - left:-1em; -} -.block_minus_sym { - position:absolute; - z-index:4; - line-height:12px; - top:13px; - left:-1em; -} - -.tic_major { - position:absolute; - top:0em; - height:0.5em; - width: 2px; - margin-left: -1px; - background-color: blue; -} -.tic_minor { - position:absolute; - top:0em; - height:0.2em; - width: 1px; - margin-left: -0.5px; - background-color: blue; -} -.tic_label { - position:absolute; - display: inline-block; - top:0.5em; - height: 1em; - color: blue; - transform: translateX(-50%); -} - -.block_needle { - position:absolute; - z-index:4; - height:30px; - width:1px; - top:-2px; - background-color:gray; -} -.block_needle.right { - height: 60px; -} -.block_handle { - position: absolute; - display: inline-block; - z-index: 5; - top: 27px; - min-width: 3ex; - text-align: center; - font-size: 12px; - line-height: 12px; - transform: translateX(-50%); - background-color: LightGrey; - border:3px outset grey; - cursor: pointer; - -webkit-user-select: none; /* Chrome/Safari */ - -moz-user-select: none; /* Firefox */ - -ms-user-select: none; /* IE10+ */ - /* Rules below not implemented in browsers yet */ - -o-user-select: none; - user-select: none; -} -.block_handle.right { - top: 47px; -} - -.legend_container { - text-align: right; -} -.legend_entry { - display: inline-block; - padding: 5px; -} -div.legend_swatch { - box-sizing: border-box; - width: 15px; - height: 15px; - border: 1px solid black; - background-color: cyan; - float: left; -} -div.legend_swatch input { - display: none; -} -.legend_text { - line-height: 15px; - margin-left: 20px; -} -</style> - <style> -/* meme output specific css */ - -div.pop_block { - position:absolute; - z-index:5; - padding: 5px; - border: 1px solid black; - display: inline-block; - background-color: white; -} - -#measure_match { - position: absolute; - visibility: hidden; - height: auto; - width: auto; - white-space: nowrap; -} - -div.template { - position: absolute; - z-index: 1; - left: 0; - top: 0; - visibility: hidden; -} - -table.block_information { - margin-left: auto; - margin-right: auto; -} - -table.block_information * th { - text-align: right; -} - -*.hide_empty_seqs * tr.empty_seq { - display: none; -} - -*.hide_only_scan * tr.only_scan { - display: none; -} - -*.hide_only_scan * div.scanned_site { - display: none; -} - -td.symaction { - text-align: center; - text-decoration: underline; - font-size: 20px; - cursor: pointer; -} -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.actionbutton { - display:inline-block; - cursor: pointer; - font-size: 18px; - line-height:20px; - padding: 5px; - margin: 10px 0; - border: 1px solid black; -} - -div.actionbutton:hover { - color:#FFF; - background-color:#000; -} - -div.param_box { - display: inline-block; - margin-right: 20px; -} - -span.param { - font-weight: bold; -} - -div.box + div.box { - margin-top: 5px; -} - -div.sites_outer { - position: relative; - padding-top: 20px; /* height of header */ - display: inline-block; -} - -div.sites_inner { - overflow-x: hidden; - overflow-y: auto; - max-height: 200px; -} -table.sites_tbl { - border-collapse: collapse; -} - -div.sites_th_inner { - position: absolute; - top: 0; - line-height: 20px; /* height of header */ - text-align: left; - padding-left: 5px; -} -th.nopad div.sites_th_inner { - padding-left: 0; -} -div.sites_th_hidden { - visibility: hidden; - height: 0; - padding: 0 10px; -} -th.nopad div.sites_th_hidden { - padding: 0; -} -div.sites_inner * th { - height: 0; -} - -table.sites_tbl { - overflow-x: hidden; - overflow-y: auto; -} - -.site_num { - text-align: right; -} -.site_name { - padding:0px 5px; - text-align:left; -} -.site_strand { - padding:0px 5px; - text-align:center; -} -.norc .site_strand, .norc .site_strand_title { - display: none; -} -.site_start { - padding:0px 15px; - text-align: right; -} -.site_pvalue { - text-align:center; - padding:0px 15px; - text-align:right; - white-space: nowrap; -} -.lflank, .rflank, .match, .alpha_symbol { - font-weight:bold; - font-size:15px; - font-family: 'Courier New', Courier, monospace; - color:gray; -} - -.site.lflank { - text-align:right; - padding-right:5px; - color:gray; -} -.site.match { - text-align:center; -} -.site.rflank { - text-align:left; - padding-left:5px; - padding-right: 20px; -} - -th.stop_reason { - text-align: left; - padding-right: 10px; -} - -th.motif_ordinal { - -} -td.motif_ordinal { - text-align: right; - 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_nsites { - text-align: right; - padding-right: 10px; -} -td.motif_nsites { - text-align: right; - padding-right: 20px; -} -th.motif_width { - text-align: right; - padding-right: 5px; -} -td.motif_width { - text-align: right; - padding-right: 15px; -} -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.motif_download { - padding-left: 5px; -} -td.motif_download { - text-align: center; - padding-left: 5px; -} - - -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.tabCenter { - max-width: 100%; - overflow-x: auto; - height: 200px; - overflow-y: hidden; -} - -canvas.logo_rc { - display:none; -} -.show_rc_logo > canvas { - display: none; -} -.show_rc_logo > canvas.logo_rc { - display: block; -} - -canvas.scan_logo { - margin-left: 10px; -} - -div.blocks_outer { - position: relative; - padding-top: 20px; /* height of header */ -} - -div.blocks_inner { - overflow-x: hidden; - overflow-y: auto; - max-height: 200px; -} -table.blocks_tbl { - border-collapse: collapse; - width: 100%; -} - -div.blocks_th_inner { - position: absolute; - top: 0; - line-height: 20px; /* height of header */ - text-align: left; - padding-left: 5px; -} -th.nopad div.blocks_th_inner { - padding-left: 0; -} -div.blocks_th_hidden { - visibility: hidden; - height: 0; - padding: 0 10px; -} -th.nopad div.blocks_th_hidden { - padding: 0; -} -div.blocks_inner * th { - height: 0; -} - -table.blocks_tbl { - overflow-x: hidden; - overflow-y: auto; -} -td.block_td { - width: 99%; -} - -*.blockdiag_num { - text-align: right; -} - -td.blockdiag_name { - text-align: left; - padding:0px 10px; -} - -td.blockdiag_pvalue { - padding:0px 10px; - text-align:right; - white-space: nowrap; -} - -div.preview_btn { - border: 2px solid white; - height: 16px; - width: 16px; - font-size: 12px; - line-height: 16px; - text-align: center; - cursor: pointer; -} -div.preview_btn + div.preview_btn { - margin-top: 3px; -} - -div.preview_btn.active { - border: 2px solid black; - cursor: default; -} - -div.preview_btn:hover { - background-color: black; - color: white; - border-color: black; -} - -div.preview_btn.active:hover { - background-color: white; - color: black; - border-color: black; -} - - -div.preview_btn_box { - position: absolute; - left: 0px; - top: 0px; - padding: 3px; -} - -div.preview_logo_box { - height: 50px; - overflow-y: hidden; -} - -div.preview_btn_box + div.preview_logo_box { - margin-left: 25px; -} - -div.preview_box { - position: relative; -} - -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; -} - -div.programs_scroll { - width: 100%; - height: 90px; - overflow-y: auto; - overflow-x: hidden; - margin: 0 auto; -} -table.inputs, table.alpha_bg_table { - margin-top: 20px; - border-collapse:collapse; -} -table.inputs * td, table.inputs * th, table.alpha_bg_table * td, table.alpha_bg_table * th { - padding-left: 15px; - padding-right: 15px; - padding-top: 1px; - padding-bottom: 1px; -} - -table.hide_psp td.col_psp, table.hide_psp th.col_psp { - display: none; -} - -/* program settings */ -span.mod_oops, span.mod_zoops, span.mod_anr { - display: none; -} -td.oops span.mod_oops,td.zoops span.mod_zoops, td.anr span.mod_anr { - display: inline; -} -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; -} -span.spmap_uni, span.spmap_pam { - display: none; -} -td.uni span.spmap_uni, td.pam span.spmap_pam { - display: inline; -} -span.prior_dirichlet, span.prior_dmix, span.prior_mega, span.prior_megap, span.prior_addone { - display: none; -} -td.dirichlet span.prior_dirichlet, td.dmix span.prior_dmix, td.mega span.prior_mega, -td.megap span.prior_megap, td.addone span.prior_addone { - display: inline; -} -span.noendgaps_on, span.noendgaps_off { - display: none; -} -td.on span.noendgaps_on, td.off span.noendgaps_off { - display: inline; -} -span.substring_on, span.substring_off { - display: none; -} -td.on span.substring_on, td.off span.substring_off { - display: inline; -} -</style> - </head> - <body onload="page_loaded()" onpageshow="page_shown(event)" onresize="page_resized()"> - <!-- --> - <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 style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_ev"> - <p>The statistical significance of the motif. MEME usually finds the most - statistically significant (low E-value) motifs first. It is unusual to - consider a motif with an E-value larger than 0.05 significant so, as an - additional indicator, MEME displays these partially transparent.</p> - <p>The E-value of a motif is based on its log likelihood ratio, width, - sites, the background letter frequencies (given in the command line - summary), and the size of the training set.</p> - <p>The E-value is an estimate of the expected number of motifs with the - given log likelihood ratio (or higher), and with the same width and site - count, that one would find in a similarly sized set of random - sequences (sequences where each position is independent and letters are - chosen according to the background letter frequencies).</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_sites"> - <p>The number of sites contributing to the construction of the motif.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_width"> - <p>The width of the motif. Each motif describes a pattern of a fixed - width, as no gaps are allowed in MEME motifs.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_more"> - <p>Click on the blue symbol below to reveal more information about this motif.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_submit_dl"> - <p>Click on the blue symbol below to reveal options allowing you - to submit this motif to another MEME Suite motif analysis program, to download this - motif in various text formats, or to download a sequence "logo" of - this motif PNG or EPS format.</p> - <h5>Supported Programs</h5> - <dl> - <dt>Tomtom</dt> - <dd>Tomtom is a tool for searching for similar known motifs. - [<a href="http://meme-suite.org/doc/tomtom.html?man_type=web">manual</a>]</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. - [<a href="http://meme-suite.org/doc/mast.html?man_type=web">manual</a>]</dd> - <dt>FIMO</dt> - <dd>FIMO is a tool for searching biological sequence databases for - sequences that contain one or more known motifs. - [<a href="http://meme-suite.org/doc/fimo.html?man_type=web">manual</a>]</dd> - <dt>GOMO</dt> - <dd>GOMO is a tool for identifying possible roles (Gene Ontology - terms) for DNA binding motifs. - [<a href="http://meme-suite.org/doc/gomo.html?man_type=web">manual</a>]</dd> - <dt>SpaMo</dt> - <dd>SpaMo is a tool for inferring possible transcription factor - complexes by finding motifs with enriched spacings. - [<a href="http://meme-suite.org/doc/spamo.html?man_type=web">manual</a>]</dd> - </dl> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_llr"> - <p>The log likelihood ratio of the motif.The log likelihood ratio is the - logarithm of the ratio of the probability of the occurrences of the motif - given the motif model (likelihood given the motif) versus their - probability given the background model (likelihood given the null model). - (Normally the background model is a 0-order Markov model using the - background letter frequencies, but higher order Markov models may be - specified via the -bfile option to MEME.).</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_ic"> - <p>The information content of the motif in bits. It is equal to the sum - of the uncorrected information content, R(), in the columns of the pwm. - This is equal relative entropy of the motif relative to a uniform - background frequency model.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_re"> - <p>The relative entropy of the motif.</p> - - <p style="font-family: monospace;">re = llr / (sites * ln(2))</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_bt"> - <p>The Bayes Threshold.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_site_strand"> - <p>The strand used for the motif site.</p> - <dl> - <dt>+</dt> - <dd>The motif site was found in the sequence as it was supplied.</dd> - <dt>-</dt> - <dd>The motif site was found in the reverse complement of the supplied sequence.</dd> - </dl> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_site_start"> - <p>The position in the sequence where the motif site starts. If a motif - started right at the begining of a sequence it would be described as - starting at position 1.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_site_pvalue"> - <p>The probability that an equal or better site would be found in a - random sequence of the same length conforming to the background letter - frequencies.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_site_match"> - <p>A motif site with the 10 flanking letters on either side.</p> - <p>When the site is not on the given strand then the site - and both flanks are reverse complemented so they align.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_seq_name"> - <p>The name of the sequences as given in the FASTA file.</p> - <p>The number to the left of the sequence name is the ordinal - of the sequence.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_motif_sites"> - <p>These are the motif sites predicted by MEME and used to build the motif.</p> - <p>These sites are shown in solid color and hovering the cursor - over a site will reveal details about the site. Only sequences - that contain a motif site are shown.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_scanned_sites"> - <p>These are the motif sites predicted by MEME plus - any additional sites detected using a motif scanning - algorithm.</p> - <p>These MEME sites are shown in solid color and - additional scanned sites are shown in transparent color. - Hovering the cursor over a site will reveal details about the site. - Only sequences containing a predicted or scanned motif site are shown.</p> - <p>The scanned sites are predicted using a - log-odds scoring matrix constructed from the MEME sites. - Only scanned sites with position <i>p</i>-values less - than 0.0001 are shown.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_all_sequences"> - <p>These are the same sites as shown by selecting the - "Motif Sites + Scanned Sites" button except that all - sequences, including those with no sites, are included - in the diagram.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_seq_pvalue"> - <p>This is the combined match <i>p</i>-value.</p> - <p>The combined match <i>p</i>-value is defined as the probability that a - random sequence (with the same length and conforming to the background) - would have position <i>p</i>-values such that the product is smaller - or equal to the value calulated for the sequence under test.</p> - <p>The position <i>p</i>-value is defined as the probability that a - random sequence (with the same length and conforming to the background) - would have a match to the motif under test with a score greater or equal - to the largest found in the sequence under test.</p> - <p>Hovering your mouse over a motif site in the motif location - block diagram will show its position <i>p</i>-value and other information - about the site.</p> - - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motif_location"> - <p>This diagram shows the location of motif sites.</p> - <p>Each block shows the position and strength of a motif - site. The height of a block gives an indication of the - significance of the site as taller blocks are more significant. - The height is calculated to be proportional to the negative - logarithm of the <i>p</i>-value of the site, truncated at - the height for a <i>p</i>-value of 1e-10.</p> - <p>For complementable alphabets (like DNA), sites on the - positive strand are shown above the line, - sites on the negative strand are shown below.</p> - <p>Placing the cursor - over a motif site will reveal more information about the site - including its position <i>p</i>-value. (See the help - for the <i>p</i>-value column for an explanation of position - <i>p</i>-values.)</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_seq_source"> - <p>The name of the file of sequences input to MEME.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_psp_source"> - <p>The position specific priors file used by MEME to find the motifs.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_seq_alph"> - <p>The alphabet used by the sequences.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_seq_count"> - <p>The number of sequences provided as input to MEME.</p> - <div style="float:right; bottom:0px;">[ - <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 style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_alph_freq"> - <p>The frequency of the alphabet symbol in the dataset with a pseudocount - so it is never zero.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_alph_bg"> - <p>The frequency of the alphabet symbol as defined by the background model.</p> - <div style="float:right; bottom:0px;">[ - <a href="javascript:help_popup()">close</a> ]</div> - </div> - - <!-- templates --> - <div id="measure_match" class="match"></div> - <div class="template pop_block" id="tmpl_block_info"> - <div> - <span class="tvar_logo_pad lflank" style="visibility:hidden;"></span> - <span class="tvar_logo"></span> - </div> - <div class="block_sequence_fragment"> - <span class="tvar_lflank lflank"></span> - <span class="tvar_match match"></span> - <span class="tvar_rflank rflank"></span> - </div> - <table class="block_information"> - <tr><th>Motif</th><td class="tvar_motif">1</td></tr> - <tr><th><i>p</i>-value</th><td class="tvar_pvalue">8.23e-7</td></tr> - <tr><th>Start</th><td class="tvar_start">23</td></tr> - <tr><th>End</th><td class="tvar_end">33</td></tr> - </table> - </div> - - <div class="template pop_block" id="tmpl_scan_info"> - <h5>Scanned Site</h5> - <div class="tvar_logo"></div> - <table class="block_information"> - <tr><th>Motif</th><td class="tvar_motif">1</td></tr> - <tr><th><i>p</i>-value</th><td class="tvar_pvalue">8.23e-7</td></tr> - <tr><th>Start</th><td class="tvar_start">23</td></tr> - <tr><th>End</th><td class="tvar_end">33</td></tr> - </table> - </div> - - <div class="template box expanded_motif" id="tmpl_motif_expanded"> - <div style="position: relative; min-height: 20px"> - <div class="param_box"> - <span class="param"><span class="tvar_ordinal"></span>.</span> - </div> - <div class="sym_btn positioned tvar_less" tabindex="0" - title="Show less information.">↥</div> - <div class="sym_btn positioned tvar_submit" tabindex="0" - title="Submit the motif to another MEME Suite program or download it.">⇢</div> - </div> - <div> - <div class="param_box"> - <span class="param"><i>E</i>-value:</span> - <span class="tvar_evalue"></span> - <div class="help" data-topic="pop_ev"></div> - </div> - <div class="param_box"> - <span class="param">Site Count:</span> - <span class="tvar_site_count"></span> - <div class="help" data-topic="pop_sites"></div> - </div> - <div class="param_box"> - <span class="param">Width:</span> - <span class="tvar_width"></span> - <div class="help" data-topic="pop_width"></div> - </div> - </div> - <div class="tabMain base"> - <div class="tabCenter tvar_logo"></div> - </div> - <div class="tabArea base"> - <span class="tvar_tab tab" tabindex="0">Standard</span><span - class="tvar_tab_rc tab middle" tabindex="0">Reverse - Complement</span> - </div> - <div style="padding: 10px 0"> - <div class="param_box"> - <span class="param">Log Likelihood Ratio:</span> - <span class="tvar_llr"></span> - <div class="help" data-topic="pop_llr"></div> - </div> - <div class="param_box"> - <span class="param">Information Content:</span> - <span class="tvar_ic"></span> - <div class="help" data-topic="pop_ic"></div> - </div> - <div class="param_box"> - <span class="param">Relative Entropy:</span> - <span class="tvar_re"></span> - <div class="help" data-topic="pop_re"></div> - </div> - <div class="param_box"> - <span class="param">Bayes Threshold:</span> - <span class="tvar_bt"></span> - <div class="help" data-topic="pop_bt"></div> - </div> - </div> - <div class="tvar_sites"></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">⇧</span><span class="active">⬆</span> - </div> - <div id="outpop_num" class="navnum"></div> - <div id="outpop_next" class="navarrow" tabindex="0"> - <span class="inactive">⇩</span><span class="active">⬇</span> - </div> - </div> - <div id="logo_box" style="height: 100px; margin-right: 40px;"> - <canvas id="outpop_logo" height="100" width="580"></canvas> - <canvas id="outpop_logo_rc" class="logo_rc" height="100" width="580"></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> - <option value="3">FASTA</option> - <option value="4">Raw</option> - </select> - </div> - <form id="text_form" method="post" action=""> - <script>$("text_form").action = site_url + "/utilities/save_generated_file";</script> - <input type="hidden" id="text_name" name="name" value="motif.txt"> - <input type="hidden" name="mime_type" value="text/plain"> - <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> - </form> - </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="MEME"/> - <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"/> 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"/> 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 src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAD4AAABGCAYAAACUsCfoAAAAAXNSR0IArs4c6QAAAAZiS0dEAP8A/wD/oL2nkwAAAAlwSFlzAAALEgAACxIB0t1+/AAAAAd0SU1FB9wLHAInL7an9JAAAA8eSURBVHja7ZpZbxv3ucZ/s3AZ7qQkypZELZS3WHKiRJbTFnHqOjZcGzCQBf0A7cUB8glOb89dz30vChRp7xK0aZo4TYq6dtKqSew6iuJWpmPJlrVFFCmKI+7LLJw5F81MFZyec5rTILJaP8AAnAty+Pzf933ebeAhHuIhHuIhHmJPo6TpaeGLfimTydhLS0sUCgWazSbVahXDMOh0Ong8HiKRCAMDAxw+fJhHH31UeFDJ/91/bHp62r558ya6rmOaJuvr6+TzeYrFIoZhAOD1epFlmWAwSDqdZnR0lCNHjjA+Ps7+/fuFPUU8k8nYV69epVKpEA6HuXPnDrOzs7RaLbxeL93d3fj9foLBIB6Ph0ajQaVSAUBRFNLpNI888ggHDhzg3Llzwp4g/vbbb9szMzPE43FyuRwffPAB2WyWnp4ehoaGiMVi2LZNvV6n3W7j8/mIRqN4vV4ajQa1Wo2trS0OHTqEaZo89dRTfO973xMeaOKvvfaaffv2bcLhMCsrK/z+979HVVWOHz/O0NAQxWIRVVVRVRW/348oihiGgSiKxGIxurq6CAQCBINB3n//fcbGxiiXyxw7dowXX3yx1Nvbm3igiBcKhY9u3rw5OTMzQzgc5vbt23zwwQfIsszExAS2bZPP55EkiVAoRCQSIRwOI8sy5XKZ7e1tWq0WnU6HTqfD4OAggUAAVVXpdDo0m01GRkb44Q9/KDxQxH/729/as7Oz+Hw+Pv30U37zm9/g9Xrp6emht7eXYDCI3+/H6/UiCALtdhvLsuh0OkiSRCAQQJZl6vU65XKZ1dVV+vv7SSQS5PN5vF4vhUKBgwcP8qMf/WjXyIs7b+7cuWMvLi4iCAL1ep133nkHXdcZHh4mlUoRDofp7+8nHo9jGAaCIBCPx+nr6yOdTtPX14fH40HTNGRZpqenh76+PrLZLMVikYGBARRFwTRN5ubm+PGPf2zvFnF5583c3BzlchlZlrl16xa1Wo2xsTGi0SiDg4OutUzTJBKJIIoiXq+XQCBAIpEgFAphmiaqqlIoFKjVaoyOjhKJRFhfXycajRKNRunp6WFhYYG33nqLQqHwUTKZPP5VE5ecD5cvX7bv37+Poijkcjl++ctfMjo6ytDQEMlkEo/HQ7lcpt1u4/F4kGUZQRDw+Xz09fVx4MABRkZGSKVSdHV10el0KJVK1Ot14vE4kiRRKpVQFIV4PI5t23z66ad0Op2+K1eu/MeuWVxVVUzTRNd17t27RzKZJJFIEI1GEUWRdruNaZqIoogkSYiiiCiK+P1+AoEA0WiUQ4cOCQCbm5vb5XI5Xi6XWVtbw7ZtZFnG7/e7D1YUhWAwSLVaJZvN2v39/cJXHuOLi4t2sVhEEAS2t7eZn59n//79JBIJwuEwlmXRbDbRdR1BEBAEAcuysCwL2/5LmIriX+Wit7c3EY/HSSQSeDweDMPA4/EQCoWwbRvbtgmFQoTDYUqlErlcbnfE7f79+64gbWxs0G63icViRCIRBEHANE0Mw0CSJLxer0vSUfVKpUKxWGRtbc12UmKr1cI0TQD3t4PBoHtwgUAAv99Ps9kkn8/vjrjlcjlkWabdbrO8vEx3dzfhcJhoNEq9XkfTNERRxOfz4fV6sW0bSZJcBS+VSqytrdFqtbh+/bq9sLBALpdje3sbXddd4jutLwh/8WzLslBVdXeI12o1RFFkc3PTLTFjsRixWAxVVbEsC1mWkSTJdVXnMgyDarWKrusUi0X8fj+WZVGtVimXyxiGgW3bblh4PB78fj/tdhvbthFF0a3tv3Liuq4jiiKFQgFZlolEInR3d6MoConEXytLp1Bx0Ol0sG0bXdfRdZ1arYYgCNi2jaZptFot1zOcQ3LSnxMGzsHvCnHH/RqNBtFoFEmSCIfDAAwNDWFZFu12m0ajgaZpWJbl/oDH4/ncoTii5xBz1N+2bTqdDrIs4/P53MxgWRaapu2exQOBgHsAnU6HdrvN5uYmgUCASCRCJBIhkUhgmibNZpNarUaj0XAt71jfET1RFN1YliTJfUa73SaZTLK1tUWtVkPTNKampnaHuFNGyrKM1+t141bTNGq1GrVazS1EIpEI8XjcLWJqtdrnYthNF58pv23beL1eJEly1VzXder1Oq1Wi2AwiK7ru0PcSSs73bBYLBIMBpEkCdM0qVQq6LpOq9UiHA673Vmn08E0TfdyRM85CNM08Xq9bkoMhULugRqGgd/v3z1Xl2X5c24aDodRVZV4PO7W406/raoqtVqNYDCIz+dDURQ3vp3LuXeEz4nlTqdDOBxG13U3TBRF2b0mJRAI0Gg0EAQBTdPw+/2Uy2VXoJzRkkPEifNWq0UgEHCLEsedLcty1X1nzIdCIRRFoVQqUSqVsCyLYDBIPB7fncotlUq5JaWu6xiGgWmabG1tuanINE0EQXAPwSlk6vU6zWaTdruNpmnud3eWsk6fnkwmMU2Tzc1NVFVFURSi0SjpdHp3iB89ehRRFOnt7XWHCNFolFwu58ar08AYhuEWNH6/H4/H8zlL71R4J5XJskwgECAWi5HP51lZWaHVajE8PEw8Hufw4cO7Q3zfvn0C4E5MNU2jq6uLarVKPp//nPA5hYgzcYlEIoRCIfcQHLd3SDvEPR4PHo+HfD5PPp9HEARGRkYIhUIMDQ0Ju0Ic4NixY3g8Hnp7e8lms8RiMcLhMNlsFk3TXHW3bZtgMOjmfScEvF6vW8s7qczxgGazSSAQ4M9//jOqqlKpVHj88cfx+XyMjY3t7ujp1KlTQrlcdicupVKJkZER1tbWuHfvHqqqEolEiMVitNtt6vW6q+iNRoNms4kkSfh8PtfC0WgURVHo7+9nc3OTjY0N3n33XQYGBkilUiSTSU6ePCnsKnGA559/nkqlwtGjR8nn8/j9fh5//HEsy+LWrVvMz8+j6zqhUAifz4dhGG7z0mq1UFUVXdeJRCIEg0F32loqlbh37x53796lq6sLRVGIRCJMTEzs2pT1c8Qfe+wxYWpqyv1j2WyWVCpFIpGgUqkwNzfHnTt33JTnDCUlSaK7u5v+/n66u7vxeDxun16r1SgUCly/fp3bt29z+vRpBgcHqdVqRKPRB2uh8LOf/cyemZlhYWGBYDBIJBIBoFgs0mw2CYfDxONxfD4fg4ODros7vXWhUKDT6bg5/v3332dlZYWhoSHS6TSnTp1i3759VKtVzpw5w1c9dvpfNymvvPKKff36dbLZLIqiuBVWs9mk0WhgWZbbn4fDYURRRNM0AoEAvb29+Hw+Go0Gly9fZmNjg4mJCcbGxti/f787mJyfn6darTI5OcmJEyeEB4J4sVj8wfT09L/Pzs6SzWbdpWEikXBJGoZBs9kkGo0iyzKmabrLhtXVVTKZDJubm5w9e5YjR44wMDDAd7/7XWF2dtZeXFzkyJEj7pZm//79pFIpenp6vhIP+D8f8NZbb9nr6+ssLy+ztbXl1t5er9fdhxeLRSRJoquri0qlQiaTYXt7m0gkwpkzZ5BlmbGxMV544QX3eR9//LE9Pz/PsWPHuHHjBouLi0iSxMDAAMePH2dqakrYVeIAKysr9u3bt1leXnZn65qmoeu6W9AYhkGj0aBYLGKaJocOHeLRRx8lkUgwOTnpjp4d5HI5++OPP6ZcLjM+Ps61a9dYWFig2Wzi9Xp5/vnnOX36tLCrxHfi1q1b9tLSkuv+9XrdbTEVRSEWi5FMJhkdHWV4eJiDBw/+j8/Y2tr6+WuvvfYdwzBIpVJIkoSqqszPz1Ov17lw4QJf+9rXziYSiau7TvxvoVQqpUul0n2n2/oibz+899579k9/+lPC4TCnTp3i61//Orlcjp/85CdomsbTTz/NiRMn/pvH/CMotrQfyF/GD8Xj8aX/7yEePnx4dnx8fPJ3v/sdiqIwODjI5OSkcOPGDfvNN9/kypUr5PN5MpmMPT4+/qWQ71Z835fZZSSTyeMrKyt2vV7n7t27vPrqq1y7ds1+8sknhT/+8Y/2pUuXuHnzJs1mk6WlJTudTn8p5EUeAAwPDwvPPfccBw4cYHV1lc+KJ3t0dPTVixcvcvDgQebn53n55ZeZmZn5h1fLalv/twfqTaRMJmP/4he/YH19nSNHjnDhwgVisRj37t3jnXfeYWFhgQMHDnD+/HmeeuopYc9b3MH4+LjwrW99C0EQuHXrFtPT09RqNfr7+zlx4gTpdJqNjQ3efPNN3njjDbtYLP5gV1X9y8bly5ft119/nUqlwsmTJzl9+jQej4ePPvqITz75hLW1NYLBIJOTk5w7d46+vr4vzEN+EImfO3dOuHr1qv3666/z3nvvoWkaZ8+e5YknnnBXU5qmcfPmTQzDYG1tzR4cHBT2vMUdTE9P25cuXaJQKDA5OcmFCxfQdZ3Z2VkWFhbY2NhAURRSqRTPPvssY2Njwp62uINvfvObwp/+9Cf7V7/6FTdu3KDT6XD+/HmmpqbcoaaqqszOzmIYxhfK9Q80cYCJiQlhbm7OFgSBubk5vF4vzzzzDBMTE+7CMRgMsrCwwEsvvcS1a9fsb3zjG8KedvWd+OSTT+y3336bubk5JicnOXnyJJZl8eGHH7K2tkahUKDRaLBv3z4uXrzI2bNnhT1tcQdHjx4VMpmM3el0WFxcJBQKMTU1xbFjx6hWqwC0221WVlb49a9/zY0bN+wnn3xS2BN5/O/J88899xzDw8NkMhnm5uaIx+M8/fTT9PT0YFkWg4ODrK6u8sorrzA/P2/veVffidXVVfvdd99lenqa8+fPMzo6iqZp/OEPf2BhYYFWq4Usy4yMjHDx4kX+luXlvUh8aGhImJmZsS3L4vr165imSSqVY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alt="MEME Logo"> - <h1>MEME</h1> - <h2>Multiple Em for Motif Elicitation</h2> - </div> - <p> - For further information on how to interpret these results or to get a - copy of the MEME software please access - <a href="http://meme-suite.org/">http://meme-suite.org</a>. - </p> - <p>If you use MEME in your research, please cite the following paper:<br /> - <span class="citation"> - Timothy L. Bailey and Charles Elkan, - "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", - <em>Proceedings of the Second International Conference on Intelligent Systems - for Molecular Biology</em>, pp. 28-36, AAAI Press, Menlo Park, California, 1994. - <a href="http://meme-suite.org/doc/ismb94.pdf">[pdf]</a> - </span> - </p> - </div> - <!-- navigation --> - <div class="pad2"> - <a class="jump" href="#motifs_sec">Discovered Motifs</a> - | - <a class="jump" href="#sites_sec">Motif Locations</a> - | - <a class="jump" href="#inputs_sec">Inputs & Settings</a> - | - <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> - <h2 class="mainh pad2" id="motifs_sec">Discovered Motifs</h2> - <div id="motifs" class="box"> - <p>Please wait... Loading...</p> - <p>If the page has fully loaded and this message does not disappear then an error may have occurred.</p> - </div> - <h2 class="mainh pad2" id="sites_sec">Motif Locations</h2> - <div id="blocks" class="box"> - <p>Please wait... Loading...</p> - <p>If the page has fully loaded and this message does not disappear then an error may have occurred.</p> - </div> - <h2 class="mainh pad2" id="inputs_sec">Inputs & Settings</h2> - <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 class="col_psp">PSP Source <div class="help" data-topic="pop_psp_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_psp" class="col_psp"></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.source; - $("ins_seq_alphabet").innerHTML = meme_alphabet.get_alphabet_name(); - $("ins_seq_count").innerHTML = db.sequences.length; - if (db.psp) { - $("ins_seq_psp").innerHTML = db.psp; - } - toggle_class($("seq_info"), "hide_psp", !(db.psp)); - } - </script> - <h4>Background</h4> - <span id="alpha_bg"></span> - <script> - { - $("alpha_bg").appendChild(make_alpha_bg_table(meme_alphabet, data.sequence_db.freqs)); - } - </script> - <h4>Other Settings</h4> - <table id="tbl_settings" class="inputs hide_advanced"> - <tr> - <th>Motif Site Distribution</th> - <td id="opt_mod"> - <span class="mod_zoops">ZOOPS: Zero or one site per sequence</span> - <span class="mod_oops">OOPS: Exactly one site per sequence</span> - <span class="mod_anr">ANR: Any number of sites per sequence</span> - </td> - </tr> - <tr> - <th>Site Strand Handling</th> - <td id="opt_strand"> - <span class="strand_none">This alphabet only has one strand</span> - <span class="strand_given">Sites must be on the given strand</span> - <span class="strand_both">Sites may be on either strand</span> - </td> - </tr> - <tr> - <th>Maximum Number of Motifs</th> - <td id="opt_nmotifs"></td> - </tr> - <tr> - <th>Motif E-value Threshold</th> - <td id="opt_evt"></td> - </tr> - <tr> - <th>Minimum Motif Width</th> - <td id="opt_minw"></td> - </tr> - <tr> - <th>Maximum Motif Width</th> - <td id="opt_maxw"></td> - </tr> - <tr> - <th>Minimum Sites per Motif</th> - <td id="opt_minsites"></td> - </tr> - <tr> - <th>Maximum Sites per Motif</th> - <td id="opt_maxsites"></td> - </tr> - <tr class="advanced"> - <th>Bias on Number of Sites</th> - <td id="opt_wnsites"></td> - </tr> - <tr class="advanced"> - <th>Sequence Prior</th> - <td id="opt_prior"> - <span class="prior_dirichlet">Simple Dirichlet</span> - <span class="prior_dmix">Dirichlets Mix</span> - <span class="prior_mega">Mega-weight Dirichlets Mix</span> - <span class="prior_megap">Mega-weight Dirichlets Mix Plus</span> - <span class="prior_addone">Add One</span> - </td> - </tr> - <tr class="advanced"> - <th>Sequence Prior Strength</th> - <td id="opt_b"></td> - </tr> - <tr class="advanced"> - <th>EM Starting Point Source</th> - <td id="opt_substring"> - <span class="substring_on">From substrings in input sequences</span> - <span class="substring_off">From strings on command line (-cons)</span> - </td> - </tr> - <tr class="advanced"> - <th>EM Starting Point Map Type</th> - <td id="opt_spmap"> - <span class="spmap_uni">Uniform</span> - <span class="spmap_pam">Point Accepted Mutation</span> - </td> - </tr> - <tr class="advanced"> - <th>EM Starting Point Fuzz</th> - <td id="opt_spfuzz"></td> - </tr> - <tr class="advanced"> - <th>EM Maximum Iterations</th> - <td id="opt_maxiter"></td> - </tr> - <tr class="advanced"> - <th>EM Improvement Threshold</th> - <td id="opt_distance"></td> - </tr> - <tr class="advanced"> - <th>Trim Gap Open Cost</th> - <td id="opt_wg"></td> - </tr> - <tr class="advanced"> - <th>Trim Gap Extend Cost</th> - <td id="opt_ws"></td> - </tr> - <tr class="advanced"> - <th>End Gap Treatment</th> - <td id="opt_noendgaps"> - <span class="noendgaps_on">No cost</span> - <span class="noendgaps_off">Same cost as other gaps</span> - </td> - </tr> - <tr> - <td colspan="2" style="text-align: center"> - <a href="javascript:toggle_class(document.getElementById('tbl_settings'), 'hide_advanced')"> - <span class="show_more">Show Advanced Settings</span> - <span class="show_less">Hide Advanced Settings</span> - </a> - </td> - </tr> - </table> - <script> - { - $("opt_mod").className = data.options.mod; - $("opt_strand").className = (meme_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none"); - $("opt_nmotifs").textContent = data.options.nmotifs; - $("opt_evt").textContent = (typeof data.options.evt === "number" ? data.options.evt : "no limit"); - $("opt_minw").textContent = data.options.minw; - $("opt_maxw").textContent = data.options.maxw; - $("opt_minsites").textContent = data.options.minsites; - $("opt_maxsites").textContent = data.options.maxsites; - $("opt_wnsites").textContent = data.options.wnsites; - $("opt_spmap").className = data.options.spmap; - $("opt_spfuzz").textContent = data.options.spfuzz; - $("opt_prior").className = data.options.prior; - $("opt_b").textContent = data.options.b; - $("opt_maxiter").textContent = data.options.maxiter; - $("opt_distance").textContent = data.options.distance; - $("opt_wg").textContent = data.options.wg; - $("opt_ws").textContent = data.options.ws; - $("opt_noendgaps").className = (data.options.noendgaps ? "on" : "off"); - $("opt_substring").className = (data.options.substring ? "on" : "off"); - } - </script> - </div> - <!-- list information on this program --> - <div id="info_sec" class="bar"> - <div class="subsection"> - <h5 id="version">MEME version</h5> - <span id="ins_version"></span> - (Release date: <span id="ins_release"></span>)<br> - </div> - <script> - $("ins_version").innerHTML = data["version"]; - $("ins_release").innerHTML = data["release"]; - </script> - <div class="subsection"> - <h5 id="reference">Reference</h5> - <span class="citation"> - Timothy L. Bailey and Charles Elkan, - "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", - <em>Proceedings of the Second International Conference on Intelligent Systems - for Molecular Biology</em>, pp. 28-36, AAAI Press, Menlo Park, California, 1994. - </span> - </div> - <div class="subsection"> - <h5 id="command">Command line</h5> - <textarea id="cmd" rows="5" style="width:100%;" readonly="readonly"> - </textarea> - <script>$("cmd").value = data["cmd"].join(" ");</script> - </div> - </div> - - </body> -</html>