Mercurial > repos > iuc > meme_meme
diff test-data/dreme_output_test1.html @ 14:3f0dd362b755 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
| author | iuc |
|---|---|
| date | Wed, 11 Dec 2019 18:05:15 -0500 |
| parents | 57e5d9382f36 |
| children | 19237efe98d1 |
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--- a/test-data/dreme_output_test1.html Thu May 17 14:10:48 2018 -0400 +++ b/test-data/dreme_output_test1.html Wed Dec 11 18:05:15 2019 -0500 @@ -7,10 +7,9 @@ // @JSON_VAR data var data = { "program": "dreme", - "version": "4.12.0", - "release": "Tue Jun 27 16:22:50 2017 -0700", + "version": "5.0.5", "cmd": [ - "dreme", "-o", "./dreme_test1_out", "-p", "dreme_test_sites.fa", + "dreme", "-o", "./dreme_out", "-p", "-norc", "-rna", "-s", "1" ], "options": { @@ -20,95 +19,19 @@ "seed": 1, "stop": { "evalue": "0.05" - } - }, "alphabet": { "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", - "aliases": "T", - "name": "Uracil", - "colour": "008000" - }, { - "symbol": "N", - "aliases": "X.", - "name": "Any base", - "equals": "ACGU" - }, { - "symbol": "V", - "name": "Not U", - "equals": "ACG" - }, { - "symbol": "H", - "name": "Not G", - "equals": "ACU" - }, { - "symbol": "D", - "name": "Not C", - "equals": "AGU" - }, { - "symbol": "B", - "name": "Not A", - "equals": "CGU" - }, { - "symbol": "M", - "name": "Amino", - "equals": "AC" - }, { - "symbol": "R", - "name": "Purine", - "equals": "AG" - }, { - "symbol": "W", - "name": "Weak", - "equals": "AU" - }, { - "symbol": "S", - "name": "Strong", - "equals": "CG" - }, { - "symbol": "Y", - "name": "Pyrimidine", - "equals": "CU" - }, { - "symbol": "K", - "name": "Keto", - "equals": "GU" - } - ] - }, "background": { "freqs": [0.221, 0.245, 0.221, 0.312] - }, - "sequence_db": { - "name": "dreme test sites", - "file": "dreme_test_sites.fa", - "lmod": "Thu Apr 26 15:09:03 CEST 2018", - "count": 1000 - }, "control_db": { "name": "shuffled positive sequences", "from": "shuffled", "count": 1000, "freqs": [0.221, 0.245, 0.221, 0.312] - }, "motifs": [ - { "db": 0, "id": "UUYUCY", "alt": "DREME-1", @@ -126,9 +49,7 @@ [0.000000, 0.000000, 0.000000, 1.000000], [0.000000, 1.000000, 0.000000, 0.000000], [0.000000, 0.474946, 0.000000, 0.525054] - ], "matches": [ - { "seq": "UUUUCC", "p": 147, "n": 75, @@ -140,6059 +61,53 @@ "n": 94, "pvalue": "2.2e-005", "evalue": "1.0e+000" - }, { "seq": "UUCUCU", "p": 94, "n": 51, "pvalue": "1.3e-004", "evalue": "6.1e+000" - }, { "seq": "UUCUCC", "p": 75, "n": 42, "pvalue": "1.1e-003", "evalue": "5.0e+001" - } - ] - }, { - "db": 0, - "id": "YAGG", - "alt": "DREME-2", - "len": 4, - "nsites": 793, - "evalue": "5.1e-012", - "p": 600, - "n": 416, - "pvalue": "1.1e-016", - "unerased_evalue": "2.4e-012", - "pwm": [ - [0.000000, 0.692308, 0.000000, 0.307692], - [1.000000, 0.000000, 0.000000, 0.000000], - [0.000000, 0.000000, 1.000000, 0.000000], - [0.000000, 0.000000, 1.000000, 0.000000] - ], - "matches": [ - { - "seq": "CAGG", - "p": 441, - "n": 304, - "pvalue": "1.5e-010", - "evalue": "6.6e-006" - }, { - "seq": "UAGG", - "p": 232, - "n": 165, - "pvalue": "1.1e-004", - "evalue": "4.7e+000" - } - ] - }, { - "db": 0, - "id": "GAAGAW", - "alt": "DREME-3", - "len": 6, - "nsites": 89, - "evalue": "3.4e-005", - "p": 81, - "n": 22, - "pvalue": "8.2e-010", - "unerased_evalue": "3.5e-004", - "pwm": [ - [0.000000, 0.000000, 1.000000, 0.000000], - [1.000000, 0.000000, 0.000000, 0.000000], - [1.000000, 0.000000, 0.000000, 0.000000], - [0.000000, 0.000000, 1.000000, 0.000000], - [1.000000, 0.000000, 0.000000, 0.000000], - [0.494382, 0.000000, 0.000000, 0.505618] - ], - "matches": [ - { - "seq": "GAAGAU", - "p": 45, - "n": 7, - "pvalue": "2.4e-008", - "evalue": "9.9e-004" - }, { - "seq": "GAAGAA", - "p": 40, - "n": 16, - "pvalue": "7.9e-004", - "evalue": "3.3e+001" - } - ] - }, { - "db": 0, - "id": "SMUGGA", - "alt": "DREME-4", - "len": 6, - "nsites": 119, - "evalue": "3.7e-003", - "p": 110, - "n": 47, - "pvalue": "9.1e-008", - "unerased_evalue": "2.6e-005", - "pwm": [ - [0.000000, 0.529412, 0.470588, 0.000000], - [0.428571, 0.571429, 0.000000, 0.000000], - [0.000000, 0.000000, 0.000000, 1.000000], - [0.000000, 0.000000, 1.000000, 0.000000], - [0.000000, 0.000000, 1.000000, 0.000000], - [1.000000, 0.000000, 0.000000, 0.000000] - ], - "matches": [ - { - "seq": "GAUGGA", - "p": 22, - "n": 6, - "pvalue": "1.7e-003", - "evalue": "7.1e+001" - }, { - "seq": "GCUGGA", - "p": 33, - "n": 14, - "pvalue": "3.6e-003", - "evalue": "1.5e+002" - }, { - "seq": "CCUGGA", - "p": 32, - "n": 15, - "pvalue": "8.6e-003", - "evalue": "3.5e+002" - }, { - "seq": "CAUGGA", - "p": 29, - "n": 13, - "pvalue": "9.1e-003", - "evalue": "3.7e+002" - } - ] - } - ], - "runtime": { - "host": "ThinkPad-T450s", - "when": "Thu May 03 13:22:29 CEST 2018", - "cpu": 13.95, - "real": 13.95, - "stop": "evalue" - } - }; - </script> <script> var site_url = "http://meme-suite.org"; </script> - <script> - -/* - * $ - * - * Shorthand function for getElementById - */ -function $(el) { - return document.getElementById(el); -} - - -/* - * See http://stackoverflow.com/a/5450113/66387 - * Does string multiplication like the perl x operator. - */ -function string_mult(pattern, count) { - if (count < 1) return ''; - var result = ''; - while (count > 1) { - if (count & 1) result += pattern; - count >>= 1, pattern += pattern; - } - return result + pattern; -} - -/* - * See http://stackoverflow.com/questions/814613/how-to-read-get-data-from-a-url-using-javascript - * Slightly modified with information from - * https://developer.mozilla.org/en/DOM/window.location - */ -function parse_params() { - "use strict"; - var search, queryStart, queryEnd, query, params, nvPairs, i, nv, n, v; - search = window.location.search; - queryStart = search.indexOf("?") + 1; - queryEnd = search.indexOf("#") + 1 || search.length + 1; - query = search.slice(queryStart, queryEnd - 1); - - if (query === search || query === "") return {}; - - params = {}; - nvPairs = query.replace(/\+/g, " ").split("&"); - - for (i = 0; i < nvPairs.length; i++) { - nv = nvPairs[i].split("="); - n = decodeURIComponent(nv[0]); - v = decodeURIComponent(nv[1]); - // allow a name to be used multiple times - // storing each value in the array - if (!(n in params)) { - params[n] = []; - } - params[n].push(nv.length === 2 ? v : null); - } - return params; -} - -/* - * coords - * - * Calculates the x and y offset of an element. - * From http://www.quirksmode.org/js/findpos.html - * with alterations to take into account scrolling regions - */ -function coords(elem) { - var myX = myY = 0; - if (elem.getBoundingClientRect) { - var rect; - rect = elem.getBoundingClientRect(); - myX = rect.left + ((typeof window.pageXOffset !== "undefined") ? - window.pageXOffset : document.body.scrollLeft); - myY = rect.top + ((typeof window.pageYOffset !== "undefined") ? - window.pageYOffset : document.body.scrollTop); - } else { - // this fall back doesn't properly handle absolutely positioned elements - // inside a scrollable box - var node; - if (elem.offsetParent) { - // subtract all scrolling - node = elem; - do { - myX -= node.scrollLeft ? node.scrollLeft : 0; - myY -= node.scrollTop ? node.scrollTop : 0; - } while (node = node.parentNode); - // this will include the page scrolling (which is unwanted) so add it back on - myX += (typeof window.pageXOffset !== "undefined") ? window.pageXOffset : document.body.scrollLeft; - myY += (typeof window.pageYOffset !== "undefined") ? window.pageYOffset : document.body.scrollTop; - // sum up offsets - node = elem; - do { - myX += node.offsetLeft; - myY += node.offsetTop; - } while (node = node.offsetParent); - } - } - return [myX, myY]; -} - -/* - * position_popup - * - * Positions a popup relative to an anchor element. - * - * The avaliable positions are: - * 0 - Centered below the anchor. - */ -function position_popup(anchor, popup, position) { - "use strict"; - var a_x, a_y, a_w, a_h, p_x, p_y, p_w, p_h; - var a_xy, spacer, margin, scrollbar, page_w; - // define constants - spacer = 5; - margin = 15; - scrollbar = 15; - // define the positions and widths - a_xy = coords(anchor); - a_x = a_xy[0]; - a_y = a_xy[1]; - a_w = anchor.offsetWidth; - a_h = anchor.offsetHeight; - p_w = popup.offsetWidth; - p_h = popup.offsetHeight; - page_w = null; - if (window.innerWidth) { - page_w = window.innerWidth; - } else if (document.body) { - page_w = document.body.clientWidth; - } - // check the position type is defined - if (typeof position !== "number") { - position = 0; - } - // calculate the popup position - switch (position) { - case 1: - p_x = a_x + a_w + spacer; - p_y = a_y + (a_h / 2) - (p_h / 2); - break; - case 0: - default: - p_x = a_x + (a_w / 2) - (p_w / 2); - p_y = a_y + a_h + spacer; - break; - } - // constrain the popup position - if (p_x < margin) { - p_x = margin; - } else if (page_w != null && (p_x + p_w) > (page_w - margin - scrollbar)) { - p_x = page_w - margin - scrollbar - p_w; - } - if (p_y < margin) { - p_y = margin; - } - // position the popup - popup.style.left = p_x + "px"; - popup.style.top = p_y + "px"; -} - -function lookup_help_popup(popup_id) { - var _body, pop, info; - pop = document.getElementById(popup_id); - if (pop == null) { - _body = document.getElementsByTagName("body")[0]; - pop = document.createElement("div"); - pop.className = "pop_content"; - pop.id = popup_id; - pop.style.backgroundColor = "#FFC"; - pop.style.borderColor = "black"; - info = document.createElement("p"); - info.style.fontWeight = "bold"; - info.appendChild(document.createTextNode("Error: No popup for topic \"" + popup_id + "\".")); - pop.appendChild(info); - // this might cause problems with the menu, but as this only happens - // when something is already wrong I don't think that's too much of a problem - _body.insertBefore(pop, _body.firstChild); - } - if (document.getElementsByTagName('body')[0].hasAttribute("data-autobtns")) { - if (!/\bauto_buttons\b/.test(pop.className)) { - pop.className += " auto_buttons"; - var back_btn_sec = document.createElement("div"); - back_btn_sec.className = "nested_only pop_back_sec"; - var back_btn = document.createElement("span"); - back_btn.className = "pop_back"; - back_btn.appendChild(document.createTextNode("<< back")); - back_btn.addEventListener("click", function(e) { - help_return(); - }, false); - back_btn_sec.appendChild(back_btn); - pop.insertBefore(back_btn_sec, pop.firstChild); - var close_btn_sec = document.createElement("div"); - close_btn_sec.className = "pop_close_sec"; - var close_btn = document.createElement("span"); - close_btn.className = "pop_close"; - close_btn.appendChild(document.createTextNode("close")); - close_btn.addEventListener("click", function(e) { - help_popup(); - }, false); - close_btn_sec.appendChild(close_btn); - pop.appendChild(close_btn_sec); - } - } - return pop; -} - -/* - * help_popup - * - * Moves around help pop-ups so they appear - * below an activator. - */ -function help_popup(activator, popup_id) { - "use strict"; - var pop; - // set default values - if (typeof help_popup.popup === "undefined") { - help_popup.popup = []; - } - if (typeof help_popup.activator === "undefined") { - help_popup.activator = null; - } - var last_pop = (help_popup.popup.length > 0 ? help_popup.popup[help_popup.popup.length - 1] : null); - if (typeof(activator) == "undefined") { // no activator so hide - if (last_pop != null) { - last_pop.style.display = 'none'; - help_popup.popup = []; - } - return; - } - pop = lookup_help_popup(popup_id); - if (pop == last_pop) { - if (activator == help_popup.activator) { - //hide popup (as we've already shown it for the current help button) - last_pop.style.display = 'none'; - help_popup.popup = []; - return; // toggling complete! - } - } else if (last_pop != null) { - //activating different popup so hide current one - last_pop.style.display = 'none'; - } - help_popup.popup = [pop]; - help_popup.activator = activator; - toggle_class(pop, "nested", false); - //must make the popup visible to measure it or it has zero width - pop.style.display = 'block'; - position_popup(activator, pop); -} - -/* - * help_refine - * - * Intended for links within a help popup. Stores a stack of state so - * you can go back. - */ -function help_refine(popup_id) { - if (help_popup.popup == null || help_popup.popup.length == 0 || help_popup.activator == null) { - throw new Error("Can not refine a help popup when one is not shown!"); - } - var pop = lookup_help_popup(popup_id); - var last_pop = help_popup.popup[help_popup.popup.length - 1]; - if (pop == last_pop) return; // slightly odd, but no real cause for alarm - help_popup.popup.push(pop); - toggle_class(pop, "nested", true); - last_pop.style.display = "none"; - //must make the popup visible to measure it or it has zero width - pop.style.display = "block"; - position_popup(help_popup.activator, pop); -} - -/* - * help_return - * - * Intended for links within a help popup. Stores a stack of state so - * you can go back. - */ -function help_return() { - if (help_popup.popup == null || help_popup.popup.length == 0 || help_popup.activator == null) { - throw new Error("Can not return to a earlier help popup when one is not shown!"); - } - var last_pop = help_popup.popup.pop(); - last_pop.style.display = "none"; - var pop = (help_popup.popup.length > 0 ? help_popup.popup[help_popup.popup.length - 1] : null); - if (pop != null) { - toggle_class(pop, "nested", help_popup.popup.length > 1); - pop.style.display = "block"; - position_popup(help_popup.activator, pop); - } else { - help_popup.activator = null; - } -} - -/* - * update_scroll_pad - * - * Creates padding at the bottom of the page to allow - * scrolling of anything into view. - */ -function update_scroll_pad() { - var page, pad; - page = (document.compatMode === "CSS1Compat") ? document.documentElement : document.body; - pad = $("scrollpad"); - if (pad === null) { - pad = document.createElement("div"); - pad.id = 'scrollpad'; - document.getElementsByTagName('body')[0].appendChild(pad); - } - pad.style.height = Math.abs(page.clientHeight - 100) + "px"; -} - -function substitute_classes(node, remove, add) { - "use strict"; - var list, all, i, cls, classes; - list = node.className.split(/\s+/); - all = {}; - for (i = 0; i < list.length; i++) { - if (list[i].length > 0) all[list[i]] = true; - } - for (i = 0; i < remove.length; i++) { - if (all.hasOwnProperty(remove[i])) { - delete all[remove[i]]; - } - } - for (i = 0; i < add.length; i++) { - all[add[i]] = true; - } - classes = ""; - for (cls in all) { - classes += cls + " "; - } - node.className = classes; -} - -/* - * toggle_class - * - * Adds or removes a class from the node. If the parameter 'enabled' is not - * passed then the existence of the class will be toggled, otherwise it will be - * included if enabled is true. - */ -function toggle_class(node, cls, enabled) { - var classes = node.className; - var list = classes.replace(/^\s+/, '').replace(/\s+$/, '').split(/\s+/); - var found = false; - for (var i = 0; i < list.length; i++) { - if (list[i] == cls) { - list.splice(i, 1); - i--; - found = true; - } - } - if (typeof enabled == "undefined") { - if (!found) list.push(cls); - } else { - if (enabled) list.push(cls); - } - node.className = list.join(" "); -} - -/* - * find_child - * - * Searches child nodes in depth first order and returns the first it finds - * with the className specified. - * TODO replace with querySelector - */ -function find_child(node, className) { - var pattern; - if (node == null || typeof node !== "object") { - return null; - } - if (typeof className === "string") { - pattern = new RegExp("\\b" + className + "\\b"); - } else { - pattern = className; - } - if (node.nodeType == Node.ELEMENT_NODE && - pattern.test(node.className)) { - return node; - } else { - var result = null; - for (var i = 0; i < node.childNodes.length; i++) { - result = find_child(node.childNodes[i], pattern); - if (result != null) break; - } - return result; - } -} - -/* - * find_parent - * - * Searches parent nodes outwards from the node and returns the first it finds - * with the className specified. - */ -function find_parent(node, className) { - var pattern; - pattern = new RegExp("\\b" + className + "\\b"); - do { - if (node.nodeType == Node.ELEMENT_NODE && - pattern.test(node.className)) { - return node; - } - } while (node = node.parentNode); - return null; -} - -/* - * find_parent_tag - * - * Searches parent nodes outwards from the node and returns the first it finds - * with the tag name specified. HTML tags should be specified in upper case. - */ -function find_parent_tag(node, tag_name) { - do { - if (node.nodeType == Node.ELEMENT_NODE && node.tagName == tag_name) { - return node; - } - } while (node = node.parentNode); - return null; -} - -/* - * __toggle_help - * - * Uses the 'topic' property of the this object to - * toggle display of a help topic. - * - * This function is not intended to be called directly. - */ -function __toggle_help(e) { - if (!e) e = window.event; - if (e.type === "keydown") { - if (e.keyCode !== 13 && e.keyCode !== 32) { - return; - } - // stop a submit or something like that - e.preventDefault(); - } - - help_popup(this, this.getAttribute("data-topic")); -} - -function setup_help_button(button) { - "use strict"; - var topic; - if (button.hasAttribute("data-topic")) { - topic = button.getAttribute("data-topic"); - if (document.getElementById(topic) != null) { - button.tabIndex = "0"; // make keyboard selectable - button.addEventListener("click", function() { - help_popup(button, topic); - }, false); - button.addEventListener("keydown", function(e) { - // toggle only on Enter or Spacebar, let other keys do their thing - if (e.keyCode !== 13 && e.keyCode !== 32) return; - // stop a submit or something like that - e.preventDefault(); - help_popup(button, topic); - }, false); - } else { - button.style.visibility = "hidden"; - } - } - button.className += " active"; -} - -/* - * help_button - * - * Makes a help button for the passed topic. - */ -function help_button(topic) { - var btn = document.createElement("div"); - btn.className = "help"; - btn.setAttribute("data-topic", topic); - setup_help_button(btn); - return btn; -} - -/* - * prepare_download - * - * Sets the attributes of a link to setup a file download using the given content. - * If no link is provided then create one and click it. - */ -function prepare_download(content, mimetype, filename, link) { - "use strict"; - // if no link is provided then create one and click it - var click_link = false; - if (!link) { - link = document.createElement("a"); - click_link = true; - } - try { - // Use a BLOB to convert the text into a data URL. - // We could do this manually with a base 64 conversion. - // This will only be supported on modern browsers, - // hence the try block. - var blob = new Blob([content], {type: mimetype}); - var reader = new FileReader(); - reader.onloadend = function() { - // If we're lucky the browser will also support the download - // attribute which will let us suggest a file name to save the link. - // Otherwise it is likely that the filename will be unintelligible. - link.setAttribute("download", filename); - link.href = reader.result; - if (click_link) { - // must add the link to click it - document.body.appendChild(link); - link.click(); - document.body.removeChild(link); - } - } - reader.readAsDataURL(blob); - } catch (error) { - if (console && console.log) console.log(error); - // probably an old browser - link.href = ""; - link.visible = false; - } -} - -/* - * add_cell - * - * Add a cell to the table row. - */ -function add_cell(row, node, cls, click_action) { - var cell = row.insertCell(row.cells.length); - if (node) cell.appendChild(node); - if (cls && cls !== "") cell.className = cls; - if (click_action) cell.addEventListener("click", click_action, false); -} - -/* - * add_header_cell - * - * Add a header cell to the table row. - */ -function add_header_cell(row, node, help_topic, cls, colspan) { - var th = document.createElement("th"); - if (node) th.appendChild(node); - if (help_topic && help_topic !== "") th.appendChild(help_button(help_topic)); - if (cls && cls !== "") th.className = cls; - if (typeof colspan == "number" && colspan > 1) th.colSpan = colspan; - row.appendChild(th); -} - -/* - * add_text_cell - * - * Add a text cell to the table row. - */ -function add_text_cell(row, text, cls, action) { - var node = null; - if (typeof(text) != 'undefined') node = document.createTextNode(text); - add_cell(row, node, cls, action); -} - -/* - * add_text_header_cell - * - * Add a text header cell to the table row. - */ -function add_text_header_cell(row, text, help_topic, cls, action, colspan) { - var node = null; - if (typeof(text) != 'undefined') { - var nbsp = (help_topic ? "\u00A0" : ""); - var str = "" + text; - var parts = str.split(/\n/); - if (parts.length === 1) { - if (action) { - node = document.createElement("span"); - node.appendChild(document.createTextNode(str + nbsp)); - } else { - node = document.createTextNode(str + nbsp); - } - } else { - node = document.createElement("span"); - for (var i = 0; i < parts.length; i++) { - if (i !== 0) { - node.appendChild(document.createElement("br")); - } - node.appendChild(document.createTextNode(parts[i])); - } - } - if (action) { - node.addEventListener("click", action, false); - node.style.cursor = "pointer"; - } - } - add_header_cell(row, node, help_topic, cls, colspan); -} - -function setup_help() { - "use strict"; - var help_buttons, i; - help_buttons = document.querySelectorAll(".help:not(.active)"); - for (i = 0; i < help_buttons.length; i++) { - setup_help_button(help_buttons[i]); - } -} - -function setup_scrollpad() { - "use strict"; - if (document.getElementsByTagName('body')[0].hasAttribute("data-scrollpad") && document.getElementById("scrollpad") == null) { - window.addEventListener("resize", update_scroll_pad, false); - update_scroll_pad(); - } -} - -// anon function to avoid polluting global scope -(function() { - "use strict"; - window.addEventListener("load", function load(evt) { - window.removeEventListener("load", load, false); - setup_help(); - setup_scrollpad(); - }, false); -})(); - -/* - * make_link - * - * Creates a text node and if a URL is specified it surrounds it with a link. - * If the URL doesn't begin with "http://" it automatically adds it, as - * relative links don't make much sense in this context. - */ -function make_link(text, url) { - var textNode = null; - var link = null; - if (typeof text !== "undefined" && text !== null) textNode = document.createTextNode(text); - if (typeof url === "string") { - if (url.indexOf("//") == -1) { - url = "http://" + url; - } - link = document.createElement('a'); - link.href = url; - if (textNode) link.appendChild(textNode); - return link; - } - return textNode; -} -</script> - <script> -function motif_logo_template(inputs) { - function _input(name) { - if (typeof inputs[name] === "undefined") { - throw new Error("Missing template variable: " + name); - } - return inputs[name]; - } - return ( -"%!PS-Adobe-3.0 EPSF-3.0\n" + -"%%Title: Sequence Logo : " + _input("TITLE") + "\n" + -"%%Creator: " + _input("CREATOR") + "\n" + -"%%CreationDate: " + _input("CREATIONDATE") + "\n" + -"%%BoundingBox: 0 0 " + _input("BOUNDINGWIDTH") + " " + _input("BOUNDINGHEIGHT") + " \n" + -"%%Pages: 0\n" + -"%%DocumentFonts: \n" + -"%%EndComments\n" + -"\n" + -"% ---- CONSTANTS ----\n" + -"\/cmfactor 72 2.54 div def % defines points -> cm conversion\n" + -"\/cm {cmfactor mul} bind def % defines centimeters\n" + -"\n" + -"% ---- VARIABLES ----\n" + -"\n" + -"% NA = Nucleic Acid, AA = Amino Acid\n" + -"\/logoType (" + _input("LOGOTYPE") + ") def \n" + -"\n" + -"\/logoTitle (" + _input("TITLE") + ") def\n" + -"\n" + -"% Dimensions in cm\n" + -"\/logoWidth " + _input("LOGOWIDTH") + " cm def\n" + -"\/logoHeight " + _input("LOGOLINEHEIGHT") + " cm def\n" + -"\/totalHeight " + _input("LOGOHEIGHT") + " cm def\n" + -"\n" + -"\/yaxis " + _input("YAXIS") + " def\n" + -"\/yaxisLabel (" + _input("YAXISLABEL") + ") def\n" + -"\/yaxisBits " + _input("BARBITS") + " def % bits\n" + -"\/yaxisTicBits " + _input("TICBITS") + " def\n" + -"\n" + -"\/xaxis " + _input("NUMBERING") + " def\n" + -"\/xaxisLabel (" + _input("XAXISLABEL") + ") def\n" + -"\/showEnds (" + _input("SHOWENDS") + ") def \n" + -"\n" + -"\/showFineprint true def\n" + -"\/fineprint (" + _input("FINEPRINT") + ") def\n" + -"\n" + -"\/charsPerLine " + _input("CHARSPERLINE") + " def\n" + -"\n" + -"\/showingBox " + _input("SHOWINGBOX") + " def \n" + -"\/shrinking false def % true falses\n" + -"\/shrink 1.0 def\n" + -"\/outline " + _input("OUTLINE") + " def\n" + -"\n" + -"\/IbeamFraction " + _input("ERRORBARFRACTION") + " def\n" + -"\/IbeamGray 0.50 def\n" + -"\/IbeamLineWidth 0.5 def\n" + -"\n" + -"\/fontsize " + _input("FONTSIZE") + " def\n" + -"\/titleFontsize " + _input("TITLEFONTSIZE") + " def\n" + -"\/smallFontsize " + _input("SMALLFONTSIZE") + " def\n" + -"\n" + -"\/topMargin " + _input("TOPMARGIN") + " cm def\n" + -"\/bottomMargin " + _input("BOTTOMMARGIN") + " cm def\n" + -"\n" + -"\/defaultColor [0 0 0] def \n" + -"\n" + -_input("COLORDICT") + "\n" + -"\n" + -"\/colorDict fullColourDict def\n" + -"\n" + -"% ---- DERIVED PARAMETERS ----\n" + -"\n" + -"\/leftMargin\n" + -" fontsize 3.5 mul\n" + -"\n" + -"def \n" + -"\n" + -"\/rightMargin \n" + -" %Add extra room if showing ends\n" + -" showEnds (false) eq { fontsize}{fontsize 1.5 mul} ifelse\n" + -"def\n" + -"\n" + -"\/yaxisHeight \n" + -" logoHeight \n" + -" bottomMargin sub \n" + -" topMargin sub\n" + -"def\n" + -"\n" + -"\/ticWidth fontsize 2 div def\n" + -"\n" + -"\/pointsPerBit yaxisHeight yaxisBits div def\n" + -"\n" + -"\/stackMargin 1 def\n" + -"\n" + -"% Do not add space aroung characters if characters are boxed\n" + -"\/charRightMargin \n" + -" showingBox { 0.0 } {stackMargin} ifelse\n" + -"def\n" + -"\n" + -"\/charTopMargin \n" + -" showingBox { 0.0 } {stackMargin} ifelse\n" + -"def\n" + -"\n" + -"\/charWidth\n" + -" logoWidth\n" + -" leftMargin sub\n" + -" rightMargin sub\n" + -" charsPerLine div\n" + -" charRightMargin sub\n" + -"def\n" + -"\n" + -"\/charWidth4 charWidth 4 div def\n" + -"\/charWidth2 charWidth 2 div def\n" + -"\n" + -"\/stackWidth \n" + -" charWidth charRightMargin add\n" + -"def\n" + -" \n" + -"\/numberFontsize \n" + -" fontsize charWidth lt {fontsize}{charWidth} ifelse\n" + -"def\n" + -"\n" + -"% movements to place 5'\/N and 3'\/C symbols\n" + -"\/leftEndDeltaX fontsize neg def\n" + -"\/leftEndDeltaY fontsize 1.5 mul neg def\n" + -"\/rightEndDeltaX fontsize 0.25 mul def\n" + -"\/rightEndDeltaY leftEndDeltaY def\n" + -"\n" + -"% Outline width is proporional to charWidth, \n" + -"% but no less that 1 point\n" + -"\/outlinewidth \n" + -" charWidth 32 div dup 1 gt {}{pop 1} ifelse\n" + -"def\n" + -"\n" + -"\n" + -"% ---- PROCEDURES ----\n" + -"\n" + -"\/StartLogo { \n" + -" % Save state\n" + -" save \n" + -" gsave \n" + -"\n" + -" % Print Logo Title, top center \n" + -" gsave \n" + -" SetStringFont\n" + -"\n" + -" logoWidth 2 div\n" + -" logoTitle\n" + -" stringwidth pop 2 div sub\n" + -" totalHeight\n" + -" titleFontsize sub\n" + -" moveto\n" + -"\n" + -" logoTitle\n" + -" show\n" + -" grestore\n" + -"\n" + -" % Print X-axis label, bottom center\n" + -" gsave\n" + -" SetStringFont\n" + -"\n" + -" logoWidth 2 div\n" + -" xaxisLabel\n" + -" stringwidth pop 2 div sub\n" + -" 0\n" + -" titleFontsize 3 div\n" + -" add\n" + -" moveto\n" + -"\n" + -" xaxisLabel\n" + -" show\n" + -" grestore\n" + -"\n" + -" % Show Fine Print\n" + -" showFineprint {\n" + -" gsave\n" + -" SetSmallFont\n" + -" logoWidth\n" + -" fineprint stringwidth pop sub\n" + -" smallFontsize sub\n" + -" smallFontsize 3 div\n" + -" moveto\n" + -" \n" + -" fineprint show\n" + -" grestore\n" + -" } if\n" + -"\n" + -" % Move to lower left corner of last line, first stack\n" + -" leftMargin bottomMargin translate\n" + -"\n" + -" % Move above first line ready for StartLine \n" + -" 0 totalHeight translate\n" + -"\n" + -" SetLogoFont\n" + -"} bind def\n" + -"\n" + -"\/EndLogo { \n" + -" grestore \n" + -" showpage \n" + -" restore \n" + -"} bind def\n" + -"\n" + -"\n" + -"\/StartLine { \n" + -" % move down to the bottom of the line:\n" + -" 0 logoHeight neg translate\n" + -" \n" + -" gsave \n" + -" yaxis { MakeYaxis } if\n" + -" xaxis { showEnds (true) eq {ShowLeftEnd} if } if\n" + -"} bind def\n" + -"\n" + -"\/EndLine{ \n" + -" xaxis { showEnds (true) eq {ShowRightEnd} if } if\n" + -" grestore \n" + -"} bind def\n" + -"\n" + -"\n" + -"\/MakeYaxis {\n" + -" gsave \n" + -" stackMargin neg 0 translate\n" + -" ShowYaxisBar\n" + -" ShowYaxisLabel\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"\/ShowYaxisBar { \n" + -" gsave \n" + -" SetStringFont\n" + -"\n" + -" \/str 10 string def % string to hold number \n" + -" \/smallgap stackMargin 2 div def\n" + -"\n" + -" % Draw first tic and bar\n" + -" gsave \n" + -" ticWidth neg 0 moveto \n" + -" ticWidth 0 rlineto \n" + -" 0 yaxisHeight rlineto\n" + -" stroke\n" + -" grestore\n" + -"\n" + -" \n" + -" % Draw the tics\n" + -" % initial increment limit proc for\n" + -" 0 yaxisTicBits yaxisBits abs %cvi\n" + -" {\/loopnumber exch def\n" + -"\n" + -" % convert the number coming from the loop to a string\n" + -" % and find its width\n" + -" loopnumber 10 str cvrs\n" + -" \/stringnumber exch def % string representing the number\n" + -"\n" + -" stringnumber stringwidth pop\n" + -" \/numberwidth exch def % width of number to show\n" + -"\n" + -" \/halfnumberheight\n" + -" stringnumber CharBoxHeight 2 div\n" + -" def\n" + -"\n" + -" numberwidth % move back width of number\n" + -" neg loopnumber pointsPerBit mul % shift on y axis\n" + -" halfnumberheight sub % down half the digit\n" + -"\n" + -" moveto % move back the width of the string\n" + -"\n" + -" ticWidth neg smallgap sub % Move back a bit more \n" + -" 0 rmoveto % move back the width of the tic \n" + -"\n" + -" stringnumber show\n" + -" smallgap 0 rmoveto % Make a small gap \n" + -"\n" + -" % now show the tic mark\n" + -" 0 halfnumberheight rmoveto % shift up again\n" + -" ticWidth 0 rlineto\n" + -" stroke\n" + -" } for\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\/ShowYaxisLabel {\n" + -" gsave\n" + -" SetStringFont\n" + -"\n" + -" % How far we move left depends on the size of\n" + -" % the tic labels.\n" + -" \/str 10 string def % string to hold number \n" + -" yaxisBits yaxisTicBits div cvi yaxisTicBits mul \n" + -" str cvs stringwidth pop\n" + -" ticWidth 1.5 mul add neg \n" + -"\n" + -"\n" + -" yaxisHeight\n" + -" yaxisLabel stringwidth pop\n" + -" sub 2 div\n" + -"\n" + -" translate\n" + -" 90 rotate\n" + -" 0 0 moveto\n" + -" yaxisLabel show\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"\/StartStack { % <stackNumber> startstack\n" + -" xaxis {MakeNumber}{pop} ifelse\n" + -" gsave\n" + -"} bind def\n" + -"\n" + -"\/EndStack {\n" + -" grestore\n" + -" stackWidth 0 translate\n" + -"} bind def\n" + -"\n" + -"\n" + -"% Draw a character whose height is proportional to symbol bits\n" + -"\/MakeSymbol{ % charbits character MakeSymbol\n" + -" gsave\n" + -" \/char exch def\n" + -" \/bits exch def\n" + -"\n" + -" \/bitsHeight \n" + -" bits pointsPerBit mul \n" + -" def\n" + -"\n" + -" \/charHeight \n" + -" bitsHeight charTopMargin sub\n" + -" dup \n" + -" 0.0 gt {}{pop 0.0} ifelse % if neg replace with zero \n" + -" def \n" + -" \n" + -" charHeight 0.0 gt {\n" + -" char SetColor\n" + -" charWidth charHeight char ShowChar\n" + -"\n" + -" showingBox { % Unfilled box\n" + -" 0 0 charWidth charHeight false ShowBox\n" + -" } if\n" + -"\n" + -"\n" + -" } if\n" + -"\n" + -" grestore\n" + -"\n" + -" 0 bitsHeight translate \n" + -"} bind def\n" + -"\n" + -"\n" + -"\/ShowChar { % <width> <height> <char> ShowChar\n" + -" gsave\n" + -" \/tc exch def % The character\n" + -" \/ysize exch def % the y size of the character\n" + -" \/xsize exch def % the x size of the character\n" + -"\n" + -" \/xmulfactor 1 def \n" + -" \/ymulfactor 1 def\n" + -" \/limmulfactor 0.01 def\n" + -" \/drawable true def\n" + -"\n" + -" \n" + -" % if ysize is negative, make everything upside down!\n" + -" ysize 0 lt {\n" + -" % put ysize normal in this orientation\n" + -" \/ysize ysize abs def\n" + -" xsize ysize translate\n" + -" 180 rotate\n" + -" } if\n" + -"\n" + -" shrinking {\n" + -" xsize 1 shrink sub 2 div mul\n" + -" ysize 1 shrink sub 2 div mul translate \n" + -"\n" + -" shrink shrink scale\n" + -" } if\n" + -"\n" + -" % Calculate the font scaling factors\n" + -" % Loop twice to catch small correction due to first scaling\n" + -" 2 {\n" + -" gsave\n" + -" xmulfactor ymulfactor scale\n" + -" \n" + -" ysize % desired size of character in points\n" + -" tc CharBoxHeight \n" + -" dup 0.0 ne {\n" + -" div % factor by which to scale up the character\n" + -" \/ymulfactor exch def\n" + -" } % end if\n" + -" {pop pop}\n" + -" ifelse\n" + -"\n" + -" xsize % desired size of character in points\n" + -" tc CharBoxWidth \n" + -" dup 0.0 ne {\n" + -" div % factor by which to scale up the character\n" + -" \/xmulfactor exch def\n" + -" } % end if\n" + -" {pop pop}\n" + -" ifelse\n" + -" grestore\n" + -" % if the multiplication factors get too small we need to avoid a crash\n" + -" xmulfactor limmulfactor lt {\n" + -" \/xmulfactor 1 def\n" + -" \/drawable false def\n" + -" } if\n" + -" ymulfactor limmulfactor lt {\n" + -" \/ymulfactor 1 def\n" + -" \/drawable false def\n" + -" } if\n" + -" } repeat\n" + -"\n" + -" % Adjust horizontal position if the symbol is an I\n" + -" tc (I) eq {\n" + -" charWidth 2 div % half of requested character width\n" + -" tc CharBoxWidth 2 div % half of the actual character\n" + -" sub 0 translate\n" + -" % Avoid x scaling for I \n" + -" \/xmulfactor 1 def \n" + -" } if\n" + -"\n" + -"\n" + -" % ---- Finally, draw the character\n" + -" drawable { \n" + -" newpath\n" + -" xmulfactor ymulfactor scale\n" + -"\n" + -" % Move lower left corner of character to start point\n" + -" tc CharBox pop pop % llx lly : Lower left corner\n" + -" exch neg exch neg\n" + -" moveto\n" + -"\n" + -" outline { % outline characters:\n" + -" outlinewidth setlinewidth\n" + -" tc true charpath\n" + -" gsave 1 setgray fill grestore\n" + -" clip stroke\n" + -" } { % regular characters\n" + -" tc show\n" + -" } ifelse\n" + -" } if\n" + -"\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"\/ShowBox { % x1 y1 x2 y2 filled ShowBox\n" + -" gsave\n" + -" \/filled exch def \n" + -" \/y2 exch def\n" + -" \/x2 exch def\n" + -" \/y1 exch def\n" + -" \/x1 exch def\n" + -" newpath\n" + -" x1 y1 moveto\n" + -" x2 y1 lineto\n" + -" x2 y2 lineto\n" + -" x1 y2 lineto\n" + -" closepath\n" + -"\n" + -" clip\n" + -" \n" + -" filled {\n" + -" fill\n" + -" }{ \n" + -" 0 setgray stroke \n" + -" } ifelse\n" + -"\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"\/MakeNumber { % number MakeNumber\n" + -" gsave\n" + -" SetNumberFont\n" + -" stackWidth 0 translate\n" + -" 90 rotate % rotate so the number fits\n" + -" dup stringwidth pop % find the length of the number\n" + -" neg % prepare for move\n" + -" stackMargin sub % Move back a bit\n" + -" charWidth (0) CharBoxHeight % height of numbers\n" + -" sub 2 div %\n" + -" moveto % move back to provide space\n" + -" show\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"\/Ibeam{ % heightInBits Ibeam\n" + -" gsave\n" + -" % Make an Ibeam of twice the given height in bits\n" + -" \/height exch pointsPerBit mul def \n" + -" \/heightDRAW height IbeamFraction mul def\n" + -"\n" + -" IbeamLineWidth setlinewidth\n" + -" IbeamGray setgray \n" + -"\n" + -" charWidth2 height neg translate\n" + -" ShowIbar\n" + -" newpath\n" + -" 0 0 moveto\n" + -" 0 heightDRAW rlineto\n" + -" stroke\n" + -" newpath\n" + -" 0 height moveto\n" + -" 0 height rmoveto\n" + -" currentpoint translate\n" + -" ShowIbar\n" + -" newpath\n" + -" 0 0 moveto\n" + -" 0 heightDRAW neg rlineto\n" + -" currentpoint translate\n" + -" stroke\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"\/ShowIbar { % make a horizontal bar\n" + -" gsave\n" + -" newpath\n" + -" charWidth4 neg 0 moveto\n" + -" charWidth4 0 lineto\n" + -" stroke\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"\/ShowLeftEnd {\n" + -" gsave\n" + -" SetStringFont\n" + -" leftEndDeltaX leftEndDeltaY moveto\n" + -" logoType (NA) eq {(5) show ShowPrime} if\n" + -" logoType (AA) eq {(N) show} if\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"\/ShowRightEnd { \n" + -" gsave\n" + -" SetStringFont\n" + -" rightEndDeltaX rightEndDeltaY moveto\n" + -" logoType (NA) eq {(3) show ShowPrime} if\n" + -" logoType (AA) eq {(C) show} if\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"\/ShowPrime {\n" + -" gsave\n" + -" SetPrimeFont\n" + -" (\\242) show \n" + -" grestore\n" + -"} bind def\n" + -"\n" + -" \n" + -"\/SetColor{ % <char> SetColor\n" + -" dup colorDict exch known {\n" + -" colorDict exch get aload pop setrgbcolor\n" + -" } {\n" + -" pop\n" + -" defaultColor aload pop setrgbcolor\n" + -" } ifelse \n" + -"} bind def\n" + -"\n" + -"% define fonts\n" + -"\/SetTitleFont {\/Times-Bold findfont titleFontsize scalefont setfont} bind def\n" + -"\/SetLogoFont {\/Helvetica-Bold findfont charWidth scalefont setfont} bind def\n" + -"\/SetStringFont{\/Helvetica-Bold findfont fontsize scalefont setfont} bind def\n" + -"\/SetPrimeFont {\/Symbol findfont fontsize scalefont setfont} bind def\n" + -"\/SetSmallFont {\/Helvetica findfont smallFontsize scalefont setfont} bind def\n" + -"\n" + -"\/SetNumberFont {\n" + -" \/Helvetica-Bold findfont \n" + -" numberFontsize\n" + -" scalefont\n" + -" setfont\n" + -"} bind def\n" + -"\n" + -"%Take a single character and return the bounding box\n" + -"\/CharBox { % <char> CharBox <lx> <ly> <ux> <uy>\n" + -" gsave\n" + -" newpath\n" + -" 0 0 moveto\n" + -" % take the character off the stack and use it here:\n" + -" true charpath \n" + -" flattenpath \n" + -" pathbbox % compute bounding box of 1 pt. char => lx ly ux uy\n" + -" % the path is here, but toss it away ...\n" + -" grestore\n" + -"} bind def\n" + -"\n" + -"\n" + -"% The height of a characters bounding box\n" + -"\/CharBoxHeight { % <char> CharBoxHeight <num>\n" + -" CharBox\n" + -" exch pop sub neg exch pop\n" + -"} bind def\n" + -"\n" + -"\n" + -"% The width of a characters bounding box\n" + -"\/CharBoxWidth { % <char> CharBoxHeight <num>\n" + -" CharBox\n" + -" pop exch pop sub neg \n" + -"} bind def\n" + -"\n" + -"% Set the colour scheme to be faded to indicate trimming\n" + -"\/MuteColour {\n" + -" \/colorDict mutedColourDict def\n" + -"} def\n" + -"\n" + -"% Restore the colour scheme to the normal colours\n" + -"\/RestoreColour {\n" + -" \/colorDict fullColourDict def\n" + -"} def\n" + -"\n" + -"% Draw the background for a trimmed section\n" + -"% takes the number of columns as a parameter\n" + -"\/DrawTrimBg { % <num> DrawTrimBox\n" + -" \/col exch def\n" + -" \n" + -" \/boxwidth \n" + -" col stackWidth mul \n" + -" def\n" + -" \n" + -" gsave\n" + -" 0.97 setgray\n" + -"\n" + -" newpath\n" + -" 0 0 moveto\n" + -" boxwidth 0 rlineto\n" + -" 0 yaxisHeight rlineto\n" + -" 0 yaxisHeight lineto\n" + -" closepath\n" + -" \n" + -" fill\n" + -" grestore\n" + -"} def\n" + -"\n" + -"\/DrawTrimEdge {\n" + -" gsave\n" + -" 0.2 setgray\n" + -" [2] 0 setdash\n" + -"\n" + -" newpath\n" + -" 0 0 moveto\n" + -" 0 yaxisHeight lineto\n" + -" \n" + -" stroke\n" + -"\n" + -"} def\n" + -"\n" + -"\n" + -"% Deprecated names\n" + -"\/startstack {StartStack} bind def\n" + -"\/endstack {EndStack} bind def\n" + -"\/makenumber {MakeNumber} bind def\n" + -"\/numchar { MakeSymbol } bind def\n" + -"\n" + -"%%EndProlog\n" + -"\n" + -"%%Page: 1 1\n" + -"StartLogo\n" + -"\n" + -_input("DATA") + "\n" + -"\n" + -"EndLogo\n" + -"\n" + -"%%EOF\n" - ); -}</script> - <script> -//====================================================================== -// start Alphabet object -//====================================================================== -var Alphabet = function(alphabet, background) { - "use strict"; - var i, j, sym, aliases, complement, comp_e_sym, ambigs, generate_background; - generate_background = (background == null); - if (generate_background) { - background = []; - for (i = 0; i < alphabet.ncore; i++) background[i] = 1.0 / alphabet.ncore; - } else if (alphabet.ncore != background.length) { - throw new Error("The background length does not match the alphabet length."); - } - this.name = alphabet.name; - this.like = (alphabet.like != null ? alphabet.like.toUpperCase() : null); - this.ncore = alphabet.ncore; - this.symbols = alphabet.symbols; - this.background = background; - this.genbg = generate_background; - this.encode = {}; - this.encode2core = {}; - this.complement = {}; - // check if all symbols are same case - var seen_uc = false; - var seen_lc = false; - var check_case = function (syms) { - var s, sym; - if (typeof syms === "string") { - for (s = 0; s < syms.length; s++) { - sym = syms.charAt(s); - if (sym >= 'a' && sym <= 'z') seen_lc = true; - else if (sym >= 'A' && sym <= 'Z') seen_uc = true; - } - } - }; - for (i = 0; i < this.symbols.length; i++) { - check_case(this.symbols[i].symbol); - check_case(this.symbols[i].aliases); - } - // now map symbols to indexes - var update_array = function(array, syms, index) { - var s, sym; - if (typeof syms === "string") { - for (s = 0; s < syms.length; s++) { - sym = syms.charAt(s); - array[sym] = index; - // when only a single case is used, then encode as case insensitive - if (seen_uc != seen_lc) { - if (sym >= 'a' && sym <= 'z') { - array[sym.toUpperCase()] = index; - } else if (sym >= 'A' && sym <= 'Z') { - array[sym.toLowerCase()] = index; - } - } - } - } - } - // map core symbols to index - for (i = 0; i < this.ncore; i++) { - update_array(this.encode2core, this.symbols[i].symbol, i); - update_array(this.encode, this.symbols[i].symbol, i); - update_array(this.encode2core, this.symbols[i].aliases, i); - update_array(this.encode, this.symbols[i].aliases, i); - } - // map ambigous symbols to index - ambigs = {}; - for (i = this.ncore; i < this.symbols.length; i++) { - update_array(this.encode, this.symbols[i].symbol, i); - update_array(this.encode, this.symbols[i].aliases, i); - ambigs[this.symbols[i].equals] = i; - } - // determine complements - for (i = 0; i < this.ncore; i++) { - complement = this.symbols[i].complement; - if (typeof complement === "string") { - this.complement[i] = this.encode2core[complement]; - } - } - next_symbol: - for (i = this.ncore; i < this.symbols.length; i++) { - complement = ""; - for (j = 0; j < this.symbols[i].equals.length; j++) { - comp_e_sym = this.complement[this.encode2core[this.symbols[i].equals.charAt(j)]]; - if (typeof comp_e_sym !== "number") continue next_symbol; - complement += this.symbols[comp_e_sym].symbol; - } - complement = complement.split("").sort().join(""); - if (typeof ambigs[complement] === "number") { - this.complement[i] = ambigs[complement]; - } - } - // determine case insensitivity - this.case_insensitive = true; - if (seen_uc == seen_lc) { - // when there is a mixture of cases it probably won't - // be case insensitive but we still need to check - loop: - for (i = 0; i < this.symbols.length; i++) { - sym = this.symbols[i].symbol; - if (sym >= 'A' && sym <= 'Z') { - if (this.encode[sym.toLowerCase()] != i) { - this.case_insensitive = false; - break loop; - } - } else if (sym >= 'a' && sym <= 'z') { - if (this.encode[sym.toUpperCase()] != i) { - this.case_insensitive = false; - break loop; - } - } - aliases = this.symbols[i].aliases; - if (aliases != null) { - for (j = 0; j < aliases.length; j++) { - sym = aliases.charAt(j); - if (sym >= 'A' && sym <= 'Z') { - if (this.encode[sym.toLowerCase()] != i) { - this.case_insensitive = false; - break loop; - } - } else if (sym >= 'a' && sym <= 'z') { - if (this.encode[sym.toUpperCase()] != i) { - this.case_insensitive = false; - break loop; - } - } - } - } - } - } - // normalise aliases to remove the prime symbol and eliminate - // the alternate cases when the alphabet is case insensitive - var seen, out; - for (i = 0; i < this.symbols.length; i++) { - sym = this.symbols[i].symbol; - aliases = this.symbols[i].aliases; - if (typeof aliases != "string") aliases = ""; - seen = {}; - out = []; - if (this.case_insensitive) { - sym = sym.toUpperCase(); - aliases = aliases.toUpperCase(); - } - seen[sym] = true; - for (j = 0; j < aliases.length; j++) { - if (!seen[aliases.charAt(j)]) { - seen[aliases.charAt(j)] = true; - out.push(aliases.charAt(j)); - } - } - this.symbols[i].aliases = out.sort().join(""); - } -}; -// return the name of the alphabet -Alphabet.prototype.get_alphabet_name = function() { - return this.name; -}; -// return if the alphabet can be complemented -Alphabet.prototype.has_complement = function() { - return (typeof this.symbols[0].complement === "string"); -}; -// return true if an uppercase letter has the same meaning as the lowercase form -Alphabet.prototype.is_case_insensitive = function() { - return this.case_insensitive; -}; -// return the information content of an alphabet letter -Alphabet.prototype.get_ic = function() { - return Math.log(this.ncore) / Math.LN2; -}; -// return the count of the core alphabet symbols -Alphabet.prototype.get_size_core = function() { - return this.ncore; -}; -// return the count of all alphabet symbols -Alphabet.prototype.get_size_full = function() { - return this.symbols.length; -}; -// return the symbol for the given alphabet index -Alphabet.prototype.get_symbol = function(alph_index) { - "use strict"; - if (alph_index < 0 || alph_index >= this.symbols.length) { - throw new Error("Alphabet index out of bounds"); - } - return this.symbols[alph_index].symbol; -}; -// return the aliases for the given alphabet index -Alphabet.prototype.get_aliases = function(alph_index) { - "use strict"; - if (alph_index < 0 || alph_index >= this.symbols.length) { - throw new Error("Alphabet index out of bounds"); - } - var sym_obj = this.symbols[alph_index]; - return (sym_obj.aliases != null ? sym_obj.aliases : ""); -}; -// return the name for the given alphabet index -Alphabet.prototype.get_name = function(alph_index) { - "use strict"; - var sym; - if (alph_index < 0 || alph_index >= this.symbols.length) { - throw new Error("Alphabet index out of bounds"); - } - sym = this.symbols[alph_index]; - return (typeof sym.name === "string" ? sym.name : sym.symbol); -}; -// return the alphabet it is like or null -Alphabet.prototype.get_like = function() { - "use strict"; - return this.like; -}; -// return the index of the complement for the given alphabet index -Alphabet.prototype.get_complement = function(alph_index) { - var comp_e_sym = this.complement[alph_index]; - if (typeof comp_e_sym === "number") { - return comp_e_sym; - } else { - return -1; - } -}; -// return a string containing the core symbols -Alphabet.prototype.get_symbols = function() { - "use strict"; - var i, core_symbols; - core_symbols = ""; - for (i = 0; i < this.ncore; i++) { - core_symbols += this.symbols[i].symbol; - } - return core_symbols; -}; -// return if the background was not a uniform generated background -Alphabet.prototype.has_bg = function() { - "use strict"; - return !this.genbg; -}; -// get the background frequency for the index -Alphabet.prototype.get_bg_freq = function(alph_index) { - "use strict"; - var freq, i, symbols; - if (alph_index >= 0) { - if (alph_index < this.ncore) { - return this.background[alph_index]; - } else if (alph_index < this.symbols.length) { - freq = 0; - symbols = this.symbols[alph_index].equals; - for (i = 0; i < symbols.length; i++) { - freq += this.background[this.encode2core[symbols.charAt(i)]]; - } - return freq; - } - } - throw new Error("The alphabet index is out of range."); -}; -// get the colour of the index -Alphabet.prototype.get_colour = function(alph_index) { - "use strict"; - if (alph_index < 0 || alph_index >= this.symbols.length) { - throw new Error("BAD_ALPHABET_INDEX"); - } - if (typeof this.symbols[alph_index].colour != "string") { - return "black"; - } - return "#" + this.symbols[alph_index].colour; -}; -// get the rgb componets of the colour at the index -Alphabet.prototype.get_rgb = function(alph_index) { - "use strict"; - if (alph_index < 0 || alph_index >= this.symbols.length) { - throw new Error("BAD_ALPHABET_INDEX"); - } - if (typeof this.symbols[alph_index].colour != "string") { - return {"red": 0, "green": 0, "blue": 0}; - } - var colour = this.symbols[alph_index].colour; - var red = parseInt(colour.substr(0, 2), 16) / 255; - var green = parseInt(colour.substr(2, 2), 16) / 255; - var blue = parseInt(colour.substr(4, 2), 16) / 255; - return {"red": red, "green": green, "blue": blue}; -}; -// convert a symbol into the index -Alphabet.prototype.get_index = function(letter) { - "use strict"; - var alph_index; - alph_index = this.encode[letter]; - if (typeof alph_index === "undefined") { - return -1; - } - return alph_index; -}; -// convert a symbol into the list of core indexes that it equals -Alphabet.prototype.get_indexes = function(letter) { - "use strict"; - var alph_index, comprise_str, i, comprise_list; - alph_index = this.encode[letter]; - if (typeof alph_index === "undefined") { - throw new Error("Unknown letter"); - } - comprise_str = this.symbols[alph_index].equals; - comprise_list = []; - if (typeof comprise_str == "string") { - for (i = 0; i < comprise_str.length; i++) { - comprise_list.push(this.encode2core[comprise_str.charAt(i)]); - } - } else { - comprise_list.push(alph_index); - } - return comprise_list; -}; -// check if a symbol is the primary way of representing the symbol in the alphabet -Alphabet.prototype.is_prime_symbol = function(letter) { - var alph_index; - alph_index = this.encode[letter]; - if (alph_index == null) return false; - if (this.is_case_insensitive()) { - return (this.symbols[alph_index].symbol.toUpperCase() == letter.toUpperCase()); - } else { - return (this.symbols[alph_index].symbol == letter); - } -}; -// compare 2 alphabets -Alphabet.prototype.equals = function(other) { - "use strict"; - var i, sym1, sym2; - // first check that it's actually an alphabet object - if (!(typeof other === "object" && other != null && other instanceof Alphabet)) { - return false; - } - // second shortcircuit if it's the same object - if (this === other) return true; - // compare - if (this.name !== other.name) return false; - if (this.ncore !== other.ncore) return false; - if (this.symbols.length !== other.symbols.length) return false; - for (i = 0; i < this.symbols.length; i++) { - sym1 = this.symbols[i]; - sym2 = other.symbols[i]; - if (sym1.symbol !== sym2.symbol) return false; - if (sym1.aliases !== sym2.aliases) return false; - if (sym1.name !== sym2.name) return false; - if (typeof sym1.colour !== typeof sym2.colour || - (typeof sym1.colour === "string" && typeof sym2.colour === "string" && - parseInt(sym1.colour, 16) != parseInt(sym2.colour, 16))) { - return false; - } - if (sym1.complement !== sym2.complement) return false; - if (sym1.equals !== sym2.equals) return false; - } - return true; -}; -Alphabet.prototype.check_core_subset = function(super_alph) { - var complement_same = true; - var seen_set = {}; - var sub_i, sub_symbol, super_i, super_symbol; - for (sub_i = 0; sub_i < this.ncore; sub_i++) { - sub_symbol = this.symbols[sub_i]; - super_i = super_alph.encode[sub_symbol.symbol]; - if (super_i == null) return 0; - super_symbol = super_alph.symbols[super_i]; - if (seen_set[super_i]) return 0; - seen_set[super_i] = true; - // check complement - if (sub_symbol.complement != null && super_symbol.complement != null) { - if (super_alph.encode[sub_symbol.complement] != super_alph.encode[super_symbol.complement]) { - complement_same = false; - } - } else if (sub_symbol.complement != null || super_symbol.complement != null) { - complement_same = false; - } - } - return (complement_same ? 1 : -1); -}; -// convert a sequence to its reverse complement -Alphabet.prototype.invcomp_seq = function(seq) { - "use strict"; - var syms, i, e_sym, comp_e_sym; - if (!this.has_complement()) throw new Error("Alphabet must be complementable"); - syms = seq.split(""); - for (i = 0; i < syms.length; i++) { - e_sym = this.encode[syms[i]]; - if (typeof e_sym === "undefined") { - e_sym = this.ncore; // wildcard - } - comp_e_sym = this.complement[e_sym]; - if (typeof comp_e_sym === "undefined") { - comp_e_sym = e_sym; // not complementable - } - syms[i] = this.symbols[comp_e_sym].symbol; - } - return syms.reverse().join(""); -}; -// convert the alphabet to the text version -Alphabet.prototype.as_text = function() { - "use strict"; - function name_as_text(name) { - var i, c, out; - out = "\""; - for (i = 0; i < name.length; i++) { - c = name.charAt(i); - if (c == "\"") { - out += "\\\""; - } else if (c == "/") { - out += "\\/"; - } else if (c == "\\") { - out += "\\\\"; - } else { - out += c; - } - } - out += "\""; - return out; - } - function symbol_as_text(sym) { - var out; - out = sym.symbol; - if (typeof sym.name === "string" && sym.name != sym.symbol) { - out += " " + name_as_text(sym.name); - } - if (typeof sym.colour === "string") { - out += " " + sym.colour; - } - return out; - } - var out, i, j, c, sym; - out = ""; - // output core symbols with 2 way complements - for (i = 0; i < this.ncore; i++) { - c = this.complement[i]; - if (typeof c === "number" && i < c && this.complement[c] === i) { - out += symbol_as_text(this.symbols[i]) + " ~ " + symbol_as_text(this.symbols[c]) + "\n"; - } - } - // output core symbols with no complement - for (i = 0; i < this.ncore; i++) { - if (typeof this.complement[i] === "undefined") { - out += symbol_as_text(this.symbols[i]) + "\n"; - } - } - // output ambiguous symbols that have comprising characters - for (i = this.ncore; i < this.symbols.length; i++) { - if (this.symbols[i].equals.length == 0) break; - out += symbol_as_text(this.symbols[i]) + " = " + this.symbols[i].equals + "\n"; - if (typeof this.symbols[i].aliases === "string") { - for (j = 0; j < this.symbols[i].aliases.length; j++) { - if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue; - out += this.symbols[i].aliases.charAt(j) + " = " + this.symbols[i].equals + "\n"; - } - } - } - // output aliases of core symbols - for (i = 0; i < this.ncore; i++) { - if (typeof this.symbols[i].aliases === "string") { - for (j = 0; j < this.symbols[i].aliases.length; j++) { - if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue; - out += this.symbols[i].aliases.charAt(j) + " = " + this.symbols[i].symbol + "\n"; - } - } - } - // output gap symbols - i = this.symbols.length - 1; - if (this.symbols[i].equals.length == 0) { - out += symbol_as_text(this.symbols[i]) + " =\n"; - if (typeof this.symbols[i].aliases === "string") { - for (j = 0; j < this.symbols[i].aliases.length; j++) { - if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue; - out += this.symbols[i].aliases.charAt(j) + " =\n"; - } - } - } - return out; -}; -// output the alphabet as it appears in minimal MEME format -Alphabet.prototype.as_meme = function() { - "use strict"; - function name_as_text(name) { - var i, c, out; - out = "\""; - for (i = 0; i < name.length; i++) { - c = name.charAt(i); - if (c == "\"") { - out += "\\\""; - } else if (c == "/") { - out += "\\/"; - } else if (c == "\\") { - out += "\\\\"; - } else { - out += c; - } - } - out += "\""; - return out; - } - if (this.equals(AlphStd.DNA)) { - return "ALPHABET= ACGT\n"; - } else if (this.equals(AlphStd.PROTEIN)) { - return "ALPHABET= ACDEFGHIKLMNPQRSTVWY\n"; - } else { - return "ALPHABET" + - (this.name != null ? " " + name_as_text(this.name) : "") + - (this.like != null ? " " + this.like + "-LIKE" : "") + "\n" + - this.as_text() + "END ALPHABET\n"; - } -}; - -// Returns a table showing all the letters in the alphabet -Alphabet.prototype.as_table = function() { - "use strict"; - var i, j, row, th, td, aliases, equals, sym; - var table = document.createElement("table"); - // create the core symbol header - row = table.insertRow(table.rows.length); - th = document.createElement("th"); - th.appendChild(document.createTextNode("Symbol(s)")); - row.appendChild(th); - th = document.createElement("th"); - th.appendChild(document.createTextNode("Name")); - row.appendChild(th); - th = document.createElement("th"); - if (this.has_complement()) { - th.appendChild(document.createTextNode("Complement")); - } - row.appendChild(th); - // list the core symbols - for (i = 0; i < this.ncore; i++) { - row = table.insertRow(table.rows.length); - td = document.createElement("td"); - if (this.symbols[i].colour != null) { - td.style.color = '#' + this.symbols[i].colour; - } - td.appendChild(document.createTextNode(this.symbols[i].symbol)); - aliases = this.get_aliases(i); - if (aliases.length > 0) { - td.appendChild(document.createTextNode(' ' + aliases.split('').join(' '))); - } - row.appendChild(td); - td = document.createElement("td"); - if (this.symbols[i].name != null) { - td.appendChild(document.createTextNode(this.symbols[i].name)); - } - row.appendChild(td); - td = document.createElement("td"); - if (this.symbols[i].complement != null) { - td.style.color = this.get_colour(this.get_index(this.symbols[i].complement)); - td.appendChild(document.createTextNode(this.symbols[i].complement)); - } - row.appendChild(td); - } - // create the ambiguous symbol header - row = table.insertRow(table.rows.length); - th = document.createElement("th"); - th.appendChild(document.createTextNode("Symbol(s)")); - row.appendChild(th); - th = document.createElement("th"); - th.appendChild(document.createTextNode("Name")); - row.appendChild(th); - th = document.createElement("th"); - th.appendChild(document.createTextNode("Matches")); - row.appendChild(th); - // list the ambiguous symbols - for (i = this.ncore; i < this.symbols.length; i++) { - row = table.insertRow(table.rows.length); - td = document.createElement("td"); - if (this.symbols[i].colour != null) { - td.style.color = '#' + this.symbols[i].colour; - } - td.appendChild(document.createTextNode(this.symbols[i].symbol)); - aliases = this.get_aliases(i); - if (aliases.length > 0) { - td.appendChild(document.createTextNode(' ' + aliases.split('').join(' '))); - } - row.appendChild(td); - td = document.createElement("td"); - if (this.symbols[i].name != null) { - td.appendChild(document.createTextNode(this.symbols[i].name)); - } - row.appendChild(td); - td = document.createElement("td"); - equals = this.symbols[i].equals.split(''); - for (j = 0; j < equals.length; j++) { - if (j != 0) td.appendChild(document.createTextNode(' ')); - sym = document.createElement("span"); - sym.style.color = this.get_colour(this.get_index(equals[j])); - sym.appendChild(document.createTextNode(equals[j])); - td.appendChild(sym); - } - row.appendChild(td); - } - return table; -}; - -// returns a dictionary of the colours for EPS -Alphabet.prototype._as_eps_dict = function() { - "use strict"; - var i, sym, rgb; - var out = "/fullColourDict <<\n"; - for (i = 0; i < this.ncore; i++) { - sym = this.get_symbol(i); - sym = sym.replace(/\\/g, "\\\\"); - sym = sym.replace(/\(/g, "\\("); - sym = sym.replace(/\)/g, "\\)"); - rgb = this.get_rgb(i); - out += " (" + sym + ") [" + rgb.red.toFixed(4) + " " + rgb.green.toFixed(4) + " " + rgb.blue.toFixed(4) + "]\n"; - } - out += ">> def\n"; - out += "/mutedColourDict <<\n"; - for (i = 0; i < this.ncore; i++) { - sym = this.get_symbol(i); - sym = sym.replace(/\\/g, "\\\\"); - sym = sym.replace(/\(/g, "\\("); - sym = sym.replace(/\)/g, "\\)"); - rgb = Alphabet.lighten_colour(this.get_rgb(i)); - out += " (" + sym + ") [" + rgb.red.toFixed(4) + " " + rgb.green.toFixed(4) + " " + rgb.blue.toFixed(4) + "]\n"; - } - out += ">> def\n"; - return out; -}; - -// return the alphabet name or a list of primary symbols -Alphabet.prototype.toString = function() { - "use strict"; - if (this.name != null) { - return this.name; - } else { - return this.get_symbols(); - } -}; - -//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -// Helper functions -//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -// Convert a colour specified in RGB colourspace values into LAB colourspace -Alphabet.rgb2lab = function(rgb) { - "use strict"; - var xyzHelper, labHelper; - // XYZ helper - xyzHelper = function(value) { - if (value > 0.0445) { - value = (value + 0.055) / 1.055; - value = Math.pow(value, 2.4); - } else { - value /= 12.92; - } - value *= 100; - return value; - }; - // lab helper - labHelper = function(value) { - if (value > 0.008856) { - value = Math.pow(value, 1.0 / 3.0); - } else { - value = (7.787 * value) + (16.0 / 116.0); - } - return value; - }; - // convert into XYZ colourspace - var c1, c2, c3; - if (typeof rgb == "number") { - c1 = xyzHelper(((rgb >> 16) & 0xFF) / 255.0); - c2 = xyzHelper(((rgb >> 8) & 0xFF) / 255.0); - c3 = xyzHelper((rgb & 0xFF) / 255.0); - } else { - c1 = xyzHelper(rgb.red); - c2 = xyzHelper(rgb.green); - c3 = xyzHelper(rgb.blue); - } - var x = (c1 * 0.4124) + (c2 * 0.3576) + (c3 * 0.1805); - var y = (c1 * 0.2126) + (c2 * 0.7152) + (c3 * 0.0722); - var z = (c1 * 0.0193) + (c2 * 0.1192) + (c3 * 0.9505); - // convert into Lab colourspace - c1 = labHelper(x / 95.047); - c2 = labHelper(y / 100.0); - c3 = labHelper(z / 108.883); - var l = (116.0 * c2) - 16; - var a = 500.0 * (c1 - c2); - var b = 200.0 * (c2 - c3); - return {"l": l, "a": a, "b": b}; -}; - -// Convert a colour specified in HSV colourspace into RGB colourspace -Alphabet.hsv2rgb = function(hue, sat, value, output_object) { - // achromatic (grey) - var r = value; - var g = value; - var b = value; - if (sat != 0) { - var h = hue / 60.0; - var i = Math.floor(h); - var f = h - i; - var p = value * (1.0 - sat); - var q = value * (1.0 - (sat * f)); - var t = value * (1.0 - (sat * (1.0 - f))); - if (i == 0) { - r = value; - g = t; - b = p; - } else if (i == 1) { - r = q; - g = value; - b = p; - } else if (i == 2) { - r = p; - g = value; - b = t; - } else if (i == 3) { - r = p; - g = q; - b = value; - } else if (i == 4) { - r = t; - g = p; - b = value; - } else { - r = value; - g = p; - b = q; - } - } - if (output_object) { - return {"red": r, "green": g, "blue": b}; - } else { - return (Math.floor(r * 255) << 15) | (Math.floor(g * 255) << 8) | (Math.floor(b * 255)); - } -}; - -// Calculate a distance score between two colours in LAB colourspace -Alphabet.lab_dist = function(lab1, lab2) { - var c1 = Math.sqrt((lab1.l * lab1.l) + (lab1.a * lab1.a)); - var c2 = Math.sqrt((lab2.l * lab2.l) + (lab2.a * lab2.a)); - var dc = c1 - c2; - var dl = lab1.l - lab2.l; - var da = lab1.a - lab2.a; - var db = lab1.b - lab2.b; - // we don't want NaN due to rounding errors so fudge things a bit... - var dh = 0; - var dh_squared = (da * da) + (db * db) - (dc * dc); - if (dh_squared > 0) { - dh = Math.sqrt(dh_squared); - } - var first = dl; - var second = dc / (1.0 + (0.045 * c1)); - var third = dh / (1.0 + (0.015 * c1)); - return Math.sqrt((first * first) + (second * second) + (third * third)); -}; - -// convert an RGB value into a HSL value -Alphabet.rgb2hsl = function(rgb) { - "use strict"; - var min, max, delta, h, s, l, r, g, b; - if (typeof rgb == "number") { - r = ((rgb >> 16) & 0xFF) / 255.0; - g = ((rgb >> 8) & 0xFF) / 255.0; - b = (rgb & 0xFF) / 255.0; - } else { - r = rgb.red; - g = rgb.green; - b = rgb.blue; - } - min = Math.min(r, g, b); - max = Math.max(r, g, b); - delta = max - min; - l = min + (delta / 2); - if (max == min) { - h = 0; // achromatic (grayscale) - s = 0; - } else { - if (l > 0.5) { - s = delta / (2 - max - min); - } else { - s = delta / (max + min); - } - if (max == r) { - h = (g - b) / delta; - if (g < b) h += 6; - } else if (max == g) { - h = ((b - r) / delta) + 2; - } else { - h = ((r - g) / delta) + 4; - } - h /= 6; - } - return {"h": h, "s": s, "l": l}; -}; - -// convert a HSL value into an RGB value -Alphabet.hsl2rgb = function(hsl, output_object) { - "use strict"; - function _hue(p, q, t) { - "use strict"; - if (t < 0) t += 1; - else if (t > 1) t -= 1; - if (t < (1.0 / 6.0)) { - return p + ((q - p) * 6.0 * t); - } else if (t < 0.5) { - return q; - } else if (t < (2.0 / 3.0)) { - return p + ((q - p) * ((2.0 / 3.0) - t) * 6.0); - } else { - return p; - } - } - var r, g, b, p, q; - if (hsl.s == 0) { - // achromatic (grayscale) - r = hsl.l; - g = hsl.l; - b = hsl.l; - } else { - if (hsl.l < 0.5) { - q = hsl.l * (1 + hsl.s); - } else { - q = hsl.l + hsl.s - (hsl.l * hsl.s); - } - p = (2 * hsl.l) - q; - r = _hue(p, q, hsl.h + (1.0 / 3.0)); - g = _hue(p, q, hsl.h); - b = _hue(p, q, hsl.h - (1.0 / 3.0)); - } - if (output_object) { - return {"red": r, "green": g, "blue": b}; - } else { - return (Math.floor(r * 255) << 15) | (Math.floor(g * 255) << 8) | (Math.floor(b * 255)); - } -}; - -Alphabet.lighten_colour = function(rgb) { - "use strict"; - var hsl = Alphabet.rgb2hsl(rgb); - hsl.l += (1.0 - hsl.l) * 2 / 3; - return Alphabet.hsl2rgb(hsl, typeof rgb != "number"); -}; - -//====================================================================== -// end Alphabet object -//====================================================================== - -//====================================================================== -// start StandardAlphabet object -//====================================================================== - -// an extension of the alphabet object to support some additional fields -// only present in standard alphabets. -var StandardAlphabet = function(enum_code, enum_name, alphabet_data) { - Alphabet.apply(this, [alphabet_data]); - this.enum_code = enum_code; - this.enum_name = enum_name; -}; -StandardAlphabet.prototype = Alphabet.prototype; -StandardAlphabet.prototype.constructor = StandardAlphabet; - -// A unique code for this standard alphabet. -// This code will be a power of 2 to enable creation of bitsets for -// a selection of standard alphabets. -StandardAlphabet.prototype.get_code = function() { - return this.enum_code; -}; - -// A unique name for this standard alphabet. -// this name will be all upper case and the same as the property that -// refers to this alphabet in the AlphStd collection. -StandardAlphabet.prototype.get_enum = function() { - return this.enum_name; -}; - -//====================================================================== -// end StandardAlphabet object -//====================================================================== - -// A collection of standard alphabets. -var AlphStd = { - RNA: new StandardAlphabet(1, "RNA", { - "name": "RNA", - "like": "RNA", - "ncore": 4, - "symbols": [ - {"symbol": "A", "name": "Adenine", "colour": "CC0000"}, - {"symbol": "C", "name": "Cytosine", "colour": "0000CC"}, - {"symbol": "G", "name": "Guanine", "colour": "FFB300"}, - {"symbol": "U", "name": "Uracil", "colour": "008000", - "aliases": "T"}, - {"symbol": "N", "name": "Any base", "equals": "ACGU", "aliases": "X."}, - {"symbol": "V", "name": "Not U", "equals": "ACG"}, - {"symbol": "H", "name": "Not G", "equals": "ACU"}, - {"symbol": "D", "name": "Not C", "equals": "AGU"}, - {"symbol": "B", "name": "Not A", "equals": "CGU"}, - {"symbol": "M", "name": "Amino", "equals": "AC"}, - {"symbol": "R", "name": "Purine", "equals": "AG"}, - {"symbol": "W", "name": "Weak", "equals": "AU"}, - {"symbol": "S", "name": "Strong", "equals": "CG"}, - {"symbol": "Y", "name": "Pyrimidine", "equals": "CU"}, - {"symbol": "K", "name": "Keto", "equals": "GU"} - ] - }), - DNA: new StandardAlphabet(2, "DNA", { - "name": "DNA", - "like": "DNA", - "ncore": 4, - "symbols": [ - {"symbol": "A", "name": "Adenine", "colour": "CC0000", "complement": "T"}, - {"symbol": "C", "name": "Cytosine", "colour": "0000CC", "complement": "G"}, - {"symbol": "G", "name": "Guanine", "colour": "FFB300", "complement": "C"}, - {"symbol": "T", "name": "Thymine", "colour": "008000", "complement": "A", - "aliases": "U"}, - {"symbol": "N", "name": "Any base", "equals": "ACGT", "aliases": "X."}, - {"symbol": "V", "name": "Not T", "equals": "ACG"}, - {"symbol": "H", "name": "Not G", "equals": "ACT"}, - {"symbol": "D", "name": "Not C", "equals": "AGT"}, - {"symbol": "B", "name": "Not A", "equals": "CGT"}, - {"symbol": "M", "name": "Amino", "equals": "AC"}, - {"symbol": "R", "name": "Purine", "equals": "AG"}, - {"symbol": "W", "name": "Weak", "equals": "AT"}, - {"symbol": "S", "name": "Strong", "equals": "CG"}, - {"symbol": "Y", "name": "Pyrimidine", "equals": "CT"}, - {"symbol": "K", "name": "Keto", "equals": "GT"} - ] - }), - PROTEIN: new StandardAlphabet(4, "PROTEIN", { - "name": "Protein", - "like": "PROTEIN", - "ncore": 20, - "symbols": [ - {"symbol": "A", "name": "Alanine", "colour": "0000CC"}, - {"symbol": "C", "name": "Cysteine", "colour": "0000CC"}, - {"symbol": "D", "name": "Aspartic acid", "colour": "FF00FF"}, - {"symbol": "E", "name": "Glutamic acid", "colour": "FF00FF"}, - {"symbol": "F", "name": "Phenylalanine", "colour": "0000CC"}, - {"symbol": "G", "name": "Glycine", "colour": "FFB300"}, - {"symbol": "H", "name": "Histidine", "colour": "FFCCCC"}, - {"symbol": "I", "name": "Isoleucine", "colour": "0000CC"}, - {"symbol": "K", "name": "Lysine", "colour": "CC0000"}, - {"symbol": "L", "name": "Leucine", "colour": "0000CC"}, - {"symbol": "M", "name": "Methionine", "colour": "0000CC"}, - {"symbol": "N", "name": "Asparagine", "colour": "008000"}, - {"symbol": "P", "name": "Proline", "colour": "FFFF00"}, - {"symbol": "Q", "name": "Glutamine", "colour": "008000"}, - {"symbol": "R", "name": "Arginine", "colour": "CC0000"}, - {"symbol": "S", "name": "Serine", "colour": "008000"}, - {"symbol": "T", "name": "Threonine", "colour": "008000"}, - {"symbol": "V", "name": "Valine", "colour": "0000CC"}, - {"symbol": "W", "name": "Tryptophan", "colour": "0000CC"}, - {"symbol": "Y", "name": "Tyrosine", "colour": "33E6CC"}, - {"symbol": "X", "name": "Any amino acid", "equals": "ACDEFGHIKLMNPQRSTVWY", "aliases": "*."}, - {"symbol": "B", "name": "Asparagine or Aspartic acid", "equals": "DN"}, - {"symbol": "Z", "name": "Glutamine or Glutamic acid", "equals": "EQ"}, - {"symbol": "J", "name": "Leucine or Isoleucine", "equals": "IL"} - ] - }) -}; - -//====================================================================== -// start Symbol object -//====================================================================== -var Symbol = function(alph_index, scale, alphabet) { - "use strict"; - //variable prototype - this.symbol = alphabet.get_symbol(alph_index); - this.scale = scale; - this.colour = alphabet.get_colour(alph_index); -}; - -Symbol.prototype.get_symbol = function() { - "use strict"; - return this.symbol; -}; - -Symbol.prototype.get_scale = function() { - "use strict"; - return this.scale; -}; - -Symbol.prototype.get_colour = function() { - "use strict"; - return this.colour; -}; - -Symbol.prototype.toString = function() { - "use strict"; - return this.symbol + " " + (Math.round(this.scale*1000)/10) + "%"; -}; - -function compare_symbol(sym1, sym2) { - "use strict"; - if (sym1.get_scale() < sym2.get_scale()) { - return -1; - } else if (sym1.get_scale() > sym2.get_scale()) { - return 1; - } else { - return 0; - } -} -//====================================================================== -// end Symbol object -//====================================================================== - -//====================================================================== -// start Pspm object -//====================================================================== -var Pspm = function(matrix, name, ltrim, rtrim, nsites, evalue, pssm, alt) { - "use strict"; - var row, col, data, row_sum, delta, evalue_re; - if (typeof name !== "string") { - name = ""; - } - this.name = name; - //construct - if (matrix instanceof Pspm) { - // copy constructor - this.alph_length = matrix.alph_length; - this.motif_length = matrix.motif_length; - this.name = matrix.name; - this.alt = matrix.alt; - this.nsites = matrix.nsites; - this.evalue = matrix.evalue; - this.ltrim = matrix.ltrim; - this.rtrim = matrix.rtrim; - this.pspm = []; - for (row = 0; row < matrix.motif_length; row++) { - this.pspm[row] = []; - for (col = 0; col < matrix.alph_length; col++) { - this.pspm[row][col] = matrix.pspm[row][col]; - } - } - if (matrix.pssm != null) { - this.pssm = []; - for (row = 0; row < matrix.motif_length; row++) { - this.pspm[row] = []; - for (col = 0; col < matrix.alph_length; col++) { - this.pssm[row][col] = matrix.pssm[row][col]; - } - } - } - } else { - // check parameters - if (ltrim == null) { - ltrim = 0; - } else if (typeof ltrim !== "number" || ltrim % 1 !== 0 || ltrim < 0) { - throw new Error("ltrim must be a non-negative integer, got: " + ltrim); - } - if (rtrim == null) { - rtrim = 0; - } else if (typeof rtrim !== "number" || rtrim % 1 !== 0 || rtrim < 0) { - throw new Error("rtrim must be a non-negative integer, got: " + rtrim); - } - if (nsites != null) { - if (typeof nsites !== "number" || nsites < 0) { - throw new Error("nsites must be a positive number, got: " + nsites); - } else if (nsites == 0) { - nsites = null; - } - } - if (evalue != null) { - if (typeof evalue === "number") { - if (evalue < 0) { - throw new Error("evalue must be a non-negative number, got: " + evalue); - } - } else if (typeof evalue === "string") { - evalue_re = /^((?:[+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)|inf)$/; - if (!evalue_re.test(evalue)) { - throw new Error("evalue must be a non-negative number, got: " + evalue); - } - } else { - throw new Error("evalue must be a non-negative number, got: " + evalue); - } - } - // set properties - this.name = name; - this.alt = alt; - this.nsites = nsites; - this.evalue = evalue; - this.ltrim = ltrim; - this.rtrim = rtrim; - if (typeof matrix === "string") { - // string constructor - data = parse_pspm_string(matrix); - this.alph_length = data["alph_length"]; - this.motif_length = data["motif_length"]; - this.pspm = data["pspm"]; - if (this.evalue == null) { - if (data["evalue"] != null) { - this.evalue = data["evalue"]; - } else { - this.evalue = 0; - } - } - if (this.nsites == null) { - if (typeof data["nsites"] === "number") { - this.nsites = data["nsites"]; - } else { - this.nsites = 20; - } - } - } else { - // assume pspm is a nested array - this.motif_length = matrix.length; - this.alph_length = (matrix.length > 0 ? matrix[0].length : 0); - if (this.nsites == null) { - this.nsites = 20; - } - if (this.evalue == null) { - this.evalue = 0; - } - this.pspm = []; - // copy pspm and check - for (row = 0; row < this.motif_length; row++) { - if (this.alph_length != matrix[row].length) { - throw new Error("COLUMN_MISMATCH"); - } - this.pspm[row] = []; - row_sum = 0; - for (col = 0; col < this.alph_length; col++) { - this.pspm[row][col] = matrix[row][col]; - row_sum += this.pspm[row][col]; - } - delta = 0.1; - if (isNaN(row_sum) || (row_sum > 1 && (row_sum - 1) > delta) || - (row_sum < 1 && (1 - row_sum) > delta)) { - throw new Error("INVALID_SUM"); - } - } - // copy pssm - if (pssm != null) { - this.pssm = []; - for (row = 0; row < this.motif_length; row++) { - this.pssm[row] = []; - for (col = 0; col < this.alph_length; col++) { - this.pssm[row][col] = pssm[row][col]; - } - } - } - } - } -}; - -Pspm.prototype.copy = function() { - "use strict"; - return new Pspm(this); -}; - -Pspm.prototype.reverse = function() { - "use strict"; - var x, y, temp, temp_trim; - //reverse - x = 0; - y = this.motif_length-1; - while (x < y) { - temp = this.pspm[x]; - this.pspm[x] = this.pspm[y]; - this.pspm[y] = temp; - x++; - y--; - } - // reverse pssm (if defined) - if (typeof this.pssm !== "undefined") { - //reverse - x = 0; - y = this.motif_length-1; - while (x < y) { - temp = this.pssm[x]; - this.pspm[x] = this.pssm[y]; - this.pssm[y] = temp; - x++; - y--; - } - } - //swap triming - temp_trim = this.ltrim; - this.ltrim = this.rtrim; - this.rtrim = temp_trim; - return this; //allow function chaining... -}; - -Pspm.prototype.reverse_complement = function(alphabet) { - "use strict"; - var x, y, temp, i, row, c, temp_trim; - if (this.alph_length != alphabet.get_size_core()) { - throw new Error("The alphabet size does not match the size of the pspm."); - } - if (!alphabet.has_complement()) { - throw new Error("The specified alphabet can not be complemented."); - } - // reverse motif - this.reverse(); - //complement - for (x = 0; x < this.motif_length; x++) { - row = this.pspm[x]; - for (i = 0; i < row.length; i++) { - c = alphabet.get_complement(i); - if (c < i) continue; - temp = row[i]; - row[i] = row[c]; - row[c] = temp; - } - } - // complement pssm (if defined) - if (typeof this.pssm !== "undefined") { - //complement - for (x = 0; x < this.motif_length; x++) { - row = this.pssm[x]; - for (i = 0; i < row.length; i++) { - c = alphabet.get_complement(i); - if (c < i) continue; - temp = row[i]; - row[i] = row[c]; - row[c] = temp; - } - } - } - return this; //allow function chaining... -}; - -Pspm.prototype.get_stack = function(position, alphabet, ssc) { - "use strict"; - var row, stack_ic, alphabet_ic, stack, i, sym; - if (this.alph_length != alphabet.get_size_core()) { - throw new Error("The alphabet size does not match the size of the pspm."); - } - row = this.pspm[position]; - stack_ic = this.get_stack_ic(position, alphabet); - if (ssc) stack_ic -= this.get_error(alphabet); - alphabet_ic = alphabet.get_ic(); - stack = []; - for (i = 0; i < this.alph_length; i++) { - sym = new Symbol(i, row[i]*stack_ic/alphabet_ic, alphabet); - if (sym.get_scale() <= 0) { - continue; - } - stack.push(sym); - } - stack.sort(compare_symbol); - return stack; -}; - -Pspm.prototype.get_stack_ic = function(position, alphabet) { - "use strict"; - var row, H, i; - if (this.alph_length != alphabet.get_size_core()) { - throw new Error("The alphabet size does not match the size fo the pspm."); - } - row = this.pspm[position]; - H = 0; - for (i = 0; i < this.alph_length; i++) { - if (row[i] === 0) { - continue; - } - H -= (row[i] * (Math.log(row[i]) / Math.LN2)); - } - return alphabet.get_ic() - H; -}; - -Pspm.prototype.get_error = function(alphabet) { - "use strict"; - if (this.nsites === 0) { - return 0; - } - return (alphabet.get_size_core()-1) / (2 * Math.LN2 * this.nsites); -}; - -Pspm.prototype.get_motif_length = function() { - "use strict"; - return this.motif_length; -}; - -Pspm.prototype.get_alph_length = function() { - "use strict"; - return this.alph_length; -}; - -Pspm.prototype.get_left_trim = function() { - "use strict"; - return this.ltrim; -}; - -Pspm.prototype.get_right_trim = function() { - "use strict"; - return this.rtrim; -}; - -Pspm.prototype.as_best_match = function(alphabet) { - "use strict"; - var match, odds, best_odds, best_index; - var i, j; - match = ""; - for (i = 0; i < this.motif_length; i++) { - best_index = 0; - best_odds = this.pspm[i][0] / alphabet.get_bg_freq(0); - for (j = 1; j < this.alph_length; j++) { - odds = this.pspm[i][j] / alphabet.get_bg_freq(j); - if (odds > best_odds) { - best_odds = odds; - best_index = j; - } - } - match += alphabet.get_symbol(best_index); - } - return match; -}; - -Pspm.prototype.as_count_matrix = function() { - "use strict"; - var count, count_text, text; - var i, j; - text = ""; - for (i = 0; i < this.motif_length; i++) { - if (i !== 0) { - text += "\n"; - } - for (j = 0; j < this.alph_length; j++) { - if (j !== 0) { - text += " "; - } - count = Math.round(this.nsites * this.pspm[i][j]); - count_text = "" + count; - // pad up to length of 4 - if (count_text.length < 4) { - text += (new Array(5 - count_text.length)).join(" ") + count_text; - } else { - text += count_text; - } - } - } - return text; -}; - -Pspm.prototype.as_probability_matrix = function() { - "use strict"; - var text; - var i, j; - text = ""; - for (i = 0; i < this.motif_length; i++) { - if (i !== 0) { - text += "\n"; - } - for (j = 0; j < this.alph_length; j++) { - if (j !== 0) { - text += " "; - } - text += this.pspm[i][j].toFixed(6); - } - } - return text; -}; - -Pspm.prototype.as_score_matrix = function(alphabet, pseudo) { - "use strict"; - var me, score, out, row, col, score_text; - me = this; - if (typeof this.pssm === "undefined") { - if (!(typeof alphabet === "object" && alphabet != null && alphabet instanceof Alphabet)) { - throw new Error("The alphabet is required to generate the pssm."); - } - if (typeof pseudo === "undefined") { - pseudo = 0.01; - } else if (typeof pseudo !== "number" || pseudo < 0) { - throw new Error("Expected positive number for pseudocount"); - } - score = function(row, col) { - "use strict"; - var p, bg, p2; - p = me.pspm[row][col]; - bg = alphabet.get_bg_freq(col); - p2 = (p * me.nsites + bg * pseudo) / (me.nsites + pseudo); - return (p2 > 0 ? Math.round((Math.log(p2 / bg) / Math.LN2) * 100) : -10000); - }; - } else { - score = function(row, col) { - "use strict"; - return me.pssm[row][col]; - }; - } - out = ""; - for (row = 0; row < this.motif_length; row++) { - for (col = 0; col < this.alph_length; col++) { - if (col !== 0) { - out += " "; - } - score_text = "" + score(row, col); - // pad out to 6 characters - if (score_text.length < 6) { - out += (new Array(7 - score_text.length)).join(" ") + score_text; - } else { - out += score_text; - } - } - out += "\n"; - } - return out; -} - -Pspm.prototype.as_pspm = function() { - "use strict"; - return "letter-probability matrix: alength= " + this.alph_length + - " w= " + this.motif_length + " nsites= " + this.nsites + - " E= " + (typeof this.evalue === "number" ? - this.evalue.toExponential() : this.evalue) + "\n" + - this.as_probability_matrix(); -}; - -Pspm.prototype.as_pssm = function(alphabet, pseudo) { - "use strict"; - return "log-odds matrix: alength= " + this.alph_length + - " w= " + this.motif_length + - " E= " + (typeof this.evalue == "number" ? - this.evalue.toExponential() : this.evalue) + "\n" + - this.as_score_matrix(alphabet, pseudo); -}; - -Pspm.prototype.as_meme = function(options) { - var with_header, with_pspm, with_pssm, version, alphabet, bg_source, pseudocount, strands; - var out, alen, i; - // get the options - if (typeof options !== "object" || options === null) { - options = {}; - } - with_header = (typeof options["with_header"] === "boolean" ? options["with_header"] : false); - with_pspm = (typeof options["with_pspm"] === "boolean" ? options["with_pspm"] : false); - with_pssm = (typeof options["with_pssm"] === "boolean" ? options["with_pssm"] : false); - if (!with_pspm && !with_pssm) with_pspm = true; - if (with_header) { - if (typeof options["version"] === "string" && /^\d+(?:\.\d+){0,2}$/.test(options["version"])) { - version = options["version"]; - } else if (typeof options["version"] === "number") { - version = options["version"].toFixed(0); - } else { - version = "4"; - } - if (typeof options["strands"] === "number" && options["strands"] === 1) { - strands = 1; - } else { - strands = 2; - } - if (typeof options["bg_source"] === "string") { - bg_source = options["bg_source"]; - } else { - bg_source = "unknown source"; - } - if (typeof options["alphabet"] === "object" && options["alphabet"] != null - && options["alphabet"] instanceof Alphabet) { - alphabet = options["alphabet"]; - } else { - throw new Error("The alphabet is required to generate the header."); - } - } - // now create the output - out = ""; - if (with_header) { - out = "MEME version " + version + "\n\n"; - out += alphabet.as_meme() + "\n"; - if (alphabet.has_complement()) { // assume DNA has both strands unless otherwise specified - out += "strands: " + (strands === 1 ? "+" : "+ -") + "\n\n"; - } - out += "Background letter frequencies (from " + bg_source + "):\n"; - alen = alphabet.get_size_core(); - for (i = 0; i < alen; i++) { - if (i !== 0) { - if (i % 9 === 0) { // maximum of nine entries per line - out += "\n"; - } else { - out += " "; - } - } - out += alphabet.get_symbol(i) + " " + alphabet.get_bg_freq(i).toFixed(3); - } - } - out += "\n\n"; - out += "MOTIF " + this.name + (this.alt == null ? "" : " " + this.alt); - if (with_pssm) { - out += "\n\n"; - out += this.as_pssm(options["alphabet"], options["pseudocount"]); - } - if (with_pspm) { - out += "\n\n"; - out += this.as_pspm(); - } - return out; -} - -Pspm.prototype.toString = function() { - "use strict"; - var str, i, row; - str = ""; - for (i = 0; i < this.pspm.length; i++) { - row = this.pspm[i]; - str += row.join("\t") + "\n"; - } - return str; -}; - -function parse_pspm_properties(str) { - "use strict"; - var parts, i, eqpos, before, after, properties, prop, num, num_re; - num_re = /^((?:[+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)|inf)$/; - parts = trim(str).split(/\s+/); - // split up words containing = - for (i = 0; i < parts.length;) { - eqpos = parts[i].indexOf("="); - if (eqpos != -1) { - before = parts[i].substr(0, eqpos); - after = parts[i].substr(eqpos+1); - if (before.length > 0 && after.length > 0) { - parts.splice(i, 1, before, "=", after); - i += 3; - } else if (before.length > 0) { - parts.splice(i, 1, before, "="); - i += 2; - } else if (after.length > 0) { - parts.splice(i, 1, "=", after); - i += 2; - } else { - parts.splice(i, 1, "="); - i++; - } - } else { - i++; - } - } - properties = {}; - for (i = 0; i < parts.length; i += 3) { - if (parts.length - i < 3) { - throw new Error("Expected PSPM property was incomplete. "+ - "Remaing parts are: " + parts.slice(i).join(" ")); - } - if (parts[i+1] !== "=") { - throw new Error("Expected '=' in PSPM property between key and " + - "value but got " + parts[i+1]); - } - prop = parts[i].toLowerCase(); - num = parts[i+2]; - if (!num_re.test(num)) { - throw new Error("Expected numeric value for PSPM property '" + - prop + "' but got '" + num + "'"); - } - properties[prop] = num; - } - return properties; -} - -function parse_pspm_string(pspm_string) { - "use strict"; - var header_re, lines, first_line, line_num, col_num, alph_length, - motif_length, nsites, evalue, pspm, i, line, match, props, parts, - j, prob; - header_re = /^letter-probability\s+matrix:(.*)$/i; - lines = pspm_string.split(/\n/); - first_line = true; - line_num = 0; - col_num = 0; - alph_length; - motif_length; - nsites; - evalue; - pspm = []; - for (i = 0; i < lines.length; i++) { - line = trim(lines[i]); - if (line.length === 0) { - continue; - } - // check the first line for a header though allow matrices without it - if (first_line) { - first_line = false; - match = header_re.exec(line); - if (match !== null) { - props = parse_pspm_properties(match[1]); - if (props.hasOwnProperty("alength")) { - alph_length = parseFloat(props["alength"]); - if (alph_length != 4 && alph_length != 20) { - throw new Error("PSPM property alength should be 4 or 20" + - " but got " + alph_length); - } - } - if (props.hasOwnProperty("w")) { - motif_length = parseFloat(props["w"]); - if (motif_length % 1 !== 0 || motif_length < 1) { - throw new Error("PSPM property w should be an integer larger " + - "than zero but got " + motif_length); - } - } - if (props.hasOwnProperty("nsites")) { - nsites = parseFloat(props["nsites"]); - if (nsites <= 0) { - throw new Error("PSPM property nsites should be larger than " + - "zero but got " + nsites); - } - } - if (props.hasOwnProperty("e")) { - evalue = props["e"]; - if (evalue < 0) { - throw new Error("PSPM property evalue should be " + - "non-negative but got " + evalue); - } - } - continue; - } - } - pspm[line_num] = []; - col_num = 0; - parts = line.split(/\s+/); - for (j = 0; j < parts.length; j++) { - prob = parseFloat(parts[j]); - if (prob != parts[j] || prob < 0 || prob > 1) { - throw new Error("Expected probability but got '" + parts[j] + "'"); - } - pspm[line_num][col_num] = prob; - col_num++; - } - line_num++; - } - if (typeof motif_length === "number") { - if (pspm.length != motif_length) { - throw new Error("Expected PSPM to have a motif length of " + - motif_length + " but it was actually " + pspm.length); - } - } else { - motif_length = pspm.length; - } - if (typeof alph_length !== "number") { - alph_length = pspm[0].length; - if (alph_length != 4 && alph_length != 20) { - throw new Error("Expected length of first row in the PSPM to be " + - "either 4 or 20 but got " + alph_length); - } - } - for (i = 0; i < pspm.length; i++) { - if (pspm[i].length != alph_length) { - throw new Error("Expected PSPM row " + i + " to have a length of " + - alph_length + " but the length was " + pspm[i].length); - } - } - return {"pspm": pspm, "motif_length": motif_length, - "alph_length": alph_length, "nsites": nsites, "evalue": evalue}; -} -//====================================================================== -// end Pspm object -//====================================================================== - -//====================================================================== -// start Logo object -//====================================================================== - -var Logo = function(alphabet, options) { - "use strict"; - this.alphabet = alphabet; - this.fine_text = ""; - this.x_axis = 1; - this.y_axis = true; - this.xlate_nsyms = 1; - this.xlate_start = null; - this.xlate_end = null; - this.pspm_list = []; - this.pspm_column = []; - this.rows = 0; - this.columns = 0; - if (typeof options === "string") { - // the old method signature had fine_text here so we support that - this.fine_text = options; - } else if (typeof options === "object" && options != null) { - this.fine_text = (typeof options.fine_text === "string" ? options.fine_text : ""); - this.x_axis = (typeof options.x_axis === "boolean" ? (options.x_axis ? 1 : 0) : 1); - if (options.x_axis_hidden != null && options.x_axis_hidden) this.x_axis = -1; - this.y_axis = (typeof options.y_axis === "boolean" ? options.y_axis : true); - this.xlate_nsyms = (typeof options.xlate_nsyms === "number" ? options.xlate_nsyms : this.xlate_nsyms); - this.xlate_start = (typeof options.xlate_start === "number" ? options.xlate_start : this.xlate_start); - this.xlate_end = (typeof options.xlate_end === "number" ? options.xlate_end : this.xlate_end); - } -}; - -Logo.prototype.add_pspm = function(pspm, column) { - "use strict"; - var col; - if (typeof column === "undefined") { - column = 0; - } else if (column < 0) { - throw new Error("Column index out of bounds."); - } - this.pspm_list[this.rows] = pspm; - this.pspm_column[this.rows] = column; - this.rows++; - col = column + pspm.get_motif_length(); - if (col > this.columns) { - this.columns = col; - } -}; - -Logo.prototype.get_columns = function() { - "use strict"; - return this.columns; -}; - -Logo.prototype.get_xlate_nsyms = function() { - "use strict"; - return this.xlate_nsyms; -}; - -Logo.prototype.get_xlate_start = function() { - "use strict"; - return (this.xlate_start != null ? this.xlate_start : 0); -}; - -Logo.prototype.get_xlate_end = function() { - "use strict"; - return (this.xlate_end != null ? this.xlate_end : this.columns * this.xlate_nsyms); -}; - -Logo.prototype.get_xlate_columns = function() { - "use strict"; - return this.get_xlate_end() - this.get_xlate_start(); -}; - -Logo.prototype.get_rows = function() { - "use strict"; - return this.rows; -}; - -Logo.prototype.get_pspm = function(row_index) { - "use strict"; - if (row_index < 0 || row_index >= this.rows) { - throw new Error("INDEX_OUT_OF_BOUNDS"); - } - return this.pspm_list[row_index]; -}; - -Logo.prototype.get_offset = function(row_index) { - "use strict"; - if (row_index < 0 || row_index >= this.rows) { - throw new Error("INDEX_OUT_OF_BOUNDS"); - } - return this.pspm_column[row_index]; -}; - -Logo.prototype._as_eps_data = function(ssc, errbars) { - var i, j, pos, stack_pos, pspm, stack, sym, out; - out = ""; - for (i = 0; i < this.rows; i++) { - out += "\nStartLine\n"; - // Indent - for (j = 0; j < this.pspm_column[i]; j++) { - out += "() startstack\nendstack\n\n"; - } - pspm = this.pspm_list[i]; - if (pspm.get_left_trim() > 0) { - out += "MuteColour\nDrawTrimEdge\n" + pspm.get_left_trim() + " DrawTrimBg\n"; - } - for (pos = 0; pos < pspm.get_motif_length(); pos++) { - if (pos != 0 && pos == pspm.get_left_trim()) { // enable full colour - out += "DrawTrimEdge\nRestoreColour\n"; - } else if (pos == (pspm.get_motif_length() - pspm.get_right_trim())) { - out += "MuteColour\n" + pspm.get_right_trim() + " DrawTrimBg\n"; - } - out += "(" + (pos + 1) + ") startstack\n"; - stack = pspm.get_stack(pos, this.alphabet, ssc); - for (stack_pos = 0; stack_pos < stack.length; stack_pos++) { - sym = stack[stack_pos]; - out += " " + (sym.get_scale() * this.alphabet.get_ic()) + " (" + sym.get_symbol() + ") numchar\n"; - } - if (errbars) { - out += " " + pspm.get_error(this.alphabet) + " Ibeam\n"; - } - out += "endstack\n\n"; - } - if (pspm.get_right_trim() > 0 || pspm.get_left_trim() == pspm.get_motif_length()) { - out += "RestoreColour\n"; - } - out += "EndLine\n"; - } - return out; -}; - -Logo.prototype.as_eps = function(options) { - "use strict"; - if (this.xlate_nsyms != 1) throw new Error("Unsupported setting xlate_nsyms for EPS"); - if (this.xlate_start != null) throw new Error("Unsupported setting xlate_start for EPS"); - if (this.xlate_end != null) throw new Error("Unsupported setting xlate_end for EPS"); - - var LOGOHEIGHT = 7.5; // default height of line in cm - var cm2pts, height, width, now, ssc, errbars; - if (typeof options === "undefined") { - options = {}; - } - cm2pts = 72 / 2.54; - if (typeof options.logo_height == "number") { - height = options.logo_height; - } else { - height = LOGOHEIGHT * this.rows; - } - if (typeof options.logo_width == "number") { - width = options.logo_width; - } else { - width = this.columns + 2; - } - now = new Date(); - ssc = (typeof options.ssc == "boolean" ? options.ssc : false); - errbars = (typeof options.show_error_bar == "boolean" ? options.show_error_bar : ssc); - var values = { - "LOGOHEIGHT": height, - "LOGOWIDTH": width, - "BOUNDINGHEIGHT": Math.round(height * cm2pts), - "BOUNDINGWIDTH": Math.round(width * cm2pts), - "LOGOLINEHEIGHT": (height / this.rows), - "CHARSPERLINE": this.columns, - "BARBITS": this.alphabet.get_ic(), - "LOGOTYPE": (this.alphabet.has_complement() ? "NA" : "AA"), - "CREATIONDATE": now.getDate() + "." + (now.getMonth() + 1) + "." + now.getFullYear() + " " + now.getHours() + ":" + now.getMinutes() + ":" + now.getSeconds(), - "ERRORBARFRACTION": (typeof options.error_bar_fraction == "number" ? options.error_bar_fraction : 1.0), - "TICBITS": (typeof options.ticbits == "number" ? options.ticbits : 1.0), - "TITLE": (typeof options.title == "string" ? options.title : ""), - "FINEPRINT": (typeof options.fineprint == "string" ? options.fineprint : this.fine_text), - "XAXISLABEL": (typeof options.xaxislabel == "string" ? options.xaxislabel : ""), - "YAXISLABEL": (typeof options.yaxislabel == "string" ? options.yaxislabel : "bits"), - "SSC": ssc, - "YAXIS": (typeof options.show_y_axis == "boolean" ? options.show_y_axis : this.y_axis), - "SHOWENDS": (typeof options.show_ends == "boolean" ? options.show_ends : false), - "ERRBAR": errbars, - "OUTLINE": (typeof options.show_outline == "boolean" ? options.show_outline : false), - "NUMBERING": (typeof options.show_numbering == "boolean" ? options.show_numbering : this.x_axis != 0), - "SHOWINGBOX": (typeof options.show_box == "boolean" ? options.show_box : false), - "CREATOR": (typeof options.creator == "string" ? options.creator : "motif_logo.js"), - "FONTSIZE": (typeof options.label_font_size == "number" ? options.label_font_size : 12), - "TITLEFONTSIZE": (typeof options.title_font_size == "number" ? options.title_font_size : 12), - "SMALLFONTSIZE": (typeof options.small_font_size == "number" ? options.small_font_size : 6), - "TOPMARGIN" : (typeof options.top_margin == "number" ? options.top_margin : 0.9), - "BOTTOMMARGIN": (typeof options.bottom_margin == "number" ? options.bottom_margin : 0.9), - "COLORDICT": this.alphabet._as_eps_dict(), - "DATA": this._as_eps_data(ssc, errbars) - }; - // now this requires that the script containing the template has been imported! - return motif_logo_template(values); -}; - -//====================================================================== -// end Logo object -//====================================================================== - -// calculate the exact size (in pixels) of an object drawn on the -// canvas assuming that the background of the canvas is transparent. -function canvas_bounds(ctx, cwidth, cheight) { - "use strict"; - var data, r, c, top_line, bottom_line, left_line, right_line, - txt_width, txt_height; - - // extract the image data - data = ctx.getImageData(0, 0, cwidth, cheight).data; - - // set initial values - top_line = -1; bottom_line = -1; left_line = -1; right_line = -1; - txt_width = 0; txt_height = 0; - - // Find the top-most line with a non-transparent pixel - for (r = 0; r < cheight; r++) { - for (c = 0; c < cwidth; c++) { - if (data[r * cwidth * 4 + c * 4 + 3]) { - top_line = r; - break; - } - } - if (top_line != -1) { - break; - } - } - - // Only bother looking if we found at least one set pixel... - if (top_line != -1) { - - //find the last line with a non-transparent pixel - for (r = cheight-1; r >= top_line; r--) { - for(c = 0; c < cwidth; c++) { - if(data[r * cwidth * 4 + c * 4 + 3]) { - bottom_line = r; - break; - } - } - if (bottom_line != -1) { - break; - } - } - // calculate height - txt_height = bottom_line - top_line + 1; - - // Find the left-most line with a non-transparent pixel - for (c = 0; c < cwidth; c++) { - for (r = top_line; r <= bottom_line; r++) { - if (data[r * cwidth * 4 + c * 4 + 3]) { - left_line = c; - break; - } - } - if (left_line != -1) { - break; - } - } - - //find the right most line with a non-transparent pixel - for (c = cwidth-1; c >= left_line; c--) { - for(r = top_line; r <= bottom_line; r++) { - if(data[r * cwidth * 4 + c * 4 + 3]) { - right_line = c; - break; - } - } - if (right_line != -1) { - break; - } - } - txt_width = right_line - left_line + 1; - } - - //return the bounds - return {bound_top: top_line, bound_bottom: bottom_line, - bound_left: left_line, bound_right: right_line, width: txt_width, - height: txt_height}; -} - -//====================================================================== -// start RasterizedAlphabet -//====================================================================== - -// Rasterize Alphabet -// 1) Measure width of text at default font for all symbols in alphabet -// 2) sort in width ascending -// 3) Drop the top and bottom 10% (designed to ignore outliers like 'W' and 'I') -// 4) Calculate the average as the maximum scaling factor (designed to stop I becoming a rectangular blob). -// 5) Assume scale of zero would result in width of zero, interpolate scale required to make perfect width font -// 6) Draw text onto temp canvas at calculated scale -// 7) Find bounds of drawn text -// 8) Paint on to another canvas at the desired height (but only scaling width to fit if larger). -var RasterizedAlphabet = function(alphabet, logo_scale, font, width) { - "use strict"; - var default_size, safety_pad, canvas, ctx, middle, baseline, widths, sizes, - i, sym, size, tenpercent, avg_width, scale, - target_width, target_height; - //variable prototypes - this.alphabet = alphabet; - this.scale = logo_scale; - this.sym_cache = {}; - this.stack_num_cache = []; - this.scale_num_cache = []; - // size of canvas - default_size = 60; // size of measuring canvas - safety_pad = 20; // pixels to pad around so we don't miss the edges - // create a canvas to do our measuring - canvas = document.createElement("canvas"); - if (!canvas.getContext) throw new Error("No canvas support"); - canvas.width = default_size + 2 * safety_pad; - canvas.height = default_size + 2 * safety_pad; - middle = Math.round(canvas.width / 2); - baseline = Math.round(canvas.height - safety_pad); - ctx = canvas.getContext('2d'); - if (!supports_text(ctx)) throw new Error("Canvas does not support text"); - ctx.font = font; - ctx.textAlign = "center"; - ctx.translate(middle, baseline); - // list of widths - widths = []; - sizes = []; - //now measure each letter in the alphabet - for (i = 0; i < alphabet.get_size_core(); ++i) { - // reset the canvas - ctx.clearRect(0, 0, canvas.width, canvas.height); - ctx.fillStyle = alphabet.get_colour(i); - // draw the test text - ctx.fillText(alphabet.get_symbol(i), 0, 0); - //measure - size = canvas_bounds(ctx, canvas.width, canvas.height); - if (size.width === 0) throw new Error("Invisible symbol!"); - widths.push(size.width); - sizes[i] = size; - } - //sort the widths - widths.sort(function(a,b) {return a - b;}); - //drop 10% of the items off each end - tenpercent = Math.floor(widths.length / 10); - for (i = 0; i < tenpercent; ++i) { - widths.pop(); - widths.shift(); - } - //calculate average width - avg_width = 0; - for (i = 0; i < widths.length; ++i) { - avg_width += widths[i]; - } - avg_width /= widths.length; - // calculate the target width - target_width = width * this.scale * 2; - // calculate scales - for (i = 0; i < alphabet.get_size_core(); ++i) { - sym = alphabet.get_symbol(i); - size = sizes[i]; - // calculate scale - scale = target_width / Math.max(avg_width, size.width); - // estimate scaled height - target_height = size.height * scale; - // create an appropriately sized canvas - canvas = document.createElement("canvas"); - canvas.width = target_width; - canvas.height = target_height + safety_pad * 2; - // calculate the middle - middle = Math.round(canvas.width / 2); - // calculate the baseline - baseline = Math.round(canvas.height - safety_pad); - // get the context and prepare to draw the rasterized text - ctx = canvas.getContext('2d'); - ctx.font = font; - ctx.fillStyle = alphabet.get_colour(i); - ctx.textAlign = "center"; - ctx.translate(middle, baseline); - ctx.save(); - ctx.scale(scale, scale); - // draw the text - ctx.fillText(sym, 0, 0); - ctx.restore(); - this.sym_cache[sym] = {"image": canvas, "size": canvas_bounds(ctx, canvas.width, canvas.height)}; - } -}; - -RasterizedAlphabet.prototype.get_alphabet = function() { - return this.alphabet; -}; - -RasterizedAlphabet.prototype.get_scale = function() { - return this.scale; -}; - -RasterizedAlphabet.prototype.draw_stack_sym = function(ctx, letter, dx, dy, dWidth, dHeight) { - "use strict"; - var entry, image, size; - entry = this.sym_cache[letter]; - image = entry.image; - size = entry.size; - ctx.drawImage(image, 0, size.bound_top -1, image.width, size.height+1, dx, dy, dWidth, dHeight); -}; - -RasterizedAlphabet.prototype.draw_stack_num = function(ctx, font, stack_width, index) { - var image, image_ctx, text_length; - if (index >= this.stack_num_cache.length) { - image = document.createElement("canvas"); - // measure the text - image_ctx = image.getContext('2d'); - image_ctx.save(); - image_ctx.font = font; - text_length = image_ctx.measureText("" + (index + 1)).width; - image_ctx.restore(); - // resize the canvas to fit - image.width = Math.ceil(stack_width); - image.height = Math.ceil(text_length); - // draw the text - image_ctx = image.getContext('2d'); - image_ctx.translate(Math.round(stack_width / 2), 0); - image_ctx.font = font; - image_ctx.textBaseline = "middle"; - image_ctx.textAlign = "right"; - image_ctx.rotate(-(Math.PI / 2)); - image_ctx.fillText("" + (index + 1), 0, 0); - this.stack_num_cache[index] = image; - } else { - image = this.stack_num_cache[index]; - } - ctx.drawImage(image, 0, 0); -} - -RasterizedAlphabet.prototype.draw_scale_num = function(ctx, font, num) { - var image, image_ctx, text_size, m_length; - if (num >= this.scale_num_cache.length) { - image = document.createElement("canvas"); - // measure the text - image_ctx = image.getContext('2d'); - image_ctx.font = font; - text_size = image_ctx.measureText("" + num); - if (text_size.actualBoundingBoxAscent && text_size.actualBoundingBoxDesent) { - // resize the canvas to fit - image.width = Math.ceil(text_size.width); - image.height = Math.ceil(text_size.actualBoundingBoxAscent + text_size.actualBoundingBoxDesent); - // draw the text - image_ctx = image.getContext('2d'); - image_ctx.font = font; - image_ctx.textAlign = "right"; - image_ctx.fillText("" + num, image.width, text_size.actualBoundingBoxAscent); - } else { - // measure width of 'm' to approximate height, we double it later anyway - m_length = image_ctx.measureText("m").width; - // resize the canvas to fit - image.width = Math.ceil(text_size.width); - image.height = Math.ceil(2 * m_length); - // draw the text - image_ctx = image.getContext('2d'); - image_ctx.font = font; - image_ctx.textAlign = "right"; - image_ctx.textBaseline = "middle"; - image_ctx.fillText("" + num, image.width, m_length); - } - this.scale_num_cache[num] = image; - } else { - image = this.scale_num_cache[num]; - } - ctx.drawImage(image, -image.width, -Math.round(image.height / 2)) -} - -//====================================================================== -// end RasterizedAlphabet -//====================================================================== - -//====================================================================== -// start LogoMetrics object -//====================================================================== - -var LogoMetrics = function(ctx, logo_columns, logo_rows, has_names, has_finetext, x_axis, y_axis) { - "use strict"; - var i, row_height; - //variable prototypes - this.pad_top = (has_names ? 5 : 0); - this.pad_left = (y_axis ? 10 : 0); - this.pad_right = (has_finetext ? 15 : 0); - this.pad_bottom = 0; - this.pad_middle = 20; - this.name_height = 14; - this.name_font = "bold " + this.name_height + "px Times, sans-serif"; - this.name_spacer = 0; - this.y_axis = y_axis; - this.y_label = "bits"; - this.y_label_height = 12; - this.y_label_font = "bold " + this.y_label_height + "px Helvetica, sans-serif"; - this.y_label_spacer = 3; - this.y_num_height = 12; - this.y_num_width = 0; - this.y_num_font = "bold " + this.y_num_height + "px Helvetica, sans-serif"; - this.y_tic_width = 5; - this.stack_pad_left = 0; - this.stack_font = "bold 25px Helvetica, sans-serif"; - this.stack_height = 90; - this.stack_width = 26; - this.stacks_pad_right = 5; - this.x_axis = x_axis; - this.x_num_above = 2; - this.x_num_height = 12; - this.x_num_width = 0; - this.x_num_font = "bold " + this.x_num_height + "px Helvetica, sans-serif"; - this.fine_txt_height = 6; - this.fine_txt_above = 2; - this.fine_txt_font = "normal " + this.fine_txt_height + "px Helvetica, sans-serif"; - this.letter_metrics = new Array(); - this.summed_width = 0; - this.summed_height = 0; - //calculate the width of the y axis numbers - ctx.font = this.y_num_font; - for (i = 0; i <= 2; i++) { - this.y_num_width = Math.max(this.y_num_width, ctx.measureText("" + i).width); - } - //calculate the width of the x axis numbers (but they are rotated so it becomes height) - if (x_axis == 1) { - ctx.font = this.x_num_font; - for (i = 1; i <= logo_columns; i++) { - this.x_num_width = Math.max(this.x_num_width, ctx.measureText("" + i).width); - } - } else if (x_axis == 0) { - this.x_num_height = 4; - this.x_num_width = 4; - } else { - this.x_num_height = 0; - this.x_num_width = 0; - } - - //calculate how much vertical space we want to draw this - //first we add the padding at the top and bottom since that's always there - this.summed_height += this.pad_top + this.pad_bottom; - //all except the last row have the same amount of space allocated to them - if (logo_rows > 1) { - row_height = this.stack_height + this.pad_middle; - if (has_names) { - row_height += this.name_height; - //the label is allowed to overlap into the spacer - row_height += Math.max(this.y_num_height/2, this.name_spacer); - //the label is allowed to overlap the space used by the other label - row_height += Math.max(this.y_num_height/2, this.x_num_height + this.x_num_above); - } else { - row_height += this.y_num_height/2; - //the label is allowed to overlap the space used by the other label - row_height += Math.max(this.y_num_height/2, this.x_num_height + this.x_num_above); - } - this.summed_height += row_height * (logo_rows - 1); - } - //the last row has the name and fine text below it but no padding - this.summed_height += this.stack_height + (this.y_axis ? this.y_num_height/2 : 0); - - var fine_txt_total = (has_finetext ? this.fine_txt_height + this.fine_txt_above : 0); - if (has_names) { - this.summed_height += fine_txt_total + this.name_height; - this.summed_height += Math.max((this.y_axis ? this.y_num_height/2 : 0), - this.x_num_height + this.x_num_above + this.name_spacer); - } else { - this.summed_height += Math.max((this.y_axis ? this.y_num_height/2 : 0), - this.x_num_height + this.x_num_above + fine_txt_total); - } - - //calculate how much horizontal space we want to draw this - //first add the padding at the left and right since that's always there - this.summed_width += this.pad_left + this.pad_right; - if (this.y_axis) { - //add on the space for the y-axis label - this.summed_width += this.y_label_height + this.y_label_spacer; - //add on the space for the y-axis - this.summed_width += this.y_num_width + this.y_tic_width; - } - //add on the space for the stacks - this.summed_width += (this.stack_pad_left + this.stack_width) * logo_columns; - //add on the padding after the stacks (an offset from the fine text) - this.summed_width += this.stacks_pad_right; - -}; - -//====================================================================== -// end LogoMetrics object -//====================================================================== - -//found this trick at http://talideon.com/weblog/2005/02/detecting-broken-images-js.cfm -function image_ok(img) { - "use strict"; - // During the onload event, IE correctly identifies any images that - // weren't downloaded as not complete. Others should too. Gecko-based - // browsers act like NS4 in that they report this incorrectly. - if (!img.complete) { - return false; - } - // However, they do have two very useful properties: naturalWidth and - // naturalHeight. These give the true size of the image. If it failed - // to load, either of these should be zero. - if (typeof img.naturalWidth !== "undefined" && img.naturalWidth === 0) { - return false; - } - // No other way of checking: assume it's ok. - return true; -} - -function supports_text(ctx) { - "use strict"; - if (!ctx.fillText) { - return false; - } - if (!ctx.measureText) { - return false; - } - return true; -} - -//draws the scale, returns the width -function draw_scale(ctx, metrics, alphabet_ic, raster) { - "use strict"; - var tic_height, i; - tic_height = metrics.stack_height / alphabet_ic; - ctx.save(); - ctx.translate(metrics.y_label_height, metrics.y_num_height/2); - //draw the axis label - ctx.save(); - ctx.font = metrics.y_label_font; - ctx.translate(0, metrics.stack_height/2); - ctx.rotate(-(Math.PI / 2)); - ctx.textAlign = "center"; - ctx.fillText("bits", 0, 0); - ctx.restore(); - - ctx.translate(metrics.y_label_spacer + metrics.y_num_width, 0); - - //draw the axis tics - ctx.save(); - ctx.translate(0, metrics.stack_height); - for (i = 0; i <= alphabet_ic; i++) { - //draw the number - ctx.save(); - ctx.translate(-1, 0); - raster.draw_scale_num(ctx, metrics.y_num_font, i); - ctx.restore(); - //draw the tic - ctx.fillRect(0, -1, metrics.y_tic_width, 2); - //prepare for next tic - ctx.translate(0, -tic_height); - } - ctx.restore(); - - ctx.fillRect(metrics.y_tic_width - 2, 0, 2, metrics.stack_height) - - ctx.restore(); -} - -function draw_stack_num(ctx, metrics, row_index, raster) { - "use strict"; - ctx.save(); - ctx.translate(0, Math.round(metrics.stack_height + metrics.x_num_above)); - if (metrics.x_axis == 1) { - raster.draw_stack_num(ctx, metrics.x_num_font, metrics.stack_width, row_index); - } else if (metrics.x_axis == 0) { - // draw dots instead of the numbers (good for small logos) - ctx.beginPath(); - var radius = Math.round(metrics.x_num_height / 2); - ctx.arc(Math.round(metrics.stack_width / 2), radius, radius, 0, 2 * Math.PI, false); - ctx.fill(); - } - ctx.restore(); -} - -function draw_stack(ctx, metrics, symbols, raster) { - "use strict"; - var preferred_pad, sym_min, i, sym, sym_height, pad; - preferred_pad = 0; - sym_min = 5; - - ctx.save();//1 - ctx.translate(0, metrics.stack_height); - for (i = 0; i < symbols.length; i++) { - sym = symbols[i]; - sym_height = metrics.stack_height * sym.get_scale(); - - pad = preferred_pad; - if (sym_height - pad < sym_min) { - pad = Math.min(pad, Math.max(0, sym_height - sym_min)); - } - sym_height -= pad; - - //translate to the correct position - ctx.translate(0, -(pad/2 + sym_height)); - - //draw - raster.draw_stack_sym(ctx, sym.get_symbol(), 0, 0, metrics.stack_width, sym_height); - //translate past the padding - ctx.translate(0, -(pad/2)); - } - ctx.restore();//1 -} - -function draw_dashed_line(ctx, pattern, start, x1, y1, x2, y2) { - "use strict"; - var x, y, len, i, dx, dy, tlen, theta, mulx, muly, lx, ly; - dx = x2 - x1; - dy = y2 - y1; - tlen = Math.pow(dx*dx + dy*dy, 0.5); - theta = Math.atan2(dy,dx); - mulx = Math.cos(theta); - muly = Math.sin(theta); - lx = []; - ly = []; - for (i = 0; i < pattern; ++i) { - lx.push(pattern[i] * mulx); - ly.push(pattern[i] * muly); - } - i = start; - x = x1; - y = y1; - len = 0; - ctx.beginPath(); - while (len + pattern[i] < tlen) { - ctx.moveTo(x, y); - x += lx[i]; - y += ly[i]; - ctx.lineTo(x, y); - len += pattern[i]; - i = (i + 1) % pattern.length; - x += lx[i]; - y += ly[i]; - len += pattern[i]; - i = (i + 1) % pattern.length; - } - if (len < tlen) { - ctx.moveTo(x, y); - x += mulx * (tlen - len); - y += muly * (tlen - len); - ctx.lineTo(x, y); - } - ctx.stroke(); -} - -function draw_trim_background(ctx, metrics, left_start, left_end, left_divider, right_start, right_end, right_divider) { - "use strict"; - var left_size = left_end - left_start; - var right_size = right_end - right_start; - var line_x; - - ctx.save();//s8 - ctx.fillStyle = "rgb(240, 240, 240)"; - if (left_size > 0) { - ctx.fillRect(left_start * metrics.stack_width, 0, left_size * metrics.stack_width, metrics.stack_height); - } - if (right_size > 0) { - ctx.fillRect(right_start * metrics.stack_width, 0, right_size * metrics.stack_width, metrics.stack_height); - } - ctx.fillStyle = "rgb(51, 51, 51)"; - if (left_size > 0 && left_divider) { - line_x = (left_end * metrics.stack_width) - 0.5; - draw_dashed_line(ctx, [3], 0, line_x, 0, line_x, metrics.stack_height); - } - if (right_size > 0 && right_divider) { - line_x = (right_start * metrics.stack_width) + 0.5; - draw_dashed_line(ctx, [3], 0, line_x, 0, line_x, metrics.stack_height); - } - ctx.restore();//s8 -} - -function size_logo_on_canvas(logo, canvas, show_names, scale) { - "use strict"; - var draw_name, draw_finetext, metrics; - draw_name = (typeof show_names === "boolean" ? show_names : (logo.get_rows() > 1)); - draw_finetext = (logo.fine_text.length > 0); - if (canvas.width !== 0 && canvas.height !== 0) { - return; - } - metrics = new LogoMetrics(canvas.getContext('2d'), - logo.get_xlate_columns(), logo.get_rows(), draw_name, draw_finetext, logo.x_axis, logo.y_axis); - if (typeof scale == "number") { - //resize the canvas to fit the scaled logo - canvas.width = metrics.summed_width * scale; - canvas.height = metrics.summed_height * scale; - } else { - if (canvas.width === 0 && canvas.height === 0) { - canvas.width = metrics.summed_width; - canvas.height = metrics.summed_height; - } else if (canvas.width === 0) { - canvas.width = metrics.summed_width * (canvas.height / metrics.summed_height); - } else if (canvas.height === 0) { - canvas.height = metrics.summed_height * (canvas.width / metrics.summed_width); - } - } -} - -function draw_logo_on_canvas(logo, canvas, show_names, scale) { - "use strict"; - var i, draw_name, draw_finetext, ctx, metrics, raster, pspm_i, pspm, - offset, col_index, motif_position, ssc; - ssc = false; - draw_name = (typeof show_names === "boolean" ? show_names : (logo.get_rows() > 1)); - draw_finetext = (logo.fine_text.length > 0); - ctx = canvas.getContext('2d'); - //assume that the user wants the canvas scaled equally so calculate what the best width for this image should be - metrics = new LogoMetrics(ctx, logo.get_xlate_columns(), logo.get_rows(), draw_name, draw_finetext, logo.x_axis, logo.y_axis); - if (typeof scale == "number") { - //resize the canvas to fit the scaled logo - canvas.width = metrics.summed_width * scale; - canvas.height = metrics.summed_height * scale; - } else { - if (canvas.width === 0 && canvas.height === 0) { - scale = 1; - canvas.width = metrics.summed_width; - canvas.height = metrics.summed_height; - } else if (canvas.width === 0) { - scale = canvas.height / metrics.summed_height; - canvas.width = metrics.summed_width * scale; - } else if (canvas.height === 0) { - scale = canvas.width / metrics.summed_width; - canvas.height = metrics.summed_height * scale; - } else { - scale = Math.min(canvas.width / metrics.summed_width, canvas.height / metrics.summed_height); - } - } - // cache the raster based on the assumption that we will be drawing a lot - // of logos the same size and alphabet - if (typeof draw_logo_on_canvas.raster_cache === "undefined") { - draw_logo_on_canvas.raster_cache = []; - } - for (i = 0; i < draw_logo_on_canvas.raster_cache.length; i++) { - raster = draw_logo_on_canvas.raster_cache[i]; - if (raster.get_alphabet().equals(logo.alphabet) && - Math.abs(raster.get_scale() - scale) < 0.1) break; - raster = null; - } - if (raster == null) { - raster = new RasterizedAlphabet(logo.alphabet, scale, metrics.stack_font, metrics.stack_width); - draw_logo_on_canvas.raster_cache.push(raster); - } - ctx = canvas.getContext('2d'); - ctx.save();//s1 - ctx.scale(scale, scale); - ctx.save();//s2 - ctx.save();//s7 - //create margin - ctx.translate(Math.round(metrics.pad_left), Math.round(metrics.pad_top)); - for (pspm_i = 0; pspm_i < logo.get_rows(); ++pspm_i) { - pspm = logo.get_pspm(pspm_i); - offset = logo.get_offset(pspm_i); - //optionally draw name if this isn't the last row or is the only row - if (draw_name && (logo.get_rows() == 1 || pspm_i != (logo.get_rows()-1))) { - ctx.save();//s4 - ctx.translate(Math.round(metrics.summed_width/2), Math.round(metrics.name_height)); - ctx.font = metrics.name_font; - ctx.textAlign = "center"; - ctx.fillText(pspm.name, 0, 0); - ctx.restore();//s4 - ctx.translate(0, Math.round(metrics.name_height + - Math.min(0, metrics.name_spacer - metrics.y_num_height/2))); - } - //draw scale - if (logo.y_axis) draw_scale(ctx, metrics, logo.alphabet.get_ic(), raster); - ctx.save();//s5 - //translate across past the scale - if (logo.y_axis) { - ctx.translate(Math.round(metrics.y_label_height + metrics.y_label_spacer + - metrics.y_num_width + metrics.y_tic_width), Math.round(metrics.y_num_height / 2)); - } - //draw the trimming background - if (pspm.get_left_trim() > 0 || pspm.get_right_trim() > 0) { - var left_start = offset * logo.get_xlate_nsyms(); - var left_end = (offset + pspm.get_left_trim()) * logo.get_xlate_nsyms(); - var left_divider = true; - if (left_end < logo.get_xlate_start() || left_start > logo.get_xlate_end()) { - // no overlap - left_start = 0; - left_end = 0; - left_divider = false; - } else { - if (left_start < logo.get_xlate_start()) { - left_start = logo.get_xlate_start(); - } - if (left_end > logo.get_xlate_end()) { - left_end = logo.get_xlate_end(); - left_divider = false; - } - left_start -= logo.get_xlate_start(); - left_end -= logo.get_xlate_start(); - if (left_end < left_start) { - left_start = 0; - left_end = 0; - left_divider = false; - } - } - var right_end = (offset + pspm.get_motif_length()) * logo.get_xlate_nsyms(); - //var right_start = right_end - (pspm.get_left_trim() * logo.get_xlate_nsyms()); - var right_start = right_end - (pspm.get_right_trim() * logo.get_xlate_nsyms()); - var right_divider = true; - if (right_end < logo.get_xlate_start() || right_start > logo.get_xlate_end()) { - // no overlap - right_start = 0; - right_end = 0; - right_divider = false; - } else { - if (right_start < logo.get_xlate_start()) { - right_start = logo.get_xlate_start(); - right_divider = false; - } - if (right_end > logo.get_xlate_end()) { - right_end = logo.get_xlate_end(); - } - right_start -= logo.get_xlate_start(); - right_end -= logo.get_xlate_start(); - if (right_end < right_start) { - right_start = 0; - right_end = 0; - right_divider = false; - } - } - draw_trim_background(ctx, metrics, left_start, left_end, left_divider, right_start, right_end, right_divider); - } - //draw letters - var xlate_col; - for (xlate_col = logo.get_xlate_start(); xlate_col < logo.get_xlate_end(); xlate_col++) { - ctx.translate(metrics.stack_pad_left,0); - col_index = Math.floor(xlate_col / logo.get_xlate_nsyms()); - if (xlate_col % logo.get_xlate_nsyms() == 0) { - if (col_index >= offset && col_index < (offset + pspm.get_motif_length())) { - motif_position = col_index - offset; - draw_stack_num(ctx, metrics, motif_position, raster); - draw_stack(ctx, metrics, pspm.get_stack(motif_position, logo.alphabet, ssc), raster); - } - } else { - if (col_index >= offset && col_index < (offset + pspm.get_motif_length())) { - ctx.save();// s5.1 - ctx.translate(0, Math.round(metrics.stack_height)); - // TODO draw a dot or dash or something to indicate continuity of the motif - ctx.restore(); //s5.1 - } - } - ctx.translate(Math.round(metrics.stack_width), 0); - } - ctx.restore();//s5 - ////optionally draw name if this is the last row but isn't the only row - if (draw_name && (logo.get_rows() != 1 && pspm_i == (logo.get_rows()-1))) { - //translate vertically past the stack and axis's - ctx.translate(0, metrics.y_num_height/2 + metrics.stack_height + - Math.max(metrics.y_num_height/2, metrics.x_num_above + metrics.x_num_width + metrics.name_spacer)); - - ctx.save();//s6 - ctx.translate(metrics.summed_width/2, metrics.name_height); - ctx.font = metrics.name_font; - ctx.textAlign = "center"; - ctx.fillText(pspm.name, 0, 0); - ctx.restore();//s6 - ctx.translate(0, metrics.name_height); - } else { - //translate vertically past the stack and axis's - ctx.translate(0, metrics.y_num_height/2 + metrics.stack_height + - Math.max(metrics.y_num_height/2, metrics.x_num_above + metrics.x_num_width)); - } - //if not the last row then add middle padding - if (pspm_i != (logo.get_rows() -1)) { - ctx.translate(0, metrics.pad_middle); - } - } - ctx.restore();//s7 - if (logo.fine_text.length > 0) { - ctx.translate(metrics.summed_width - metrics.pad_right, metrics.summed_height - metrics.pad_bottom); - ctx.font = metrics.fine_txt_font; - ctx.textAlign = "right"; - ctx.fillText(logo.fine_text, 0,0); - } - ctx.restore();//s2 - ctx.restore();//s1 -} - -function create_canvas(c_width, c_height, c_id, c_title, c_display) { - "use strict"; - var canvas = document.createElement("canvas"); - //check for canvas support before attempting anything - if (!canvas.getContext) { - return null; - } - var ctx = canvas.getContext('2d'); - //check for html5 text drawing support - if (!supports_text(ctx)) { - return null; - } - //size the canvas - canvas.width = c_width; - canvas.height = c_height; - canvas.id = c_id; - canvas.title = c_title; - canvas.style.display = c_display; - return canvas; -} - -function logo_1(alphabet, fine_text, pspm) { - "use strict"; - var logo = new Logo(alphabet, fine_text); - logo.add_pspm(pspm); - return logo; -} - -function logo_2(alphabet, fine_text, target, query, query_offset) { - "use strict"; - var logo = new Logo(alphabet, fine_text); - if (query_offset < 0) { - logo.add_pspm(target, -query_offset); - logo.add_pspm(query); - } else { - logo.add_pspm(target); - logo.add_pspm(query, query_offset); - } - return logo; -} - -/* - * Specifies an alternate source for an image. - * If the image with the image_id specified has - * not loaded then a generated logo will be used - * to replace it. - * - * Note that the image must either have dimensions - * or a scale must be set. - */ -function alternate_logo(logo, image_id, scale) { - "use strict"; - var image = document.getElementById(image_id); - if (!image) { - alert("Can't find specified image id (" + image_id + ")"); - return; - } - //if the image has loaded then there is no reason to use the canvas - if (image_ok(image)) { - return; - } - //the image has failed to load so replace it with a canvas if we can. - var canvas = create_canvas(image.width, image.height, image_id, image.title, image.style.display); - if (canvas === null) { - return; - } - //draw the logo on the canvas - draw_logo_on_canvas(logo, canvas, null, scale); - //replace the image with the canvas - image.parentNode.replaceChild(canvas, image); -} - -/* - * Specifes that the element with the specified id - * should be replaced with a generated logo. - */ -function replace_logo(logo, replace_id, scale, title_txt, display_style) { - "use strict"; - var element = document.getElementById(replace_id); - if (!replace_id) { - alert("Can't find specified id (" + replace_id + ")"); - return; - } - //found the element! - var canvas = create_canvas(50, 120, replace_id, title_txt, display_style); - if (canvas === null) { - return; - } - //draw the logo on the canvas - draw_logo_on_canvas(logo, canvas, null, scale); - //replace the element with the canvas - element.parentNode.replaceChild(canvas, element); -} - -/* - * Fast string trimming implementation found at - * http://blog.stevenlevithan.com/archives/faster-trim-javascript - * - * Note that regex is good at removing leading space but - * bad at removing trailing space as it has to first go through - * the whole string. - */ -function trim (str) { - "use strict"; - var ws, i; - str = str.replace(/^\s\s*/, ''); - ws = /\s/; i = str.length; - while (ws.test(str.charAt(--i))); - return str.slice(0, i + 1); -} -</script> - <script> -var current_motif = 0; -var dreme_alphabet = new Alphabet(data.alphabet, data.control_db.freqs); - -/* - * Create a pspm for the given motif data - */ -function motif_pspm(m) { - return new Pspm(m.pwm, m.id, 0, 0, m.nsites, m.evalue); -} - -/* - * Create a count matrix from the given motif data - */ -function motif_count_matrix(motif) { - return motif_pspm(motif).as_count_matrix(); -} - -/* - * Create a probablity matrix from the given motif data - */ -function motif_prob_matrix(motif) { - return motif_pspm(motif).as_probability_matrix(); -} - -/* - * Create a minimal meme format motif from the given motif data - */ -function motif_minimal_meme(motif) { - return motif_pspm(motif).as_meme({ - "with_header": true, - "with_pspm": true, - "with_pssm": false, - "version": data["version"], - "alphabet": dreme_alphabet, - "strands": (data.options.revcomp ? 2 : 1) - }); -} - -/* - * Fill in a template variable - */ -function set_tvar(template, tvar, value) { - var node; - node = find_child(template, tvar); - if (node === null) { - throw new Error("Template does not contain variable " + tvar); - } - node.innerHTML = ""; - if (typeof value !== "object") { - node.appendChild(document.createTextNode(value)); - } else { - node.appendChild(value); - } -} - -/* - * Make a canvas with the motif logo drawn on it. - */ -function make_logo(motif, height, rc) { - var pspm = new Pspm(motif["pwm"]); - if (rc) pspm = pspm.copy().reverse_complement(dreme_alphabet); - var logo = new Logo(dreme_alphabet); - logo.add_pspm(pspm, 0); - var canvas = document.createElement('canvas'); - canvas.height = height; - canvas.width = 0; - draw_logo_on_canvas(logo, canvas, false); - return canvas; -} - -/* - * Create a button designed to contain a single symbol - */ -function make_sym_btn(symbol, title, action) { - var box, sbox; - box = document.createElement("div"); - box.tabIndex = 0; - box.className = "sym_btn"; - sbox = document.createElement("span"); - if (typeof symbol == "string") { - sbox.appendChild(document.createTextNode(symbol)); - } else { - sbox.appendChild(symbol); - } - box.appendChild(sbox); - box.title = title; - box.addEventListener('click', action, false); - box.addEventListener('keydown', action, false); - return box; -} - -/* - * Create a pair of text spans with different classes. - * This is useful when using CSS to only display one of them. - */ -function text_pair(txt1, cls1, txt2, cls2) { - var container, part1, part2; - container = document.createElement("span"); - part1 = document.createElement("span"); - part1.appendChild(document.createTextNode(txt1)); - part1.className = cls1; - container.appendChild(part1); - part2 = document.createElement("span"); - part2.appendChild(document.createTextNode(txt2)); - part2.className = cls2; - container.appendChild(part2); - return container; -} - -/* - * Make a colourised sequence. - */ -function make_seq(seq) { - var i, j, letter, lbox, sbox; - sbox = document.createElement("span"); - for (i = 0; i < seq.length; i = j) { - letter = seq.charAt(i); - for (j = i+1; j < seq.length; j++) { - if (seq.charAt(j) !== letter) { - break; - } - } - lbox = document.createElement("span"); - lbox.style.color = dreme_alphabet.get_colour(dreme_alphabet.get_index(letter)); - lbox.appendChild(document.createTextNode(seq.substring(i, j))); - sbox.appendChild(lbox); - } - return sbox; -} - -/* - * Create a description element taking into account the newlines in the source text. - */ -function make_description(text) { - var i, j, lines, p; - var container = document.createElement("div"); - var paragraphs = text.split(/\n\n+/); - for (i = 0; i < paragraphs.length; i++) { - lines = paragraphs[i].split(/\n/); - p = document.createElement("p"); - p.appendChild(document.createTextNode(lines[0])); - for (j = 1; j < lines.length; j++) { - p.appendChild(document.createElement("br")); - p.appendChild(document.createTextNode(lines[j])); - } - container.appendChild(p); - } - return container; -} - -/* - * Make the table header for the discovered motifs. - */ -function make_motif_header() { - var row = document.createElement("tr"); - add_text_header_cell(row, "", "", "motif_ordinal"); - add_text_header_cell(row, "Motif", "pop_motifs_word", "motif_word"); - add_text_header_cell(row, "Logo", "pop_motifs_logo", "motif_logo"); - if (data.options.revcomp) { - add_text_header_cell(row, "RC Logo", "pop_motifs_rc_logo", "motif_logo"); - } - add_text_header_cell(row, "E-value", "pop_motifs_evalue", "motif_evalue"); - add_text_header_cell(row, "Unerased E-value", "pop_motifs_uevalue", "motif_evalue"); - add_text_header_cell(row, "More", "pop_more", "motif_more"); - add_text_header_cell(row, "Submit/Download", "pop_submit_dl", "motif_submit"); - row.className = "more"; - return row; -} - -/* - * Make a compact motif summary row for the discovered motifs. - */ -function make_motif_row(tbody, ordinal, motif) { - var row = document.createElement("tr"); - add_text_cell(row, "" + ordinal + ".", "motif_ordinal"); - add_text_cell(row, motif["id"], "motif_word"); - add_cell(row, make_logo(motif, 50, false), "motif_logo"); - if (data.options.revcomp) { - add_cell(row, make_logo(motif, 50, true), "motif_logo"); - } - add_text_cell(row, motif["evalue"], "motif_evalue"); - add_text_cell(row, motif["unerased_evalue"], "motif_evalue"); - add_cell(row, make_sym_btn(text_pair("\u21A7", "less", "\u21A5", "more"), "Show more information.", function(e) { toggle_class(tbody, "collapsed"); }, "\u21A5", ""), "motif_more"); - add_cell(row, make_sym_btn("\u21E2", "Submit the motif to another MEME Suite program or download it.", function(e) { action_show_outpop(e, ordinal); }), "motif_submit"); - return row; -} - -/* - * Make a sortable table of enriched matching rows. - */ -function make_motif_words(motif) { - var row, i, match; - var table = document.createElement("table"); - var thead = document.createElement("thead"); - row = document.createElement("tr"); - add_text_header_cell(row, "Word", "pop_match_word", "match_word", function(e) {sort_table(this, compare_words);}); - add_text_header_cell(row, "Positives", "pop_match_pos", "match_count", function(e) {sort_table(this, compare_counts);}); - add_text_header_cell(row, "Negatives", "pop_match_neg", "match_count", function(e) {sort_table(this, compare_counts);}); - add_text_header_cell(row, "P-value", "pop_match_pval", "match_evalue", function(e) {sort_table(this, compare_evalues);}); - add_text_header_cell(row, "E-value", "pop_match_eval", "match_evalue", function(e) {sort_table(this, compare_evalues);}); - thead.appendChild(row); - table.appendChild(thead); - var tbody = document.createElement("tbody"); - for (i = 0; i < motif.matches.length; i++) { - match = motif.matches[i]; - row = document.createElement("tr"); - add_cell(row, make_seq(match.seq), "match_word"); - add_text_cell(row, match.p + " / " + data.sequence_db.count, "match_count"); - add_text_cell(row, match.n + " / " + data.control_db.count, "match_count"); - add_text_cell(row, match.pvalue, "match_evalue"); - add_text_cell(row, match.evalue, "match_evalue"); - tbody.appendChild(row); - } - table.appendChild(tbody); - return table; -} - -/* - * Make an expanded view of a discovered motif. - */ -function make_motif_exp(tbody, ordinal, motif) { - "use strict"; - var box, pspm, logo_box; - box = $("tmpl_motif_expanded").cloneNode(true); - toggle_class(box, "template", false); - box.id = ""; - find_child(box, "tvar_logo").appendChild(make_logo(motif, 150, false)); - if (data.options.revcomp) { - find_child(box, "tvar_rclogo").appendChild(make_logo(motif, 150, true)); - } - set_tvar(box, "tvar_p", motif["p"]); - set_tvar(box, "tvar_p_total", data.sequence_db.count); - set_tvar(box, "tvar_n", motif["n"]); - set_tvar(box, "tvar_n_total", data.control_db.count); - set_tvar(box, "tvar_pvalue", motif["pvalue"]); - set_tvar(box, "tvar_evalue", motif["evalue"]); - set_tvar(box, "tvar_uevalue", motif["unerased_evalue"]); - set_tvar(box, "tvar_words", make_motif_words(motif)); - var cell = document.createElement("td"); - cell.colSpan = 8; - cell.appendChild(box); - var row = document.createElement("tr"); - row.className = "more"; - row.appendChild(cell); - return row; -} - -/* - * Convert a string containing a scientific number into the log of that number - * without having an intermediate representation of the number. - * This is intended to avoid underflow problems with the tiny evalues that - * MEME and DREME can create. - */ -function sci2log(scinum) { - "use strict"; - var ev_re, match, sig, exp; - ev_re = /^(.*)e(.*)$/; - if (match = ev_re.exec(scinum)) { - sig = parseFloat(match[1]); - exp = parseInt(match[2]); - return Math.log(sig) + (exp * Math.log(10)); - } - return 0; -} - -/* - * Create a table of discovered motifs. A fresh table body is used for each - * motif to make hiding/showing rows with css easier. - */ -function make_motifs() { - "use strict"; - var i, row, tbody, motif, ordinal; - // make the motifs table - var container = $("motifs"); - container.innerHTML = ""; // clear content - var table = document.createElement("table"); - // add a header that is always shown - var thead = document.createElement("thead"); - thead.appendChild(make_motif_header()); - table.appendChild(thead); - for (i = 0; i < data.motifs.length; i++) { - ordinal = i + 1; - motif = data.motifs[i]; - tbody = document.createElement("tbody"); - tbody.className = "collapsed"; - tbody.appendChild(make_motif_row(tbody, ordinal, motif)); - tbody.appendChild(make_motif_exp(tbody, ordinal, motif)); - // create a following header for every row except the last one - if ((i + 1) < data.motifs.length) tbody.appendChild(make_motif_header()); - table.appendChild(tbody); - } - container.appendChild(table); -} - -/* - * Create a table showing all the alphabet symbols, their names and frequencies. - */ -function make_alpha_bg(alph, freqs) { - function colour_symbol(index) { - var span = document.createElement("span"); - span.appendChild(document.createTextNode(alph.get_symbol(index))); - span.style.color = alph.get_colour(index); - span.className = "alpha_symbol"; - return span; - } - var table, thead, tbody, row, th, span, i; - // create table - table = document.createElement("table"); - table.className = "inputs"; - // create header - thead = document.createElement("thead"); - table.appendChild(thead); - row = thead.insertRow(thead.rows.length); - if (alph.has_complement()) { - add_text_header_cell(row, "Name", "pop_alph_name"); - add_text_header_cell(row, "Bg.", "pop_alph_control"); - add_text_header_cell(row, ""); - add_text_header_cell(row, ""); - add_text_header_cell(row, ""); - add_text_header_cell(row, "Bg.", "pop_alph_control"); - add_text_header_cell(row, "Name", "pop_alph_name"); - } else { - add_text_header_cell(row, ""); - add_text_header_cell(row, "Name", "pop_alph_name"); - add_text_header_cell(row, "Bg.", "pop_alph_control"); - } - // add alphabet entries - tbody = document.createElement("tbody"); - table.appendChild(tbody); - if (alph.has_complement()) { - for (i = 0; i < alph.get_size_core(); i++) { - var c = alph.get_complement(i); - if (i > c) continue; - row = tbody.insertRow(tbody.rows.length); - add_text_cell(row, alph.get_name(i)); - add_text_cell(row, "" + freqs[i].toFixed(3)); - add_cell(row, colour_symbol(i)); - add_text_cell(row, "~"); - add_cell(row, colour_symbol(c)); - add_text_cell(row, "" + freqs[c].toFixed(3)); - add_text_cell(row, alph.get_name(c)); - } - } else { - for (i = 0; i < alph.get_size_core(); i++) { - row = tbody.insertRow(tbody.rows.length); - add_cell(row, colour_symbol(i)); - add_text_cell(row, alph.get_name(i)); - add_text_cell(row, "" + freqs[i].toFixed(3)); - } - } - return table; -} - -/* - * Updates the format download text in the popup. - * This is called when either the format or current motif changes. - */ -function update_outpop_format(index) { - var motif = data.motifs[index]; - var fn = [motif_count_matrix, motif_prob_matrix, motif_minimal_meme]; - var suffix = ["_counts.txt", "_freqs.txt", ".meme"]; - var format = parseInt($("text_format").value); - var text = fn[format](motif); - prepare_download(text, "text/plain", motif.id + suffix[format], $("outpop_text_dl")); - $("outpop_text").value = text; -} - -/* - * Updates the motif logos and format download text in the popup. - * This is called whenever the current motif changes. - */ -function update_outpop_motif(index) { - "use strict"; - var motifs, motif, pspm, logo, canvas, num; - motifs = data["motifs"]; - if (index < 0 || index >= motifs.length) {return;} - current_motif = index; - motif = motifs[index]; - pspm = new Pspm(motif["pwm"]); - logo = new Logo(dreme_alphabet, ""); - logo.add_pspm(pspm, 0); - canvas = $("outpop_logo"); - canvas.width = canvas.width; // clear canvas - draw_logo_on_canvas(logo, canvas, false); - canvas = $("outpop_logo_rc"); - canvas.width = canvas.width; // clear rc canvas - if (data.options.revcomp) { - pspm.reverse_complement(dreme_alphabet); - logo = new Logo(dreme_alphabet, ""); - logo.add_pspm(pspm, 0); - draw_logo_on_canvas(logo, canvas, false); - } - num = $("outpop_num"); - num.innerHTML = ""; - num.appendChild(document.createTextNode("" + (index + 1))); - update_outpop_format(index); -} - - -/* - * Initialise and display the download popup. - */ -function action_show_outpop(e, ordinal) { - "use strict"; - function init() { - "use strict"; - var close_btn, next_btn, prev_btn, cancel_btn, do_btn; - var tab1, tab2, tab3; - var pnl1, pnl2, pnl3; - var format_list; - var tbl_submit, inputs, i, default_prog; - close_btn = $("outpop_close"); - close_btn.addEventListener("click", action_hide_outpop, false); - close_btn.addEventListener("keydown", action_hide_outpop, false); - next_btn = $("outpop_next"); - next_btn.addEventListener("click", action_outpop_next, false); - next_btn.addEventListener("keydown", action_outpop_next, false); - prev_btn = $("outpop_prev"); - prev_btn.addEventListener("click", action_outpop_prev, false); - prev_btn.addEventListener("keydown", action_outpop_prev, false); - cancel_btn = $("outpop_cancel"); - cancel_btn.addEventListener("click", action_hide_outpop, false); - do_btn = $("outpop_do"); - do_btn.addEventListener("click", action_outpop_submit, false); - tab1 = $("outpop_tab_1"); - tab1.tabIndex = 0; - tab1.addEventListener("click", action_outpop_tab, false); - tab1.addEventListener("keydown", action_outpop_tab, false); - tab2 = $("outpop_tab_2"); - tab2.tabIndex = 0; - tab2.addEventListener("click", action_outpop_tab, false); - tab2.addEventListener("keydown", action_outpop_tab, false); - tab3 = $("outpop_tab_3"); - tab3.tabIndex = 0; - tab3.addEventListener("click", action_outpop_tab, false); - tab3.addEventListener("keydown", action_outpop_tab, false); - pnl1 = $("outpop_pnl_1"); - pnl2 = $("outpop_pnl_2"); - pnl3 = $("outpop_pnl_3"); - toggle_class(tab1, "activeTab", true); - toggle_class(tab2, "activeTab", false); - toggle_class(tab3, "activeTab", false); - pnl1.style.display = "block"; - pnl2.style.display = "none"; - pnl3.style.display = "none"; - format_list = $("text_format"); - format_list.addEventListener("change", action_outpop_format, false); - // setup program selection - tbl_submit = $("programs"); - // when not dna, hide the inputs for programs that require dna motifs - toggle_class(tbl_submit, "alphabet_dna", dreme_alphabet.has_complement());//TODO FIXME alphabet_dna is a bad name for a field when allowing custom alphabets - // add a click listener for the radio buttons - inputs = tbl_submit.querySelectorAll("input[type='radio']"); - for (i = 0; i < inputs.length; i++) { - inputs[i].addEventListener("click", action_outpop_program, false); - } - // ensure that a default program option is selected for DNA and Protein - default_prog = document.getElementById(dreme_alphabet.has_complement() ? "submit_tomtom" : "submit_fimo"); - default_prog.checked = true; - action_outpop_program.call(default_prog); - // disable reverse-complement when not DNA - $("logo_rc_option").disabled = !dreme_alphabet.has_complement(); - // set errorbars on when ssc is on - $("logo_ssc").addEventListener("change", action_outpop_ssc, false); - } - // store the focused element - action_hide_outpop.last_active = document.activeElement; - if (!e) e = window.event; - if (e.type === "keydown") { - if (e.keyCode !== 13 && e.keyCode !== 32) { - return; - } - // stop a submit or something like that - e.preventDefault(); - } - // hide the help popup - help_popup(); - // on first load initilize the popup - if (!action_show_outpop.ready) { - init(); - action_show_outpop.ready = true; - } - update_outpop_motif(ordinal - 1); - // display the download popup - $("grey_out_page").style.display = "block"; - $("download").style.display = "block"; - $("outpop_close").focus(); -} - -/* - * Hide the download popup. - */ -function action_hide_outpop(e) { - if (!e) e = window.event; - if (e.type === "keydown") { - if (e.keyCode !== 13 && e.keyCode !== 32) { - return; - } - // stop a submit or something like that - e.preventDefault(); - } - $("download").style.display = "none"; - $("grey_out_page").style.display = "none"; - if (typeof action_hide_outpop.last_active !== "undefined") { - action_hide_outpop.last_active.focus(); - } -} - -/* - * Show the next motif in the download popup. - */ -function action_outpop_next(e) { - if (!e) e = window.event; - if (e.type === "keydown") { - if (e.keyCode !== 13 && e.keyCode !== 32) { - return; - } - // stop a submit or something like that - e.preventDefault(); - } - update_outpop_motif(current_motif + 1); -} - -/* - * Show the previous motif in the download popup. - */ -function action_outpop_prev(e) { - if (!e) e = window.event; - if (e.type === "keydown") { - if (e.keyCode !== 13 && e.keyCode !== 32) { - return; - } - // stop a submit or something like that - e.preventDefault(); - } - update_outpop_motif(current_motif - 1); -} - -/* - * Highlight the selected row in the program list. - */ -function action_outpop_program() { - "use strict"; - var table, tr, rows, i; - tr = find_parent_tag(this, "TR"); - table = find_parent_tag(tr, "TABLE"); - rows = table.querySelectorAll("tr"); - for (i = 0; i < rows.length; i++) { - toggle_class(rows[i], "selected", rows[i] === tr); - } -} - -/* - * Enable error bars when small sample correction is enabled. - */ -function action_outpop_ssc() { - "use strict"; - $("logo_err").value = $("logo_ssc").value; -} - -/* - * Submit the motif to the selected program. - */ -function action_outpop_submit(e) { - "use strict"; - var form, input, program, motifs; - // find out which program is selected - var radios, i; - radios = document.getElementsByName("program"); - program = "fimo"; // default to fimo, since it works with all alphabet types - for (i = 0; i < radios.length; i++) { - if (radios[i].checked) program = radios[i].value; - } - - motifs = motif_minimal_meme(data.motifs[current_motif]); - form = document.createElement("form"); - form.setAttribute("method", "post"); - form.setAttribute("action", site_url + "/tools/" + program); - - input = document.createElement("input"); - input.setAttribute("type", "hidden"); - input.setAttribute("name", "motifs_embed"); - input.setAttribute("value", motifs); - form.appendChild(input); - - document.body.appendChild(form); - form.submit(); - document.body.removeChild(form); -} - -/* - * Download the format text. - * Wire the link containing the data URI text to a download button so it looks - * the same as the server submit stuff. - */ -function action_outpop_download_motif(e) { - $("outpop_text_dl").click(); -} - -/* - * Download the motif logo. - * The EPS format can be calculated locally in Javascript - */ -function action_outpop_download_logo(e) { - "use strict"; - var pspm, logo, eps; - var logo_rc, logo_ssc, logo_width, logo_height; - var motif = data.motifs[current_motif]; - if ($("logo_format").value == "0") { // EPS - logo_rc = ($("logo_rc").value == "1"); - logo_ssc = ($("logo_ssc").value == "1"); - logo_width = parseFloat($("logo_width").value); - if (isNaN(logo_width) || !isFinite(logo_width) || logo_width <= 0) logo_width = null; - logo_height = parseFloat($("logo_height").value); - if (isNaN(logo_height) || !isFinite(logo_height) || logo_height <= 0) logo_height = null; - // create a PSPM from the motif - pspm = motif_pspm(motif); - if (logo_rc) pspm.reverse_complement(dreme_alphabet); - logo = new Logo(dreme_alphabet); - logo.add_pspm(pspm, 0); - eps = logo.as_eps({"ssc": logo_ssc, "logo_width": logo_width, "logo_height": logo_height}); - prepare_download(eps, "application/postscript", motif.id + ".eps"); - } else { - $("logo_motifs").value = motif_minimal_meme(motif); - $("logo_form").submit(); - } -} - -/* - * Change the selected tab in the download popup. - */ -function action_outpop_tab(e) { - "use strict"; - var tab1, tab2, tab3, pnl1, pnl2, pnl3, do_btn; - if (!e) e = window.event; - if (e.type === "keydown") { - if (e.keyCode !== 13 && e.keyCode !== 32) { - return; - } - // stop a submit or something like that - e.preventDefault(); - } - tab1 = $("outpop_tab_1"); - tab2 = $("outpop_tab_2"); - tab3 = $("outpop_tab_3"); - pnl1 = $("outpop_pnl_1"); - pnl2 = $("outpop_pnl_2"); - pnl3 = $("outpop_pnl_3"); - do_btn = $("outpop_do"); - - toggle_class(tab1, "activeTab", (this === tab1)); - toggle_class(tab2, "activeTab", (this === tab2)); - toggle_class(tab3, "activeTab", (this === tab3)); - pnl1.style.display = ((this === tab1) ? "block" : "none"); - pnl2.style.display = ((this === tab2) ? "block" : "none"); - pnl3.style.display = ((this === tab3) ? "block" : "none"); - do_btn.value = ((this === tab1) ? "Submit" : "Download"); - do_btn.removeEventListener("click", action_outpop_submit, false); - do_btn.removeEventListener("click", action_outpop_download_logo, false); - do_btn.removeEventListener("click", action_outpop_download_motif, false); - if (this === tab1) { - do_btn.addEventListener("click", action_outpop_submit, false); - } else if (this === tab2) { - do_btn.addEventListener("click", action_outpop_download_motif, false); - } else { - do_btn.addEventListener("click", action_outpop_download_logo, false); - } -} - -/* - * Update the text in the download format popup. - */ -function action_outpop_format() { - update_outpop_format(current_motif); -} - -/* - * Find all text nodes in the given container. - */ -function text_nodes(container) { - var textNodes = []; - var stack = [container]; - // depth first search to maintain ordering when flattened - while (stack.length > 0) { - var node = stack.pop(); - if (node.nodeType == Node.TEXT_NODE) { - textNodes.push(node); - } else { - for (var i = node.childNodes.length-1; i >= 0; i--) { - stack.push(node.childNodes[i]); - } - } - } - return textNodes; -} - -/* - * Get the text out of a specific text node. - */ -function node_text(node) { - if (node === undefined) { - return ''; - } else if (node.textContent) { - return node.textContent; - } else if (node.innerText) { - return node.innerText; - } else { - return ''; - } -} - -/* - * Get the text contained within the element. - */ -function elem_text(elem, separator) { - if (separator === undefined) separator = ''; - return text_nodes(elem).map(node_text).join(separator); -} - -/* - * Sort all rows in the first table body based on the column of the given element and the comparison function. - * The sort is not very fast and is intended for small tables only. - */ -function sort_table(colEle, compare_function) { - //find the parent of colEle that is either a td or th - var i, j; - var cell = colEle; - while (true) { - if (cell == null) return; - if (cell.nodeType == Node.ELEMENT_NODE && - (cell.tagName.toLowerCase() == "td" || cell.tagName.toLowerCase() == "th")) { - break; - } - cell = cell.parentNode; - } - //find the parent of cell that is a tr - var row = cell; - while (true) { - if (row == null) return; - if (row.nodeType == Node.ELEMENT_NODE && row.tagName.toLowerCase() == "tr") { - break; - } - row = row.parentNode; - } - //find the parent of row that is a table - var table = row; - while (true) { - if (table == null) return; - if (table.nodeType == Node.ELEMENT_NODE && table.tagName.toLowerCase() == "table") { - break; - } - table = table.parentNode; - } - var column_index = cell.cellIndex; - // do a bubble sort, because the tables are so small it doesn't matter - var change; - var trs = table.tBodies[0].getElementsByTagName('tr'); - var already_sorted = true; - var reverse = false; - while (true) { - do { - change = false; - for (i = 0; i < trs.length -1; i++) { - var v1 = elem_text(trs[i].cells[column_index]); - var v2 = elem_text(trs[i+1].cells[column_index]); - if (reverse) { - var tmp = v1; - v1 = v2; - v2 = tmp; - } - if (compare_function(v1, v2) > 0) { - exchange(trs[i], trs[i+1], table); - change = true; - already_sorted = false; - trs = table.tBodies[0].getElementsByTagName('tr'); - } - } - } while (change); - if (reverse) break;// we've sorted twice so exit - if (!already_sorted) break;// sort did something so exit - // when it's sorted one way already then sort the opposite way - reverse = true; - } - // put arrows on the headers - var headers = table.tHead.getElementsByTagName('tr'); - for (i = 0; i < headers.length; i++) { - for (j = 0; j < headers[i].cells.length; j++) { - var cell = headers[i].cells[j]; - var arrows = cell.getElementsByClassName("sort_arrow"); - var arrow; - if (arrows.length == 0) { - arrow = document.createElement("span"); - arrow.className = "sort_arrow"; - cell.insertBefore(arrow, cell.firstChild); - } else { - arrow = arrows[0]; - } - arrow.innerHTML = ""; - if (j == column_index) { - arrow.appendChild(document.createTextNode(reverse ? "\u25B2" : "\u25BC")); - } - } - } -} - -/* - * Swap two rows in a table. - */ -function exchange(oRowI, oRowJ, oTable) { - var i = oRowI.rowIndex; - var j = oRowJ.rowIndex; - if (i == j+1) { - oTable.tBodies[0].insertBefore(oRowI, oRowJ); - } if (j == i+1) { - oTable.tBodies[0].insertBefore(oRowJ, oRowI); - } else { - var tmpNode = oTable.tBodies[0].replaceChild(oRowI, oRowJ); - if(typeof(oRowI) != "undefined") { - oTable.tBodies[0].insertBefore(tmpNode, oRowI); - } else { - oTable.appendChild(tmpNode); - } - } -} - -/* - * Compare two E-values which may be very small. - */ -function compare_evalues(v1, v2) { - var e1 = sci2log(v1); - var e2 = sci2log(v2); - if (e1 < e2) return -1; - else if (e1 > e2) return 1; - return 0; -} - -/* - * Compare two counts. - */ -function compare_counts(v1, v2) { - var re = /(\d+)\s*\/\s*\d+/; - var m1 = re.exec(v1); - var m2 = re.exec(v2); - if (m1 == null && m2 == null) return 0; - if (m1 == null) return -1; - if (m2 == null) return 1; - return parseInt(m2[1]) - parseInt(m1[1]); -} - -/* - * Compare two sequence words. - */ -function compare_words(v1, v2) { - return v1.localeCompare(v2); -} - - -</script> - <style> -/* The following is the content of meme.css */ -body { background-color:white; font-size: 12px; font-family: Verdana, Arial, Helvetica, sans-serif;} - -div.help { - display: inline-block; - margin: 0px; - padding: 0px; - width: 12px; - height: 13px; - cursor: pointer; - background-image: url(data:image/gif;base64,R0lGODlhDAANAIABANR0AP///yH5BAEAAAEALAAAAAAMAA0AAAIdhI8Xy22MIFgv1DttrrJ7mlGNNo4c+aFg6SQuUAAAOw==); -} - -div.help:hover { - background-image: url(data:image/gif;base64,R0lGODlhDAANAKEAANR0AP///9R0ANR0ACH+EUNyZWF0ZWQgd2l0aCBHSU1QACH5BAEAAAIALAAAAAAMAA0AAAIdDGynCe3PgoxONntvwqz2/z2K2ImjR0KhmSIZUgAAOw==); -} - -p.spaced { line-height: 1.8em;} - -span.citation { font-family: "Book Antiqua", "Palatino Linotype", serif; color: #004a4d;} - -p.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;} - 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#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 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20px; -} -th.motif_more { - padding: 0 5px; -} -td.motif_more { - text-align: center; - padding: 0 5px; -} -th.motif_submit { - padding: 0 5px; -} -td.motif_submit { - text-align: center; - padding: 0 5px; -} -th.match_word { - padding-right: 10px; -} -td.match_word { - padding-right: 10px; - font-weight: bold; - font-size: large; - font-family: 'Courier New', Courier, monospace; -} -th.match_evalue, th.match_count { - text-align: right; - padding-right: 10px; -} -td.match_evalue, td.match_count { - text-align: right; - white-space: nowrap; - padding-right: 20px; -} - -div.tabArea { - font-size: 80%; - font-weight: bold; -} - -.norc div.tabArea { - display: none; -} - -span.tab, span.tab:visited { - cursor: pointer; - color: #888; - background-color: #ddd; - border: 2px solid #ccc; - padding: 2px 1em; - text-decoration: none; -} -span.tab.middle { - border-left-width: 0px; -} -div.tabArea.base span.tab { - border-top-width: 0px; -} -div.tabArea.top span.tab { - border-bottom-width: 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-} -div.close { - cursor: pointer; - border: 1px solid black; - width:15px; - height:15px; - line-height:15px; /* this causes vertical centering */ - text-align:center; - background-color:#FFF; - color:#000; - font-size:15px; - font-family:monospace; -} - -div.close:hover { - color:#FFF; - background-color:#000; -} - -div.navnum { - width:100%; - height:20px; - line-height:20px; - text-align:center; - font-size:medium; -} - -div.navarrow { - font-size: 30px; - text-decoration:none; - cursor: pointer; - -moz-user-select: none; - -webkit-user-select: none; - -ms-user-select: none; -} - -div.navarrow > span.inactive { - display: inline; -} -div.navarrow > span.active { - display: none; -} - -div.navarrow:hover > span.active { - display: inline; -} -div.navarrow:hover > span.inactive { - display: none; -} - -table.programs { - width: 100%; -} - -table.programs tr { - background-color: #EFE; -} - -table.programs tr.selected { - background-color: #262; - color: #FFF; -} - -table.programs tr.dna_only { - display: none; -} - -table.programs.alphabet_dna tr.dna_only { - display: table-row; -} - -table.inputs { - margin-top: 20px; - border-collapse:collapse; -} -table.inputs * td, table.inputs * th { - padding-left: 15px; - padding-right: 15px; - padding-top: 1px; - padding-bottom: 1px; -} - /* program settings */ -span.strand_none, span.strand_given, span.strand_both { - display: none; -} -td.none span.strand_none, td.given span.strand_given, td.both span.strand_both { - display: inline; -} - -/* show the expanded motif only when the collapsed one is hidden */ -tbody *.less, tbody.collapsed *.more { - display: none; -} - -tbody.collapsed *.less { - display: inline; -} - </style> </head> <body data-scrollpad="true"> - <!-- --> - <div id="grey_out_page" class="grey_background" style="display:none;"> - </div> - - <!-- Help popups --> - <div class="pop_content" id="pop_"> - <p>Help poup.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_motifs_word"> - <p> The name of the motif uses the IUPAC codes for nucleotides which has a different letter to represent each of the 15 possible combinations. - </p> - <p> The name is itself a representation of the motif though the position - weight matrix is not directly equalivant as it is generated from the + weight matrix is not directly equivalent as it is generated from the sites found that matched the letters given in the name. - </p> - <p> - <a id="doc_alphabets_url" href="#"> - Read more about the MEME suite's use of the IUPAC alphabets. - </a> - <script>$("doc_alphabets_url").href = site_url + "/doc/alphabets.html";</script> - </p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motifs_logo"> - <p>The logo of the motif.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motifs_rc_logo"> - <p>The logo of the reverse complement motif.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motifs_evalue"> <p>The E-value is the enrichment p-value times the number of candidate motifs tested.</p> <p>The enrichment p-value is calculated using Fisher's Exact Test for enrichment of the motif in the positive sequences.</p> <p>Note that the counts used in Fisher's Exact Test are made after erasing sites that match previously found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motifs_uevalue"> <p>The E-value of the motif calculated without erasing the sites of previously found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_more"> <p>Show more information on the motif.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_submit_dl"> <p>Submit your motif to another MEME Suite program or download your motif.</p> <h5>Supported Programs</h5> - <dl> <dt>Tomtom</dt> <dd>Tomtom is a tool for searching for similar known motifs. - </dd> <dt>MAST</dt> <dd>MAST is a tool for searching biological sequence databases for sequences that contain one or more of a group of known motifs. - </dd> <dt>FIMO</dt> <dd>FIMO is a tool for searching biological sequence databases for sequences that contain one or more known motifs. - </dd> - <dt>GOMO</dt> - <dd>GOMO is a tool for identifying possible roles (Gene Ontology + <dt>GOMo</dt> + <dd>GOMo is a tool for identifying possible roles (Gene Ontology terms) for DNA binding motifs. - </dd> <dt>SpaMo</dt> <dd>SpaMo is a tool for inferring possible transcription factor complexes by finding motifs with enriched spacings. - </dd> - </dl> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motif_positives"> - <p># positive sequences matching the motif / # positive sequences.</p> - <p>Note these counts are made after erasing sites that match previously - found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motif_negatives"> - <p># negative sequences matching the motif / # negative sequences.</p> - <p>Note these counts are made after erasing sites that match previously - found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motif_pvalue"> - <p>The p-value of Fisher's Exact Test for enrichment of the motif in - the positive sequences.</p> - <p>Note that the counts used in Fisher's Exact Test are made after - erasing sites that match previously found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motif_evalue"> - <p>The E-value is the motif p-value times the number of candidate motifs - tested.</p> - <p>Note that the p-value was calculated with counts made after - erasing sites that match previously found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_motif_uevalue"> - <p>The E-value of the motif calculated without erasing the sites of - previously found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_match_word"> - <p>All words matching the motif whose uncorrected p-value is less than - <span id="help_add_pv_thresh"></span>.</p> - <script>$("help_add_pv_thresh").innerHTML = data.options.add_pv_thresh;</script> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_match_pos"> - <p># positive sequences with matches to the word / # positive sequences.</p> - <p>Note these counts are made after erasing sites that match previously - found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_match_neg"> - <p># negative sequences with matches to the word / # negative sequences.</p> - <p>Note these counts are made after erasing sites that match previously - found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_match_pval"> - <p>The p-value of Fisher's Exact Test for enrichment of the word in - the positive sequences.</p> - <p>Note that the counts used in Fisher's Exact Test are made after - erasing sites that match previously found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_match_eval"> - <p>The word p-value times the number of candidates tested.</p> - <p>Note that the p-value was calculated with counts made after - erasing sites that match previously found motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_seq_source"> - <p>The sequence file used by DREME to find the motifs.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_seq_alph"> - <p>The alphabet of the sequences.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - <div class="pop_content" id="pop_seq_count"> - <p>The count of the sequences.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_alph_name"> - <p>The name of the alphabet symbol.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - - <div class="pop_content" id="pop_alph_control"> - <p>The frequency of the alphabet symbol in the control dataset.</p> - <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div> - </div> - - <!-- templates --> - - <div class="template box expanded_motif" id="tmpl_motif_expanded"> - <div> - <span class="tvar_logo"></span> - <span class="tvar_rclogo"></span> - </div> - <h4>Details</h4> - <table class="details"> - <thead> - <tr> - <th class="match_count">Positives <div class="help" data-topic="pop_motif_positives"></div></th> - <th class="match_count">Negatives <div class="help" data-topic="pop_motif_negatives"></div></th> - <th class="match_evalue">P-value <div class="help" data-topic="pop_motif_pvalue"></div></th> - <th class="match_evalue">E-value <div class="help" data-topic="pop_motif_evalue"></div></th> - <th class="match_evalue">Unerased E-value <div class="help" data-topic="pop_motif_uevalue"></div></th> - </tr> - </thead> - <tbody> - <tr> - <td class="match_count"> - <span class="tvar_p"></span> / <span class="tvar_p_total"></span> - </td> - <td class="match_count"> - <span class="tvar_n"></span> / <span class="tvar_n_total"></span> - </td> - <td class="tvar_pvalue match_evalue"></td> - <td class="tvar_evalue match_evalue"></td> - <td class="tvar_uevalue match_evalue"></td> - </tr> - </tbody> - </table> - <h4>Enriched Matching Words</h4> - <div class="tvar_words"></div> - </div> - - - <div class="popup_wrapper"> - <div class="popup" style="display:none; top: -150px;" id="download"> - <div> - <div style="float:right; "> - <div id="outpop_close" class="close" tabindex="0">x</div> - </div> - <h2 class="mainh" style="margin:0; padding:0;">Submit or Download</h2> - <div style="clear:both"></div> - </div> - <div style="height:100px"> - <div style="float:right; width: 30px;"> - <div id="outpop_prev" class="navarrow" tabindex="0"> - <span class="inactive">⇧</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="250"></canvas> - <canvas id="outpop_logo_rc" height="100" width="250"></canvas> - </div> - </div> - <div> - <!-- tabs start --> - <div class="tabArea top"> - <span id="outpop_tab_1" class="tab">Submit Motif</span><span - id="outpop_tab_2" class="tab middle">Download Motif</span><span - id="outpop_tab_3" class="tab middle">Download Logo</span> - </div> - <div class="tabMain top"> - <!-- Submit to another program --> - <div id="outpop_pnl_1"> - <h4 class="compact">Submit to program</h4> - <table id="programs" class="programs"> - <tr class="dna_only"> - <td><input type="radio" name="program" value="tomtom" id="submit_tomtom"></td> - <td><label for="submit_tomtom">Tomtom</label></td> - <td><label for="submit_tomtom">Find similar motifs in - published libraries or a library you supply.</label></td> - </tr> - <tr> - <td><input type="radio" name="program" value="fimo" id="submit_fimo"></td> - <td><label for="submit_fimo">FIMO</label></td> - <td><label for="submit_fimo">Find motif occurrences in - sequence data.</label></td> - </tr> - <tr> - <td><input type="radio" name="program" value="mast" id="submit_mast"></td> - <td><label for="submit_mast">MAST</label></td> - <td><label for="submit_mast">Rank sequences by affinity to - groups of motifs.</label></td> - </tr> - <tr class="dna_only"> - <td><input type="radio" name="program" value="gomo" id="submit_gomo"></td> - <td><label for="submit_gomo">GOMo</label></td> - <td><label for="submit_gomo">Identify possible roles (Gene - Ontology terms) for motifs.</label></td> - </tr> - <tr class="dna_only"> - <td><input type="radio" name="program" value="spamo" id="submit_spamo"></td> - <td><label for="submit_spamo">SpaMo</label></td> - <td><label for="submit_spamo">Find other motifs that are - enriched at specific close spacings which might imply the existance of a complex.</label></td> - </tr> - </table> - </div> - <!-- download text format --> - <div id="outpop_pnl_2"> - <div> - <label for="text_format">Format:</label> - <select id="text_format"> - <option value="0">Count Matrix</option> - <option value="1">Probability Matrix</option> - <option value="2">Minimal MEME</option> - </select> - </div> - <textarea id="outpop_text" name="content" - style="width:99%; white-space: pre; word-wrap: normal; overflow-x: scroll;" - rows="8" readonly="readonly" wrap="off"></textarea> - <a id="outpop_text_dl" download="meme.txt" href=""></a> - </div> - <!-- download logo format --> - <div id="outpop_pnl_3"> - <form id="logo_form" method="post" action=""> - <script>$("logo_form").action = site_url + "/utilities/generate_logo";</script> - <input type="hidden" name="program" value="DREME"/> - <input type="hidden" id="logo_motifs" name="motifs" value=""/> - <table> - <tr> - <td><label for="logo_format">Format:</label></td> - <td> - <select id="logo_format" name="png"> - <option value="1">PNG (for web)</option> - <option value="0">EPS (for publication)</option> - </select> - </td> - </tr> - <tr> - <td><label for="logo_rc">Orientation:</label></td> - <td> - <select id="logo_rc" name="rc1"> - <option value="0">Normal</option> - <option value="1" id="logo_rc_option">Reverse Complement</option> - </select> - </td> - </tr> - <tr> - <td><label for="logo_ssc">Small Sample Correction:</label></td> - <td> - <input type="hidden" id="logo_err" name="errbars" value="0"/> - <select id="logo_ssc" name="ssc"> - <option value="0">Off</option> - <option value="1">On</option> - </select> - </td> - </tr> - <tr> - <td><label for="logo_width">Width:</label></td> - <td> - <input type="text" id="logo_width" size="4" placeholder="default" name="width"/> 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 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" alt="DREME Logo"/> - <h1>DREME</h1> - <h2>Discriminative Regular Expression Motif Elicitation</h2> - </div> - <p class="spaced"> - For further information on how to interpret these results or to get a - copy of the MEME software please access - <a href="http://meme.nbcr.net/">http://meme.nbcr.net</a>. - </p> - <p> - If you use DREME in your research please cite the following paper:<br /> - <span class="citation"> - Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011. - <a href="http://bioinformatics.oxfordjournals.org/content/27/12/1653">[full text]</a> - </span> - </p> - </div> - <!-- navigation --> - <div class="pad2"> - <a class="jump" href="#motifs_sec">Discovered Motifs</a> - | - <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> - <!-- description --> - <div id="description_section" style="display:none"> - <div id="description" class="header"> - <h2>Description</h2> - </div> - <div id="description_text" class="box"> - </div> - </div> - <script> - if (data.description) { - $("description_text").innerHTML = ""; - $("description_text").appendChild(make_description(data.description)); - $("description_section").style.display = "block"; - } - </script> - <!-- motifs --> - <div id="motifs_sec" class="header"> - <h2>Discovered Motifs</h2> - <span><a href="#inputs_sec">Next</a> <a href="#">Top</a></span> - </div> - <div id="motifs" class="box"> - <p>No motifs were discovered!</p> - </div> - <script>make_motifs();</script> - <!-- inputs and settings --> - <div id="inputs_sec" class="header"> - <h2>Inputs & Settings</h2> - <span><a href="#motifs_sec">Previous</a> <a href="#info_sec">Next</a> <a href="#">Top</a></span> - </div> - <div class="box"> - <h4>Sequences</h4> - <table id="seq_info" class="inputs"> - <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th> - <th>Alphabet <div class="help" data-topic="pop_seq_alph"></div></th> - <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th> - </tr> - <tr> - <td id="ins_seq_source"></td> - <td id="ins_seq_alphabet"></td> - <td id="ins_seq_count"></td> - </tr> - </table> - <script> - { - var db = data.sequence_db; - $("ins_seq_source").innerHTML = db.file; - $("ins_seq_alphabet").innerHTML = dreme_alphabet.get_alphabet_name(); - $("ins_seq_count").innerHTML = db.count; - } - </script> - <h4>Control Sequences</h4> - <table id="seq_info" class="inputs"> - <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th> - <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th> - </tr> - <tr> - <td id="ins_cseq_source"></td> - <td id="ins_cseq_count"></td> - </tr> - </table> - <script> - { - var db = data.control_db; - if (db.from == "shuffled") { - $("ins_cseq_source").innerHTML = "Shuffled Sequences"; - } else { - $("ins_cseq_source").innerHTML = db.file; - } - $("ins_cseq_count").innerHTML = db.count; - } - </script> - <h4>Background</h4> - <span id="alpha_bg"></span> - <script> - { - $("alpha_bg").appendChild(make_alpha_bg(dreme_alphabet, data.control_db.freqs)); - } - </script> - <h4>Other Settings</h4> - <table id="tbl_settings" class="inputs hide_advanced"> - <tr> - <th>Strand Handling</th> - <td id="opt_strand"> - <span class="strand_none">This alphabet only has one strand</span> - <span class="strand_given">Only the given strand is processed</span> - <span class="strand_both">Both the given and reverse complement strands are processed</span> - </td> - </tr> - <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr> - <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr> - <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr> - <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr> - <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr> - </table> - <script> - { - $("opt_strand").className = (dreme_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none"); - $("opt_ngen").innerHTML = data.options.ngen; - $("opt_seed").innerHTML = data.options.seed; - $("opt_stop_evalue").innerHTML = data.options.stop.evalue; - $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count."); - $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time."); - } - </script> - </div> - <!-- list information on this program --> - <div id="info_sec" class="bar" style="position:relative"> - <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div> - <div class="subsection"> - <h5 id="version">DREME version</h5> - <span id="ins_version"></span> - (Release date: <span id="ins_release"></span>)<br> - </div> - <script> - $("ins_version").innerHTML = data["version"]; - $("ins_release").innerHTML = data["release"]; - </script> - <div class="subsection"> - <h5 id="reference">Reference</h5> - <span class="citation"> - Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011. - <a href="http://bioinformatics.oxfordjournals.org/content/27/12/1653">[full text]</a> - </span> - </div> - <div class="subsection"> - <h5 id="command">Command line</h5> - <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly"> - </textarea> - <script>$("cmd").value = data["cmd"].join(" ");</script> - </div> - </div> - </body> </html>