<!doctype html> <html> <head> <meta charset="UTF-8"> <title>Centrimo</title> <script type="text/javascript"> //@JSON_VAR data var data = { "version": "4.11.2", "revision": "4898e0907d161db4041c7e01536ae57feb300b24", "release": "Thu Sep 08 11:34:04 2016 -0400", "program": "CentriMo", "cmd": [ "centrimo-neg", "-seqlen", "500", "-verbosity", "1", "-oc", "/mnt/work1/users/home2/ddenisko/workDir/2019-02-14-peaKO/MEF2D/without-de-novo///centrimo-1/", "-bfile", "KOIN-MEF2D-macs2-wt-ko-updated-optimal_peak/background", "KOIN-MEF2D-macs2-wt-ko-updated-optimal_peak/MEF2D-macs2-wt-ko-updated-optimal_peak.fa", "/mnt/work1/users/home2/ddenisko/motif_databases/JASPAR/JASPAR_CORE_2016_vertebrates.meme" ], "options": { "motif-pseudo": 0.1, "score": 5, "optimize_score": false, "ethresh": 10, "minbin": 0, "maxbin": 0, "local": false, "norc": false, "sep": true, "flip": false, "noseq": false, "neg_sequences": false, "disc": false, "mcc": false }, "seqlen": 500, "tested": 519, "alphabet": { "name": "DNA", 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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 type="text/javascript"> function rad2deg(rad) { return rad * 180 / Math.PI; } function parse_line_join(line_join) { line_join = line_join.toLowerCase(); if (line_join == "bevel") { return 2; } else if (line_join == "round") { return 1; } else { // miter return 0; } } function parse_line_cap(line_cap) { line_cap = line_cap.toLowerCase(); if (line_cap == "square") { return 2; } else if (line_cap == "round") { return 1; } else { // butt return 0; } } function parse_text_align(text_align) { text_align = text_align.toLowerCase(); if (text_align == "center") { return "center"; } else if (text_align == "end" || text_align == "right") { return "right"; } else { // start or left return "left"; } } function parse_text_baseline(text_baseline) { text_baseline = text_baseline.toLowerCase(); if (text_baseline == "top" || text_baseline == "hanging") { return "top"; } else if (text_baseline == "middle") { return "middle"; } else if (text_baseline == "bottom") { return "bottom"; } else { // alphabetic or ideographic return "alphabetic"; } } function parse_colour(colour) { var hex6_re = /^#([0-9a-f][0-9a-f])([0-9a-f][0-9a-f])([0-9a-f][0-9a-f])$/; var hex3_re = /^#([0-9a-f])([0-9a-f])([0-9a-f])$/; var rgb_re = /^\s*rgb\s*\(\s*(\d{1,3})(%?)\s*,\s*(\d{1,3})(%?)\s*,\s*(\d{1,3})(%?)\s*\)\s*$/; var rgba_re = /^\s*rgba\s*\(\s*(\d{1,3})(%?)\s*,\s*(\d{1,3})(%?)\s*,\s*(\d{1,3})(%?)\s*,\s*(\d{1,3})(%?)\s*\)\s*$/; if (colour == null || colour == "") { return {'red': 0, 'green': 0, 'blue': 0, 'alpha': 255}; } colour = colour.replace(/^\s\s*/, '').replace(/\s\s*$/, ''); //trim colour = colour.toLowerCase(); if (colour == "maroon") {// #800000 return {'red': 128, 'green': 0, 'blue': 0, 'alpha': 255}; } else if (colour == "red") { // #FF0000 return {'red': 255, 'green': 0, 'blue': 0, 'alpha': 255}; } else if (colour == "orange") { // FFA500 return {'red': 255, 'green': 165, 'blue': 0, 'alpha': 255}; } else if (colour == "yellow") { // #FFFF00 return {'red': 255, 'green': 255, 'blue': 0, 'alpha': 255}; } else if (colour == "olive") { // #808000 return {'red': 128, 'green': 128, 'blue': 0, 'alpha': 255}; } else if (colour == "purple") { // #800080 return {'red': 128, 'green': 0, 'blue': 128, 'alpha': 255}; } else if (colour == "fuchsia" || colour == "magenta") { // #FF00FF return {'red': 255, 'green': 0, 'blue': 255, 'alpha': 255}; } else if (colour == "white") { // #FFFFFF return {'red': 255, 'green': 255, 'blue': 255, 'alpha': 255}; } else if (colour == "lime") { // #00FF00 return {'red': 0, 'green': 255, 'blue': 0, 'alpha': 255}; } else if (colour == "green") { // #008000 return {'red': 0, 'green': 128, 'blue': 0, 'alpha': 255}; } else if (colour == "navy") { // #000080 return {'red': 0, 'green': 0, 'blue': 128, 'alpha': 255}; } else if (colour == "blue") { // #0000FF return {'red': 0, 'green': 0, 'blue': 255, 'alpha': 255}; } else if (colour == "aqua" || colour == "cyan") { // #00FFFF return {'red': 0, 'green': 255, 'blue': 255, 'alpha': 255}; } else if (colour == "teal") { // #008080 return {'red': 0, 'green': 128, 'blue': 128, 'alpha': 255}; } else if (colour == "black") { // #000000 return {'red': 0, 'green': 0, 'blue': 0, 'alpha': 255}; } else if (colour == "silver") { // #C0C0C0 return {'red': 192, 'green': 192, 'blue': 192, 'alpha': 255}; } else if (colour == "gray") { // #808080 return {'red': 128, 'green': 128, 'blue': 128, 'alpha': 255}; } var matches; matches = hex6_re.exec(colour); if (matches) { var red = parseInt(matches[1], 16); var green = parseInt(matches[2], 16); var blue = parseInt(matches[3], 16); return {'red': red, 'green': green, 'blue': blue, 'alpha': 255}; } matches = hex3_re.exec(colour); if (matches) { var red = parseInt(matches[1] + matches[1], 16); var green = parseInt(matches[2] + matches[2], 16); var blue = parseInt(matches[3] + matches[3], 16); return {'red': red, 'green': green, 'blue': blue, 'alpha': 255}; } matches = rgb_re.exec(colour); if (matches) { var red = parseInt(matches[1]); if (matches[2] == "%") red = Math.round((red * 255) / 100); var green = parseInt(matches[3]); if (matches[4] == "%") green = Math.round((green * 255) / 100); var blue = parseInt(matches[5]); if (matches[6] == "%") blue = Math.round((blue * 255) / 100); return {'red': red, 'green': green, 'blue': blue, 'alpha': 255}; } matches = rgba_re.exec(colour); if (matches) { var red = parseInt(matches[1]); if (matches[2] == "%") red = Math.round((red * 255) / 100); var green = parseInt(matches[3]); if (matches[4] == "%") green = Math.round((green * 255) / 100); var blue = parseInt(matches[5]); if (matches[6] == "%") blue = Math.round((blue * 255) / 100); var alpha = parseInt(matches[7]); if (matches[8] == "%") alpha = Math.round((alpha * 255) / 100); return {'red': red, 'green': green, 'blue': blue, 'alpha': alpha}; } // default to black throw new Error("Failed to parse colour: " + colour); } function colour_equals(colour1, colour2) { if (colour1.red != colour2.red) return false; if (colour1.green != colour2.green) return false; if (colour1.blue != colour2.blue) return false; if (colour1.alpha != colour2.alpha) return false; return true; } // splits a font string into words function split_words(str) { var words = []; var start = -1; var space = /\s/; var single_quote = false; var double_quote = false; // read words for (var i = 0; i < str.length; i++) { if (start == -1) { if (!space.test(str.charAt(i))) { switch (str.charAt(i)) { case "'": single_quote = true; start = i + 1; break; case '"': double_quote = true; start = i + 1; break; default: start = i; } } } else { if (!single_quote && !double_quote) { if (space.test(str.charAt(i))) { var len = i - start; if (len > 0) words.push(str.substr(start, len)); start = -1; } else if (str.charAt(i) == "'" || str.charAt(i) == '"') { throw new Error("Quote in the middle of an unquoted word!"); } } else if (single_quote) { if (str.charAt(i) == "'") { var len = i - start; if (len > 0) words.push(str.substr(start, len)); start = -1; single_quote = false; } } else if (double_quote) { if (str.charAt(i) == '"') { var len = i - start; if (len > 0) words.push(str.substr(start, len)); start = -1; double_quote = false; } } } } if (start != -1) { if (single_quote || double_quote) throw new Error("Unterminated quoted region"); words.push(str.substr(start)); } return words; } function add_intercepts(ctx2d, eps_callback) { ctx2d.eps_callback = eps_callback; ctx2d.save = function() { this.eps_callback.save(); Object.getPrototypeOf(this).save.call(this); }; ctx2d.restore = function() { this.eps_callback.restore(); Object.getPrototypeOf(this).restore.call(this); }; ctx2d.beginPath = function() { this.eps_callback.beginPath(); Object.getPrototypeOf(this).beginPath.call(this); }; ctx2d.closePath = function() { this.eps_callback.closePath(); Object.getPrototypeOf(this).closePath.call(this); }; ctx2d.moveTo = function(x, y) { this.eps_callback.moveTo(x, y); Object.getPrototypeOf(this).moveTo.call(this, x, y); }; ctx2d.lineTo = function(x, y) { this.eps_callback.lineTo(x, y); Object.getPrototypeOf(this).lineTo.call(this, x, y); }; ctx2d.rect = function(x, y, w, h) { this.eps_callback.rect(x, y, w, h); Object.getPrototypeOf(this).rect.call(this, x, y, w, h); }; ctx2d.arc = function(x, y, radius, startAngle, endAngle, anticlockwise) { this.eps_callback.arc(x, y, radius, startAngle, endAngle, anticlockwise); Object.getPrototypeOf(this).arc.call(this, x, y, radius, startAngle, endAngle, anticlockwise); }; ctx2d.arcTo = function(cpx1, cpy1, cpx2, cpy2, radius) { this.eps_callback.arcTo(cpx1, cpy1, cpx2, cpy2, radius); Object.getPrototypeOf(this).arcTo.call(this, cpx1, cpy1, cpx2, cpy2, radius); }; ctx2d.quadraticArcTo = function(cpx, cpy, x, y) { this.eps_callback.quadraticArcTo(cpx, cpy, x, y); Object.getPrototypeOf(this).quadraticArcTo.call(this, cpx, cpy, x, y); }; ctx2d.bezierCurveTo = function(cp1x, cp1y, cp2x, cp2y, x, y) { this.eps_callback.bezierCurveTo(cp1x, cp1y, cp2x, cp2y, x, y); Object.getPrototypeOf(this).bezierCurveTo.call(this, cp1x, cp1y, cp2x, cp2y, x, y); }; ctx2d.stroke = function() { this.eps_callback.stroke(); Object.getPrototypeOf(this).stroke.call(this); }; ctx2d.fill = function() { this.eps_callback.fill(); Object.getPrototypeOf(this).fill.call(this); }; ctx2d.clip = function() { this.eps_callback.clip(); Object.getPrototypeOf(this).clip.call(this); }; ctx2d.fillRect = function(x, y, width, height) { this.eps_callback.fillRect(x, y, width, height); Object.getPrototypeOf(this).fillRect.call(this, x, y, width, height); }; ctx2d.strokeRect = function(x, y, width, height) { this.eps_callback.strokeRect(x, y, width, height); Object.getPrototypeOf(this).strokeRect.call(this, x, y, width, height); }; ctx2d.clearRect = function(x, y, width, height) { this.eps_callback.clearRect(x, y, width, height); Object.getPrototypeOf(this).clearRect.call(this, x, y, width, height); }; ctx2d.fillText = function(string, x, y) { this.eps_callback.fillText(string, x, y); Object.getPrototypeOf(this).fillText.call(this, string, x, y); }; ctx2d.translate = function(dx, dy) { this.eps_callback.translate(dx, dy); Object.getPrototypeOf(this).translate.call(this, dx, dy); }; ctx2d.rotate = function(angle) { this.eps_callback.rotate(angle); Object.getPrototypeOf(this).rotate.call(this, angle); }; ctx2d.scale = function(sx, sy) { this.eps_callback.scale(sx, sy); Object.getPrototypeOf(this).scale.call(this, sx, sy); }; ctx2d.transform = function(m11, m12, m21, m22, dx, dy) { this.eps_callback.transform(m11, m12, m21, m22, dx, dy); Object.getPrototypeOf(this).transform.call(this, m11, m12, m21, m22, dx, dy); }; ctx2d.setTransform = function(m11, m12, m21, m22, dx, dy) { this.eps_callback.setTransform(m11, m12, m21, m22, dx, dy); Object.getPrototypeOf(this).setTransform.call(this, m11, m12, m21, m22, dx, dy); }; } var EpsState = function(copy) { // canvas vars this.activeStyle = {'red': 0, 'green': 0, 'blue': 0, 'alpha': 255}; this.fillStyle = {'red': 0, 'green': 0, 'blue': 0, 'alpha': 255}; this.strokeStyle = {'red': 0, 'green': 0, 'blue': 0, 'alpha': 255}; this.lineWidth = 1.0; this.lineCap = 0; this.lineJoin = 0; this.miterLimit = 10.0; this.font = null; this.textAlign = "left"; this.textBaseline = "alphabetic"; if (copy) { this.activeStyle = copy.activeStyle; this.fillStyle = copy.fillStyle; this.strokeStyle = copy.strokeStyle; this.lineWidth = copy.lineWidth; this.lineCap = copy.lineCap; this.lineJoin = copy.lineJoin; this.miterLimit = copy.miterLimit; this.font = copy.font; this.textAlign = copy.textAlign; this.textBaseline = copy.textBaseline; } }; var EpsContext = function(ctx, width, height) { var title = "Image Title"; var creator = "Image Creator"; var date = new Date(); // private parameters this.ctx = ctx; this.width = width; this.height = height; this.stack = []; this.current_state = new EpsState(); this.font_lookup = {}; this.indent = ""; this.eps_text = "%!PS-Adobe-3.0 EPSF-3.0\n" + "%%Title: " + title + "\n" + "%%Creator: " + creator + "\n" + "%%CreationDate: " + date.toUTCString() + "\n" + "%%BoundingBox: 0 0 " + (width * 0.75) + " " + (height * 0.75) + "\n" + "%%Pages: 0\n" + "%%DocumentFonts:\n" + "%%EndComments\n" + "0.75 0.75 scale\n" + "0 " + height + " translate\n" + "1 -1 scale\n"; add_intercepts(ctx, this); }; // look for differences between the current state and the settings to see // what has changed. Apply the changes to the eps file. EpsContext.prototype.detect = function() { var state = this.current_state; var ctx = this.ctx; if (ctx.lineWidth != state.lineWidth) { state.lineWidth = ctx.lineWidth; this.eps_text += this.indent + state.lineWidth + " setlinewidth\n"; } var cap = parse_line_cap(ctx.lineCap); if (cap != state.lineCap) { state.lineCap = cap; this.eps_text += this.indent + state.lineCap + " setlinecap\n"; } var join = parse_line_join(ctx.lineJoin); if (join != state.lineJoin) { state.lineJoin = join; this.eps_text += this.indent + state.lineJoin + " setlinejoin\n"; } var miterLimit = parseInt(ctx.miterLimit); if (miterLimit != state.miterLimit) { state.miterLimit = miterLimit; this.eps_text += this.indent + state.miterLimit + " setmiterlimit\n"; } var strokeStyle = parse_colour(ctx.strokeStyle); if (!colour_equals(strokeStyle, state.strokeStyle)) { state.strokeStyle = strokeStyle; this.activateStyle(false); } var fillStyle = parse_colour(ctx.fillStyle); if (!colour_equals(fillStyle, state.fillStyle)) { state.fillStyle = fillStyle; this.activateStyle(true); } var textAlign = parse_text_align(ctx.textAlign); if (textAlign != state.textAlign) { state.textAlign = textAlign; } var textBaseline = parse_text_baseline(ctx.textBaseline); if (textBaseline != state.textBaseline) { state.textBaseline = textBaseline; } var font = this.lookup_font(ctx.font); if (font != null && font !== state.font) { state.font = font; this.eps_text += this.indent + "/" + font.name + " findfont " + font.size + " scalefont setfont\n"; } }; EpsContext.prototype.activateStyle = function(useFillStyle) { var state = this.current_state; var style = (useFillStyle ? state.fillStyle : state.strokeStyle); if (!colour_equals(state.activeStyle, style)) { this.eps_text += this.indent + (style.red / 255) + " " + (style.green / 255) + " " + (style.blue / 255) + " setrgbcolor\n"; state.activeStyle = style; } }; // saves the current state on the stack EpsContext.prototype.save = function() { this.detect(); // gsave this.eps_text += this.indent + "gsave\n"; this.stack.push(new EpsState(this.current_state)); this.indent += " "; }; // restores the last saved state EpsContext.prototype.restore = function() { if (this.stack.length == 0) throw new Error("Call to restore not matched with call to save."); this.detect(); this.current_state = this.stack.pop(); this.indent = Array(this.stack.length + 1).join(" "); // grestore this.eps_text += this.indent + "grestore\n"; }; // start a path EpsContext.prototype.beginPath = function() { this.detect(); // newpath this.eps_text += this.indent + "newpath\n"; }; // join the current position to the path start EpsContext.prototype.closePath = function() { this.detect(); // closepath this.eps_text += this.indent + "closepath\n"; }; // move the current position EpsContext.prototype.moveTo = function(x, y) { this.detect(); // moveto this.eps_text += this.indent + x + " " + y + " moveto\n"; }; // join the current position to a new position and update the current position EpsContext.prototype.lineTo = function(x, y) { this.detect(); // lineto this.eps_text += this.indent + x + " " + y + " lineto\n"; }; // add a rectangle to the path EpsContext.prototype.rect = function(x, y, width, height) { this.moveTo(x, y); this.lineTo(x + width, y); this.lineTo(x + width, y + height); this.lineTo(x, y + height); this.closePath(); }; // add an arc to the path EpsContext.prototype.arc = function(x, y, radius, startAngle, endAngle, anticlockwise) { this.detect(); if (anticlockwise) { // command "X Y RADIUS START_ANGLE END_ANGLE arc" this.eps_text += this.indent + x + " " + y + " " + radius + " " + rad2deg(startAngle) + " " + rad2deg(endAngle) + " arcn\n"; } else { // command "X Y RADIUS START_ANGLE END_ANGLE arcn" this.eps_text += this.indent + x + " " + y + " " + radius + " " + rad2deg(startAngle) + " " + rad2deg(endAngle) + " arc\n"; } }; // imagine two lines, one going from the current position to point 1 and // another going from point 1 to point 2. // Now imagine a circle of the given radius which touches the two lines at at // two tangental points T01 and T12. Add a line to the path that goes from // the current position to T01 and add the arc which goes from T01 to T12. // see http://www.dbp-consulting.com/tutorials/canvas/CanvasArcTo.html EpsContext.prototype.arcTo = function(cpx1, cpy1, cpx2, cpy2, radius) { this.detect(); // command "X1 Y1 X2 Y2 RADIUS arct" this.eps_text += this.indent + cpx1 + " " + cpy1 + " " + cpx2 + " " + cpy2 + " " + radius + " arct\n"; }; EpsContext.prototype.quadraticArcTo = function(cpx, cpy, x, y) { /* For the equations below the following variable name prefixes are used: qp0 is the quadratic curve starting point (you must keep this from your last point sent to moveTo(), lineTo(), or bezierCurveTo() ). qp1 is the quadratic curve control point (this is the cpx,cpy you would have sent to quadraticCurveTo() ). qp2 is the quadratic curve ending point (this is the x,y arguments you would have sent to quadraticCurveTo() ). We will convert these points to compute the two needed cubic control points (the starting/ending points are the same for both the quadratic and cubic curves. The exact equations for the two cubic control points are: cp0 = qp0 and cp3 = qp2 cp1 = qp0 + (qp1 - qp0) * ratio cp2 = cp1 + (qp2 - qp0) * (1 - ratio) where ratio = (sqrt(2) - 1) * 4 / 3 exactly (approx. 0.5522847498307933984022516322796) if the quadratic is an approximation of an elliptic arc, and the cubic must approximate the same arc, or ratio = 2.0 / 3.0 for keeping the same quadratic curve. In the code below, we must compute both the x and y terms for each point separately. cp1x = qp0x + (qp1x - qp0x) * ratio; cp1y = qp0y + (qp1y - qp0y) * ratio; cp2x = cp1x + (qp2x - qp0x) * (1 - ratio); cp2y = cp1y + (qp2y - qp0y) * (1 - ratio); We will now a) replace the qp0x and qp0y variables with currentX and currentY (which *you* must store for each moveTo/lineTo/bezierCurveTo) b) replace the qp1x and qp1y variables with cpx and cpy (which we would have passed to quadraticCurveTo) c) replace the qp2x and qp2y variables with x and y. which leaves us with: */ var ratio = 2.0 / 3.0; // 0.5522847498307933984022516322796 if the Bezier is // approximating an elliptic arc with best fitting var cp1x = this.currentX + (cpx - this.currentX) * ratio; var cp1y = this.currentY + (cpy - this.currentY) * ratio; var cp2x = cp1x + (x - this.currentX) * (1 - ratio); var cp2y = cp1y + (y - this.currentY) * (1 - ratio); // and now call cubic Bezier curve to function this.bezierCurveTo( cp1x, cp1y, cp2x, cp2y, x, y ); }; // add a bezier curve to the path EpsContext.prototype.bezierCurveTo = function(cp1x, cp1y, cp2x, cp2y, x, y) { this.detect(); // command "CP1X CP1Y CP2X CP2Y X Y curveto" this.eps_text += this.indent + cp1x + " " + cp1y + " " + cp2x + " " + cp2y + " " + x + " " + y + " curveto"; }; // stroke the current path EpsContext.prototype.stroke = function() { this.detect(); this.activateStyle(false); // stroke this.eps_text += this.indent + "stroke\n"; }; // fill the current path EpsContext.prototype.fill = function() { this.detect(); this.activateStyle(true); // fill this.eps_text += this.indent + "fill\n"; }; // create a clipping region from the current path EpsContext.prototype.clip = function() { this.detect(); // clip this.eps_text += this.indent + "clip\n"; }; // Draws a filled rectangle EpsContext.prototype.fillRect = function(x, y, width, height) { this.detect(); this.activateStyle(true); // rectfill this.eps_text += this.indent + x + " " + y + " " + width + " " + height + " rectfill\n"; }; // Draws a rectangular outline EpsContext.prototype.strokeRect = function(x, y, width, height) { this.detect(); this.activateStyle(false); // rectstroke this.eps_text += this.indent + x + " " + y + " " + width + " " + height + " rectstroke\n"; }; // Clears the specified area and makes it transparent. EpsContext.prototype.clearRect = function(x, y, width, height) { this.detect(); // fill a rectangle with white in the cleared region // EPS doesn't do transparency so this is as close as it can get // command "1 setgray X Y WIDTH HEIGHT rectfill" this.eps_text += this.indent + "gsave\n"; this.eps_text += this.indent + " 1 setgray\n"; this.eps_text += this.indent + " " + x + " " + y + " " + width + " " + height + " rectfill\n"; this.eps_text += this.indent + "grestore\n"; }; // Draws a filled string EpsContext.prototype.fillText = function(string, x, y) { var state = this.current_state; this.detect(); this.activateStyle(true); // lookup the font with "/FONT_NAME findfont" (leaves FONT on stack) // scale the font with "FONT SIZE scalefont" (leaves FONT on stack // set the font with "FONT setfont" // move the printing location with "X Y moveto" // various measurement commands will be needed to do center alignment etc // like "stringwidth" // show the text with "(STRING) show" string = string.replace(/\\/g, "\\\\"); string = string.replace(/\(/g, "\\("); string = string.replace(/\)/g, "\\)"); this.save(); this.translate(x, y); this.scale(1, -1); this.eps_text += this.indent + "(" + string + ")\n"; if (state.textBaseline != "alphabetic") { this.beginPath(); this.moveTo(0,0); this.eps_text += this.indent + "dup true charpath flattenpath pathbbox %bounding box\n"; this.eps_text += this.indent + "/ascent exch def pop /decent exch def pop\n"; if (state.textBaseline == "top") { this.eps_text += this.indent + "0 ascent neg translate %vertical align top\n"; } else if (state.textBaseline == "middle") { this.eps_text += this.indent + "0 ascent decent sub 2 div decent sub neg translate %vertical align middle\n"; } else if (state.textBaseline == "bottom") { this.eps_text += this.indent + "0 decent neg translate %vertical align bottom\n"; } } if (state.textAlign == "right") { this.eps_text += this.indent + "dup stringwidth pop neg 0 translate %right align\n" } else if (state.textAlign == "center") { this.eps_text += this.indent + "dup stringwidth pop 2 div neg 0 translate %center align\n" } this.moveTo(0,0); this.eps_text += this.indent + "show\n"; this.restore(); }; // move the canvas origin EpsContext.prototype.translate = function(dx, dy) { this.detect(); // command "DELTA_X DELTA_Y translate" this.eps_text += this.indent + dx + " " + dy + " translate\n"; }; // rotate around the canvas origin EpsContext.prototype.rotate = function(angle) { this.detect(); // command "DEGREES rotate" (note need to convert angle from radians to degrees) this.eps_text += this.indent + rad2deg(angle) + " rotate\n"; }; // scale EpsContext.prototype.scale = function(scale_x, scale_y) { this.detect(); // command "SCALE_X SCALE_Y scale this.eps_text += this.indent + scale_x + " " + scale_y + " scale\n"; }; // multiplies the current transform matrix by the matrix described by: // m11 m21 dx // m12 m22 dy // 0 0 1 EpsContext.prototype.transform = function(m11, m12, m21, m22, dx, dy) { this.detect(); // command "[M11 M12 M21 M22 DX DY] concat" this.eps_text += this.indent + "[" + m11 + " " + m12 + " " + m21 + " " + m22 + " " + dx + " " + dy + "] concat\n"; }; // reset transform matrix to the identity matrix then call transform EpsContext.prototype.setTransform = function(m11, m12, m21, m22, dx, dy) { // command: // "[1 0 0 1 0 0] defaultmatrix setmatrix 0 height translate 1 -1 scale " // "[M11 M12 M21 M22 DX DY] concat" this.eps_text += this.indent + "[1 0 0 1 0 0] defaultmatrix setmatrix\n"; this.eps_text += this.indent + "0 " + this.height + " translate\n"; this.eps_text += this.indent + "1 -1 scale\n"; this.transform(m11, m12, m21, m22, dx, dy); }; EpsContext.prototype.register_font = function(font_str, eps_font, size) { font_str = font_str.replace(/\s+/g, ""); // remove spaces font_str = font_str.toLowerCase(); // lower case this.font_lookup[font_str] = {'name': eps_font, 'size': size}; }; EpsContext.prototype.lookup_font = function(font_str) { font_str = font_str.replace(/\s+/g, ""); // remove spaces font_str = font_str.toLowerCase(); // lower case return this.font_lookup[font_str]; }; // return the EPS text EpsContext.prototype.eps = function() { return this.eps_text + this.indent + "showpage\n"; }; </script> <script type="text/javascript"> //====================================================================== // 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 type="text/javascript"> var LEGEND_LINE = 16; var LEGEND_FONT = "Helvetica"; var LEGEND_PAD = 5; var Dasher = function(ctx, start_x, start_y, pattern) { if (typeof pattern === "undefined") pattern = []; this.ctx = ctx; this.x = start_x; this.y = start_y; this.pattern = pattern; this.index = 0; // where in the pattern are we up to? this.fragment = 0; // how much of the current pattern have we drawn this.on = true; // pen on paper? ctx.moveTo(start_x, start_y); }; Dasher.prototype.dashTo = function(x, y) { var dx = x - this.x; var dy = y - this.y; var d = Math.pow(dx * dx + dy * dy, 0.5); if (this.pattern.length == 0) { // when no pattern is specified this just draws lines this.ctx.lineTo(x, y); } else { // calculate distance to complete dash var dc = this.pattern[this.index] - this.fragment; while (dc <= d) { // calculate the fraction of the line needed var f = dc / d; this.x += dx * f; this.y += dy * f; if (this.on) { this.ctx.lineTo(this.x, this.y); } else { this.ctx.moveTo(this.x, this.y); } // move to the next dash this.fragment = 0; // skip empty dashes, just toggling on state do { this.index = (this.index + 1) % this.pattern.length; this.on = !this.on; } while (this.pattern[this.index] <= 0); // update variables dc = this.pattern[this.index]; dx = x - this.x; dy = y - this.y; d = Math.pow(dx * dx + dy * dy, 0.5); } this.fragment += d; this.x = x; this.y = y; if (this.on) { this.ctx.lineTo(this.x, this.y); } else { this.ctx.moveTo(this.x, this.y); } } } var CentrimoResult = function(name, sig, colour, motif_length, total_sites, site_counts, neg_total_sites, neg_site_counts) { "use strict"; if (typeof name === "undefined") { name = ""; } if (typeof sig === "undefined") { sig = ""; } if (typeof colour == "undefined") { colour = "#000000"; } this.name = name; this.sig = sig; this.colour = colour; this.motif_length = motif_length; this.total_sites = total_sites; this.site_counts = site_counts; this.has_neg = (typeof neg_total_sites === "number" && typeof neg_site_counts === "object" && neg_site_counts instanceof Array); this.neg_total_sites = neg_total_sites; this.neg_site_counts = neg_site_counts; }; CentrimoResult.prototype.get_site_count = function (index, mirror, neg) { count = neg ? this.neg_site_counts[index] : this.site_counts[index]; if (mirror) { i_mirror = this.site_counts.length - 1 - index; return (count + (neg ? this.neg_site_counts[i_mirror] : this.site_counts[i_mirror])); } else { return count; } }; /* * CentrimoRSet * Construct a centrimo result set. */ var CentrimoRSet = function(sequence_length) { "use strict"; this.sequence_length = sequence_length; this.results = []; }; /* * seq_len * Get the sequence length of the result set. */ CentrimoRSet.prototype.seq_len = function() { "use strict"; return this.sequence_length; }; /* * add * Add a centrimo result to the set */ CentrimoRSet.prototype.add = function(name, sig, colour, motif_length, total_sites, site_counts, neg_total_sites, neg_site_counts) { "use strict"; this.results.push(new CentrimoResult(name, sig, colour, motif_length, total_sites, site_counts, neg_total_sites, neg_site_counts)); }; /* * count * Return the count of centrimo results. */ CentrimoRSet.prototype.count = function() { "use strict"; return this.results.length; }; /* * get * Get an entry in the result set. */ CentrimoRSet.prototype.get = function(index) { "use strict"; return this.results[index]; }; /* * CentrimoLine */ var CentrimoLine = function(name, sig, colour, dash, thickness, show_on_legend, xlist, ylist) { "use strict"; if (xlist.length != ylist.length) { throw new Error("The list of x and y points must be the same length."); } this.xlist = xlist; this.ylist = ylist; this.name = name; this.sig = sig; this.colour = colour; this.dash = dash; this.thickness = thickness; this.show_on_legend = show_on_legend; this.max_prob = -1; }; /* * trim * * Removes points from the ends so the lines are the same length. */ CentrimoLine.prototype.trim = function(left, right) { "use strict"; var lefti, righti, gradient, gap, left_y, right_y; if (this.xlist.length == 0) return; if (typeof left !== "number"|| isNaN(left)) { throw new Error("left trim is not a number"); } if (typeof right !== "number" || isNaN(right)) { throw new Error("right trim is not a number"); } for (lefti = 0; lefti < this.xlist.length; lefti++) { if (this.xlist[lefti] >= left) { break; } } if (lefti === 0 && this.xlist[0] !== left) { throw new Error("Attempt to undertrim line on the left."); } for (righti = this.xlist.length - 1; righti >= 0; righti--) { if (this.xlist[righti] <= right) { break; } } if (righti === (this.xlist.length - 1) && this.xlist[righti] !== right) { throw new Error("Attempt to undertrim line on the right."); } if (lefti == this.xlist.length || righti == -1) { // all points outside of drawable region this.xlist = []; this.ylist = []; return; } if (this.xlist[lefti] != left) { // create a new point that is exactly at left by interpolating gradient = (this.ylist[lefti] - this.ylist[lefti-1]) / (this.xlist[lefti] - this.xlist[lefti-1]); gap = left - this.xlist[lefti-1]; left_y = this.ylist[lefti-1] + gradient * gap; this.xlist.splice(0, lefti, left); this.ylist.splice(0, lefti, left_y); righti = righti - lefti + 1; } else { this.xlist.splice(0, lefti); this.ylist.splice(0, lefti); righti -= lefti; } if (this.xlist[righti] != right) { // create a new point that is exactly at right by interpolating gradient = (this.ylist[righti + 1] - this.ylist[righti]) / (this.xlist[righti + 1] - this.xlist[righti]); gap = right - this.xlist[righti]; right_y = this.ylist[righti] + gradient * gap; // truncate the lists this.xlist.length = righti + 1; this.ylist.length = righti + 1; // push the new item on the end of the lists this.xlist.push(right); this.ylist.push(right_y); } else { // truncate the lists this.xlist.length = righti + 1; this.ylist.length = righti + 1; } this.max_prob = -1; }; CentrimoLine.prototype.max = function() { "use strict"; var y_max, i; if (this.max_prob != -1) { return this.max_prob; } y_max = 0; for (i = 0; i < this.xlist.length; i++) { if (this.ylist[i] > y_max) { y_max = this.ylist[i]; } } this.max_prop = y_max; return this.max_prop; }; /* * CentrimoScale * * Calculates the increments on the y axis */ var CentrimoScale = function(max_prob) { "use strict"; var decimals, inc, rounder, max, inc_plus; if (max_prob === 0) { this.max = 0.01; this.inc = 0.002; this.digits = 3; return; } // find the minimum number of decimals needed to display the largest // digit of the maximum probability decimals = Math.ceil(-(Math.log(max_prob) / Math.log(10))); // calculate an increment which is (at minimum) 10 times smaller the the max inc = Math.pow(10, -(decimals+1)); // round-up the maximum probabilty to its largest digit rounder = Math.pow(10, decimals); max = Math.ceil(max_prob * rounder) / rounder; // adjust the increment so it's between 5 and 12 times the maximum // probability if (inc * 5 < max && inc * 12 > max) { inc *= 1; } else if (inc * 10 < max && inc * 24 > max) { inc *= 2; } else if (inc * 25 < max && inc * 60 > max) { inc *= 5; } else if (inc * 50 < max && inc * 120 > max) { inc *= 10; } max += inc; inc_plus = (1.125 * inc); while (max - inc_plus > max_prob) { max -= inc; } max = Math.min(max, 1.0); this.max = max; this.inc = inc; this.digits = decimals+1; }; var CentrimoLegendMetrics = function(lw, lh, id_w, pv_w, sq_w) { "use strict"; this.width = lw; this.height = lh; this.id_width = id_w; this.pv_width = pv_w; this.sq_width = sq_w; }; var CentrimoGraphMetrics = function(legend_metrics, top_edge, bottom_edge, left_mark, left_val, right_mark, right_val) { if (typeof legend_metrics !== "object" || legend_metrics === null) { this.legend_width = 10; this.legend_height = 10; } else { this.legend_width = legend_metrics.width; this.legend_height = legend_metrics.height; } this.top_edge = top_edge; this.bottom_edge = bottom_edge; this.left_mark = left_mark; this.left_val = left_val; this.right_mark = right_mark; this.right_val = right_val; }; /* * CentrimoGraph * Takes a results set and a window weight array and produces a graph. * The weights in the window_weights should be non-negative and sum to 1. */ var CentrimoGraph = function(rset, window_weights, fine_text, start, end, mirror) { "use strict"; var trim_left, trim_right, i, j, k, result, x, y, xpos, ypos, positions; var y_neg, ypos_neg, line_thickness; line_thickness = (window_weights.length < 10 ? 1 : 3); if (typeof fine_text !== "string") { fine_text = ""; } if (typeof mirror !== "boolean") mirror = false; this.mirror = mirror; if (mirror) { if (typeof start === "number") { start = Math.max(0, start); } else { start = 0; } } this.fine_text = fine_text; this.lines = []; for (i = 0; i < rset.count(); i++) { result = rset.get(i); x = []; y = []; if (result.has_neg) { y_neg = []; } xpos = (result.motif_length - rset.seq_len() + (window_weights.length - 1)) / 2; if (typeof trim_left === "undefined") { trim_left = xpos; } else if (trim_left < xpos) { trim_left = xpos; } positions = result.site_counts.length - window_weights.length + 1; for (j = 0; j < positions; j++, xpos += 1) { ypos = 0; // avoid division by zero when no sites are found if (result.total_sites > 0) { for (k = 0; k < window_weights.length; k++) { ypos += window_weights[k] * result.get_site_count(j + k, mirror, 0); } ypos /= result.total_sites; } x.push(xpos); y.push(ypos); // handle the negative dataset if (result.has_neg) { ypos_neg = 0; if (result.neg_total_sites > 0) { for (k = 0; k < window_weights.length; k++) { ypos_neg += window_weights[k] * result.get_site_count(j + k, mirror, 1); } ypos_neg /= result.neg_total_sites; } y_neg.push(ypos_neg); } } // subtract 1 from xpos because for loop will increment it one more than needed. xpos -= 1; this.lines.push(new CentrimoLine(result.name, result.sig, result.colour, [], line_thickness, true, x, y)); if (result.has_neg) { this.lines.push(new CentrimoLine(result.name, result.sig, result.colour, [6,4], 2, false, x.slice(0), y_neg)); } if (positions > 0) { if (typeof trim_right === "undefined") { trim_right = xpos; } else if (trim_right > xpos) { trim_right = xpos; } } } if (typeof start !== "undefined" && start != null) { if (start > trim_left) { trim_left = start; } this.start = start; } else { this.start = -Math.ceil(rset.seq_len() / 2); } if (typeof end !== "undefined" && end != null) { if (end < trim_right) { trim_right = end; } this.end = end; } else { this.end = Math.floor(rset.seq_len() / 2); } this.max_prob = 0; for (i = 0; i < this.lines.length; i++) { this.lines[i].trim(trim_left, trim_right); this.max_prob = Math.max(this.max_prob, this.lines[i].max()); } this.scale = new CentrimoScale(this.max_prob); }; /* * draw_graph * * Draws a motif probability graph */ CentrimoGraph.prototype.draw_graph = function (ctx, w, h, draw_legend, legend_x, legend_y) { "use strict"; var gap, l_margin, t_margin, b_margin, r_margin, legend_metrics, legend_width, legend_height; gap = 10; l_margin = gap + 30 + 10 * (2 + this.scale.digits); t_margin = 20; b_margin = 60; r_margin = 30; legend_metrics = this.measure_legend(ctx); // setting global legend_width = legend_metrics.width; legend_height = legend_metrics.height; // constrain legend to within graph area legend_x = Math.round(legend_x); legend_y = Math.round(legend_y); if (legend_x < (l_margin + gap)) { legend_x = l_margin + gap; } else if ((legend_x + legend_metrics.width) > (w - r_margin - gap)) { legend_x = w - r_margin - legend_metrics.width - gap; } if (legend_y < (t_margin + gap)) { legend_y = t_margin + gap; } else if ((legend_y + legend_metrics.height) > (h - b_margin - gap)) { legend_y = h - b_margin - legend_metrics.height - gap; } // draw graph ctx.save(); // draw border ctx.beginPath(); ctx.moveTo(l_margin - 0.5, t_margin +0.5); ctx.lineTo(l_margin - 0.5, h - (b_margin - 0.5)); ctx.lineTo(w - r_margin - 0.5, h - (b_margin - 0.5)); ctx.lineTo(w - r_margin - 0.5, t_margin +0.5); ctx.closePath(); ctx.stroke(); // draw fineprint ctx.save(); ctx.font = "9px Helvetica"; ctx.textAlign = "right"; ctx.textBaseline = "bottom"; ctx.fillText(this.fine_text, w - 1, h - 2); ctx.restore(); // draw y axis ctx.save(); ctx.translate(l_margin, t_margin); this.draw_y_axis(ctx, 0, h - (t_margin + b_margin)); ctx.restore(); // draw y labels ctx.save(); ctx.translate(gap, t_margin); this.draw_y_axis_label(ctx, l_margin, h - (t_margin + b_margin)); ctx.restore(); // draw x axis ctx.save(); ctx.translate(l_margin, h - b_margin); this.draw_x_axis(ctx, w - (l_margin + r_margin), b_margin); ctx.restore(); // draw top axis ctx.save(); ctx.translate(l_margin, t_margin); this.draw_top_axis(ctx, w - (l_margin + r_margin), 0); ctx.restore(); // draw x axis labels ctx.save(); ctx.translate(l_margin, h - b_margin); this.draw_x_axis_label(ctx, w - (l_margin + r_margin), b_margin - gap); ctx.restore(); // draw lines ctx.save(); ctx.translate(l_margin, t_margin); this.draw_lines(ctx, w - (l_margin + r_margin), h - (t_margin + b_margin), 8); ctx.restore(); // draw legend if (draw_legend) { ctx.save(); ctx.translate(legend_x, legend_y); this.draw_legend(ctx, legend_metrics); ctx.restore(); } ctx.restore(); return new CentrimoGraphMetrics(legend_metrics, t_margin, h - b_margin, l_margin, this.start, w - r_margin, this.end); }; /* * draw_x_axis * */ CentrimoGraph.prototype.draw_x_axis = function(ctx, w, h) { "use strict"; var scale_x, length, tic_inc, tic_min, tic_max, i, x; // pixels per unit scale_x = w / (this.end - this.start); // calcuate a good tic increment length = this.end - this.start; if (length > 50) { // multiple of 10 tic_inc = Math.max(1, Math.round(length / 100)) * 10; } else if (length > 25) { tic_inc = 5; } else if (length > 10) { tic_inc = 2; } else { tic_inc = 1; } // work out the min and max values within the start and end tic_min = Math.round(this.start / tic_inc) * tic_inc; if (tic_min < this.start) { tic_min += tic_inc; } tic_max = Math.round(this.end / tic_inc) * tic_inc; if (tic_max > this.end) { tic_max -= tic_inc; } // draw the tics ctx.save(); ctx.font = "14pt Helvetica"; ctx.textBaseline = "top"; ctx.textAlign = "center"; for (i = tic_min; i <= tic_max; i+= tic_inc) { x = Math.round((i - this.start) * scale_x) + 0.5; ctx.fillText(""+i, x, 5); if (i == this.start || i == this.end) continue; ctx.beginPath(); ctx.moveTo(x, -5); ctx.lineTo(x, 3); ctx.stroke(); } ctx.restore(); }; /* * draw_top_axis * */ CentrimoGraph.prototype.draw_top_axis = function(ctx, w, h) { "use strict"; var scale_x, length, tic_inc, tic_min, tic_max, i, x; // pixels per unit scale_x = w / (this.end - this.start); // calcuate a good tic increment length = this.end - this.start; if (length > 50) { // multiple of 10 tic_inc = Math.max(1, Math.round(length / 100)) * 10; } else if (length > 25) { tic_inc = 5; } else { tic_inc = 1; } // work out the min and max values within the start and end tic_min = Math.round(this.start / tic_inc) * tic_inc; if (tic_min < this.start) { tic_min += tic_inc; } tic_max = Math.round(this.end / tic_inc) * tic_inc; if (tic_max > this.end) { tic_max -= tic_inc; } // draw the tics ctx.save(); ctx.font = "14pt Helvetica"; ctx.textBaseline = "top"; ctx.textAlign = "center"; for (i = tic_min; i <= tic_max; i+= tic_inc) { if (i == this.start || i == this.end) continue; x = Math.round((i - this.start) * scale_x) + 0.5; ctx.beginPath(); ctx.moveTo(x, 0); ctx.lineTo(x, 8); ctx.stroke(); } ctx.restore(); }; /* * draw_x_axis_label */ CentrimoGraph.prototype.draw_x_axis_label = function(ctx, w, h) { "use strict"; ctx.save(); ctx.font = "14pt Helvetica"; ctx.textAlign = "center"; ctx.textBaseline = "bottom"; ctx.fillText((this.mirror ? "Distance of Best Site from Sequence Center" : "Position of Best Site in Sequence"), w/2, h); ctx.restore(); }; /* * draw_y_axis * * TODO some work needs to be done to allow moving the zero */ CentrimoGraph.prototype.draw_y_axis = function(ctx, w, h) { "use strict"; var y_scale, p, y; ctx.save(); ctx.font = "14pt Helvetica"; ctx.textBaseline = "middle"; ctx.textAlign = "right"; y_scale = h / this.scale.max; for (p = 0; p < this.scale.max; p += this.scale.inc) { y = Math.round(h - p * y_scale) + 0.5; this.draw_y_tic(ctx, this.scale.digits, y, p); } this.draw_y_tic(ctx, this.scale.digits, 0.5, this.scale.max); ctx.restore(); }; /* * draw_y_tic */ CentrimoGraph.prototype.draw_y_tic = function(ctx, digits, y, p) { "use strict"; ctx.beginPath(); ctx.moveTo(5, y); ctx.lineTo(-3, y); ctx.stroke(); ctx.fillText(p.toFixed(digits), -5, y); }; /* * draw_y_axis_label */ CentrimoGraph.prototype.draw_y_axis_label = function(ctx, w, h) { "use strict"; ctx.save(); ctx.translate(0, h/2); ctx.rotate(-Math.PI / 2); ctx.font = "14pt Helvetica"; ctx.textBaseline = "top"; ctx.textAlign = "center"; ctx.fillText("Probability", 0, 0); ctx.restore(); }; /* * draw_lines */ CentrimoGraph.prototype.draw_lines = function(ctx, w, h, tic_size) { "use strict"; var scale_y, scale_x, i, line, x_points, y_points, j, x, y, dasher; if (typeof tic_size === "undefined") { tic_size = 0; } scale_y = h / this.scale.max; scale_x = w / (this.end - this.start); // draw the central line if (0 > this.start && 0 < this.end) { ctx.save(); ctx.translate((-this.start) * scale_x, 0); ctx.strokeStyle = '#DDD'; ctx.beginPath(); ctx.moveTo(0.5, tic_size); ctx.lineTo(0.5, h - tic_size); ctx.stroke(); ctx.restore(); } // draw the lines ctx.save(); ctx.lineJoin = "bevel"; ctx.miterLimit = 0; for (i = 0; i < this.lines.length; i++) { line = this.lines[i]; ctx.lineWidth = line.thickness; x_points = line.xlist; y_points = line.ylist; if (x_points.length > 1) { ctx.strokeStyle = line.colour; ctx.beginPath(); for (j = 0; j < x_points.length; j++) { if (isNaN(x_points[j])) { throw new Error("X NaN!"); } if (isNaN(y_points[j])) { throw new Error("Y NaN!"); } x = (x_points[j] - this.start) * scale_x; y = h - y_points[j] * scale_y; if (j === 0) { dasher = new Dasher(ctx, x, y, line.dash); } else { dasher.dashTo(x, y); } } ctx.stroke(); } else if (x_points.length == 1) { if (isNaN(x_points[0])) { throw new Error("X NaN!"); } if (isNaN(y_points[0])) { throw new Error("Y NaN!"); } x = (x_points[0] - this.start) * scale_x; y = h - y_points[0] * scale_y; ctx.fillStyle = line.colour; ctx.beginPath(); ctx.arc(x, y, 2, 0, 2*Math.PI, false); ctx.fill(); } } ctx.restore(); }; /* * measure_legend */ CentrimoGraph.prototype.measure_legend = function(ctx) { "use strict"; var lw, lh, sq_w, id_w, pv_w, lines, i, line, len; // initilise the line height to the size of the padding lh = 2 * LEGEND_PAD; // calculate the column widths sq_w = LEGEND_LINE - 2; id_w = 0; pv_w = 0; ctx.save(); ctx.font = "" + LEGEND_LINE + "px " + LEGEND_FONT; for (i = 0; i < this.lines.length; i++) { line = this.lines[i]; if (!line.show_on_legend) { continue; } lh += LEGEND_LINE * 1.2; len = ctx.measureText(line.name).width; if (id_w < len) { id_w = len; } len = ctx.measureText(line.sig).width; if (pv_w < len) { pv_w = len; } } lh = Math.round(lh); ctx.restore(); // legend width is a function of the column widths lw = id_w + pv_w + sq_w + 4 * LEGEND_PAD; return new CentrimoLegendMetrics(lw, lh, id_w, pv_w, sq_w); }; /* * draw_legend */ CentrimoGraph.prototype.draw_legend = function(ctx, metrics) { "use strict"; var ln_h, pad, w, h, id_w, pv_w, sq_w, id_x, pv_x, sq_x, i, line; if (this.lines.length === 0) { return; } ln_h = LEGEND_LINE; pad = LEGEND_PAD; w = metrics.width; h = metrics.height; id_w = metrics.id_width; pv_w = metrics.pv_width; sq_w = metrics.sq_width; id_x = 0; pv_x = id_x + id_w + pad; sq_x = pv_x + pv_w + pad; ctx.save(); ctx.font = "" + ln_h + "px " + LEGEND_FONT; ctx.textAlign = "left"; ctx.textBaseline = "alphabetic"; // draw it ctx.save(); ctx.fillStyle = 'white'; ctx.fillRect(0.5, 0.5, w-1, h-1); ctx.strokeStyle = 'black'; ctx.strokeRect(0.5, 0.5, w-1, h-1); ctx.restore(); ctx.translate(pad, pad); ctx.fillStyle = "black"; for (i = 0; i < this.lines.length; i++) { line = this.lines[i]; if (!line.show_on_legend) { continue; } ctx.translate(0, ln_h); ctx.save(); ctx.fillStyle = line.colour; ctx.fillRect(sq_x, -sq_w + 0.1 * ln_h, sq_w, sq_w); ctx.restore(); ctx.fillText(line.name, id_x, 0); ctx.fillText(line.sig, pv_x, 0); ctx.translate(0, 0.2 * ln_h); } ctx.restore(); }; /* * triangular_weights * Returns an array of length n containing normalized weights. * */ function triangular_weights(n) { "use strict"; var weights, half, half_i, sum, i, unscaled_weight; weights = []; half = n/2; half_i = Math.floor(half); sum = 0; for (i = 0; i < half_i; i++) { unscaled_weight = (i + 0.5) / half; weights[i] = unscaled_weight; weights[n - i -1] = unscaled_weight; sum += 2 * unscaled_weight; } if (n % 2 == 1) { weights[half_i] = 1; sum += 1; } // normalize for (i = 0; i < n; i++) { weights[i] /= sum; } return weights; } /* * uniform_weights * Returns an array of length n containing normalized weights. * */ function uniform_weights(n) { "use strict"; var weights, weight, i; weights = []; weight = 1.0 / n; for (i = 0; i < n; i++) { weights[i] = weight; } return weights; } </script> <script type="text/javascript"> var palate = ["white", "cyan", "blue", "#FF00FF", "#00FF00", "red", "orange", "#008000", "#8A2BE2", "black"]; var text_palate = ["black", "black", "white", "white", "black", "white", "black", "white", "white", "white"]; var INT_MAX = 9007199254740992; var s_motifs = []; var s_swatches = []; var s_logos = [] var s_count = 0; var swap = null; var alphabet = new Alphabet(data.alphabet, data.background); var logo_timer = null; // timer to draw motif when the mouse pauses on a row var logo_motif = null; // motif to draw when timer expires var logo_row = null; // the row (or tbody) that the mouse is over var legend_x = 1000; var legend_y = 1000; var union_seq_ids = []; var intersect_seq_ids = []; var graph_metrics = new CentrimoGraphMetrics(null, 0, 0, 0, 0, 0, 0); var graph_click = {"start": 0, "stop": 0}; var zooms = []; var sort_table = { "motif": [ {"name": "<i>E</i>-value", "fn": sort_motif_evalue, "priority": 1, "pair": "evalue"}, {"name": "Fisher <i>E</i>-value", "fn": sort_motif_fisherpv, "priority": 2, "show": data['options']['neg_sequences'], "pair": "fisherpv"}, {"name": "Region Position", "fn": sort_motif_position, "pair": "position"}, {"name": "Region Distance", "fn": sort_motif_center, "pair": "center"}, {"name": "Region Width", "fn": sort_motif_spread, "pair": "spread"}, {"name": "Region Matches", "fn": sort_motif_sites, "pair": "sites"}, {"name": "<i>p</i>-value (Neg Data)", "fn": sort_motif_neg_pvalue, "show": data['options']['neg_sequences'], "pair": "neg_pvalue"}, {"name": "Region Matches in (Neg Data)", "fn": sort_motif_neg_sites, "show": data['options']['neg_sequences'], "pair": "neg_sites"}, {"name": "Matthew's Correlation Coefficient", "fn": sort_motif_mcc, "show": data['options']['mcc'], "pair": "mcc"}, {"name": "Total Matches", "fn": sort_motif_total_sites, "pair": "evalue"}, {"name": "Max Probability", "fn": sort_motif_probability, "pair": "evalue"}, {"name": "ID", "fn": sort_motif_id, "pair": "evalue"}, {"name": "Name", "fn": sort_motif_alt, "pair": "evalue"}, ], "region": [ {"id": "evalue", "name": "<i>E</i>-value", "fn": sort_peak_evalue, "priority": 1}, {"id": "fisherpv", "name": "Fisher <i>E</i>-value", "fn": sort_peak_fisherpv, "priority": 2, "show": data['options']['neg_sequences']}, {"id": "position", "name": "Region Position", "fn": sort_peak_position}, {"id": "center", "name": "Region Distance", "fn": sort_peak_center}, {"id": "spread", "name": "Region Width", "fn": sort_peak_spread}, {"id": "sites", "name": "Region Matches", "fn": sort_peak_sites}, {"id": "neg_pvalue", "name": "<i>p</i>-value (Neg Data)", "fn": sort_peak_neg_pvalue, "show": data['options']['neg_sequences']}, {"id": "neg_sites", "name": "Region Matches in (Neg Data)", "fn": sort_peak_neg_sites, "show": data['options']['neg_sequences']}, {"id": "mcc", "name": "Matthew's Correlation Coefficient", "fn": sort_peak_mcc, "show": data['options']['mcc']} ], }; pre_load_setup(); /* * name_from_source * * Makes a file name more human friendly to read. */ function name_from_source(source) { "use strict"; var file, noext; if (source == "-") { return "-" } //assume source is a file name file = source.replace(/^.*\/([^\/]+)$/,"$1"); noext = file.replace(/\.[^\.]+$/, ""); return noext.replace(/_/g, " "); } /* * pre_load_setup * * Sets up initial variables which may be * required for the HTML document creation. */ function pre_load_setup() { "use strict"; var i, motifs, params, showlist, show, parts, db_i, id, j, motif; var seq_db, db, dbs, sites, max_site, max_site_pos; for (i = 0; i < palate.length -1; i++) { s_motifs[i] = null; s_swatches[i] = null; s_logos[i] = null; } s_count = 0; motifs = data["motifs"]; if (data["options"]["neg_sequences"]) { motifs.sort(sort_motif_fisherpv); } else { motifs.sort(sort_motif_evalue); } // put a copy of the best evalue in the motif for (i = 0; i < motifs.length; i++) { motif = motifs[i]; motif["best_log_adj_pvalue"] = motif["peaks"][0]["log_adj_pvalue"]; // calculate the best probability max_site = 0; max_site_pos = 0; sites = motif["sites"]; for (j = 0; j < sites.length; j++) { if (sites[j] > max_site) { max_site = sites[j]; max_site_pos = j; } } motif["max_prob"] = max_site / motif["total_sites"]; motif["max_prob_loc"] = max_site_pos + (motif["len"] / 2) - (data["seqlen"] / 2); } params = parse_params(); if (params["show"]) { showlist = params["show"]; for (i = 0; i < showlist.length; i++) { show = showlist[i]; parts = show.match(/^db(\d+) (.+)$/); db_i = parseInt(parts[1]); id = parts[2]; // loop over the motifs looking for a match for (j = 0; j < motifs.length; j++) { motif = motifs[j]; if (motif["db"] == db_i && motif["id"] == id) { motif["colouri"] = s_count + 1; s_motifs[s_count] = motif; s_count++; break; } } // give up if we've used all the available colours if ((s_count + 1) >= palate.length) break; } } else { s_count = Math.min(3, motifs.length); for (i = 0; i < s_count; i++) { motif = motifs[i]; motif["colouri"] = i+1; s_motifs[i] = motif; } } calculate_seq_ids(); // get the name of the sequence db seq_db = data['sequence_db']; if (!seq_db['name']) seq_db['name'] = name_from_source(seq_db['source']); // get the names of the motif databases dbs = data['motif_dbs']; for (i = 0; i < dbs.length; i++) { db = dbs[i]; if (!db['name']) db['name'] = name_from_source(db['source']); } } function num_keys(e) { if (!e) var e = window.event; var code = (e.keyCode ? e.keyCode : e.which); var keychar = String.fromCharCode(code); var numre = /\d/; // only allow 0-9 and various control characters (Enter, backspace, delete) if (code != 8 && code != 9 && code != 13 && code != 46 && !numre.test(keychar)) { e.preventDefault(); } } /* * toggle_column * * Adds or removes a class from the table displaying the * centrally enriched motifs. This is primary used to set the visibility * of columns by using css rules. If the parameter 'show' is not passed * then the existence of the class will be toggled, otherwise it will be * included if show is false. */ function toggle_column(cls) { toggle_class($("motifs"), cls); } /* * toggle_filter * * Called when the user clicks a checkbox * to enable/disable a filter option. */ function toggle_filter(chkbox, filter_id) { var filter = $(filter_id); filter.disabled = !(chkbox.checked); if (!filter.disabled) { filter.focus(); if (filter.select) filter.select(); } } /* * enable_filter * * Called when the user clicks a filter label. * Enables the filter. */ function enable_filter(chkbox_id, filter_id) { var chkbox = $(chkbox_id); if (!chkbox.checked) { var filter = $(filter_id); $(chkbox_id).checked = true; filter.disabled = false; filter.focus(); if (filter.select) filter.select(); } } /* * update_filter * * If the key event is an enter key press then * update the filter on the CEM table */ function update_filter(e) { if (!e) var e = window.event; var code = (e.keyCode ? e.keyCode : e.which); if (code == 13) { e.preventDefault(); make_CEM_table(); } } /* * toggle_lock * */ /* * clear_selection * * Called when the user clicks the X in the * title of the centrally enriched motifs and * causes all the motifs to be deselected. */ function clear_selection() { for (var i = 1; i < palate.length; i++) { var motif = s_motifs[i-1]; var swatch = s_swatches[i-1]; s_motifs[i-1] = null; s_swatches[i-1] = null; s_logos[i-1] = null; if (motif) delete motif['colouri']; if (swatch) swatch.style.backgroundColor = palate[0]; } s_count = 0; if (!data['options']['noseq']) { //reset_sequences_IDs_list(); union_seq_ids = []; intersect_seq_ids = []; display_seq_ids(); } make_PM_table(); make_MP_graph(); } /* * toggle_graph_motif * * Activated when the user clicks on a swatch in the centrally enriched motifs * table. If the motif is already selected it deselects it otherwise it picks * an unused colour and selects it for graphing. */ function toggle_graph_motif(e) { "use strict"; var swatch; if (!e) var e = window.event; if (e.target) swatch = e.target; else if (e.srcElement) swatch = e.srcElement; // in case we land on a text node if (swatch.nodeType == 3) swatch = swatch.parentNode; // find the containing tbody var group = find_parent(swatch.parentNode, "peak_group"); // get the attached motif var motif = group['data_motif']; if (motif['colouri'] && motif['colouri'] != 0) { // deselect the motif var i = motif['colouri']; s_motifs[i-1] = null; s_swatches[i-1] = null; s_logos[i-1] = null; delete motif['colouri']; swatch.style.backgroundColor = palate[0]; s_count--; if (!data['options']['noseq']) calculate_seq_ids(); } else { // select an unused colour var i; for (i = 1; i < palate.length; i++) { if (!s_motifs[i-1]) break; } if (i == palate.length) { alert("All graph colours used. Please deselect motifs before adding more."); return; } s_motifs[i-1] = motif; s_swatches[i-1] = swatch; motif['colouri'] = i; swatch.style.backgroundColor = palate[i]; s_count++; if (!data['options']['noseq']) { if (s_count == 1) { union_seq_ids = motif["seqs"].slice(0); intersect_seq_ids = union_seq_ids.slice(0); } else { union_seq_ids = union_nums(union_seq_ids, motif["seqs"]); intersect_nums(intersect_seq_ids, motif["seqs"]); } } } if (!data['options']['noseq']) display_seq_ids(); make_PM_table(); make_MP_graph(); } /* * move_legend * * Called when the user clicks on the graph * to move the legend location. */ function move_legend(e) { var target; if (!e) var e = window.event; if (e.target) target = e.target; else if (e.srcElement) target = e.srcElement; var elemXY = coords(target); var posx = 0; var posy = 0; if (e.pageX || e.pageY) { posx = e.pageX; posy = e.pageY; } else if (e.clientX || e.clientY) { posx = e.clientX + document.body.scrollLeft + document.documentElement.scrollLeft; posy = e.clientY + document.body.scrollTop + document.documentElement.scrollTop; } var x = posx - elemXY[0]; var y = posy - elemXY[1]; legend_x = x - graph_metrics.legend_width/2; legend_y = y - graph_metrics.legend_height/2; if (parseInt($("legend").value) != 0) make_MP_graph(); } function highlight_peak(e) { var target, pop; pop = $("pop_peak"); if (pop.style.visibility === "visible") return; if (!e) var e = window.event; if (e.target) target = e.target; else if (e.srcElement) target = e.srcElement; while (!target['data_peak']) { if (target.nodeName == 'BODY') return; target = target.parentNode; } var peak = target['data_peak']; var l = graph_metrics.left_mark; var w = graph_metrics.right_mark - graph_metrics.left_mark; var d = graph_metrics.right_val - graph_metrics.left_val; var unit = w / d; var peak_width = peak["spread"]; var peak_left = peak["center"] - (peak["spread"] / 2); var peak_offscreen = 0; if (peak_left < graph_metrics.left_val) { peak_offscreen = graph_metrics.left_val - peak_left; peak_width = Math.max(0, peak_width - peak_offscreen); peak_left = graph_metrics.left_val; } else if ((peak_left + peak_width) > graph_metrics.right_val) { peak_offscreen = (peak_left + peak_width) - graph_metrics.right_val; peak_width = Math.max(0, peak_width - peak_offscreen); peak_left = Math.min(peak_left, graph_metrics.right_val); } if (peak_width > 0) { pop.style.width = (peak_width * unit) + "px"; pop.style.left = (l + ((peak_left - graph_metrics.left_val) * unit)) + "px"; pop.style.visibility = "visible"; } } function dehighlight_peak(e) { $("pop_peak").style.visibility = "hidden"; } /* * hover_logo * * Activated when the user hovers their cursor over a row in the centrally * enriched motifs table. After a fifth of a second delay, displays a box with * the logo and reverse complement logo. */ function hover_logo(e) { var popup; if (this === logo_row) return; logo_row = this; if (logo_timer) clearTimeout(logo_timer); logo_row.addEventListener('mousemove', move_logo, false); popup = $("logo_popup"); if (popup["data_motif"] != logo_row["data_motif"]) { logo_timer = setTimeout(popup_logo, 200); } else { popup.style.display = "block"; } } /* * dehover_logo * * Activated when the user moves their cursor off a row in the centrally * enriched motifs table. Hides the logo box (or stops it from being displayed). */ function dehover_logo(e) { var popup = $("logo_popup"); popup.style.display = "none"; if (logo_timer) clearTimeout(logo_timer); if (logo_row) logo_row.removeEventListener('mousemove', move_logo, false); logo_row = null; logo_timer = null; } /* * move_logo * * keeps the motif logo at a set distance from the cursor. */ function move_logo(e) { var popup = $("logo_popup"); popup.style.left = (e.pageX + 20) + "px"; popup.style.top = (e.pageY + 20) + "px"; } /* * popup_logo * * Activated when the user has had the cursor over a row in the centrally * enriched motifs table for longer than 1/5th of a second. It draws the * motif logos in a popup and displays the popup. */ function popup_logo() { if (logo_row == null) return; var motif = logo_row["data_motif"]; var pspm = new Pspm(motif['pwm'], motif['id'], 0, 0, motif['motif_nsites'], motif['motif_evalue']); var canvas = $("logo_popup_canvas"); var logo = logo_1(alphabet, "", pspm); draw_logo_on_canvas(logo, canvas, false, 0.5); if (!data["options"]["norc"]) { // draw RC motif var canvas_rc = $("logo_popup_canvas_rc"); var pspm_rc = pspm.copy().reverse_complement(alphabet); var logo_rc = logo_1(alphabet, "", pspm_rc); draw_logo_on_canvas(logo_rc, canvas_rc, false, 0.5); } var popup = $("logo_popup"); popup.style.display = "block"; popup['data_motif'] = motif; logo_timer = null; } /* * swap_colour * * Activated when the user clicks a swatch in the plotted motifs table. * If a swatch has already been selected then swap colours with this one, * otherwise record which swatch has been selected. */ function swap_colour(e) { var swatch; if (!e) var e = window.event; if (e.target) swatch = e.target; else if (e.srcElement) swatch = e.srcElement; var row = swatch; while (!row['motif']) row = row.parentNode; var motif = row['motif']; if (swap == null) { swatch.appendChild(document.createTextNode("\u21c5")); swap = motif; } else if (swap == motif) { while (swatch.firstChild) swatch.removeChild(swatch.firstChild); swap = null; } else { var swapi = swap['colouri']; var motifi = motif['colouri']; motif['colouri'] = swapi; swap['colouri'] = motifi; // swap swatches var temp = s_swatches[swapi-1]; s_swatches[swapi-1] = s_swatches[motifi-1]; s_swatches[motifi-1] = temp; // swap motifs temp = s_motifs[swapi-1]; s_motifs[swapi-1] = s_motifs[motifi-1]; s_motifs[motifi-1] = temp; // swap logos temp = s_logos[swapi-1]; s_logos[swapi-1] = s_logos[motifi-1]; s_logos[motifi-1] = temp; // update swatch colours s_swatches[swapi-1].style.backgroundColor = palate[swapi]; s_swatches[motifi-1].style.backgroundColor = palate[motifi]; swap = null; make_PM_table(); make_MP_graph(); } } /* * set_colour * * Activated when the user clicks a swatch in the unused colours section. * If a swatch has already been selected then set its colour to this one, * otherwise warn the user that they must select a motif swatch first. */ function set_colour(e) { var swatch; if (!e) var e = window.event; if (e.target) swatch = e.target; else if (e.srcElement) swatch = e.srcElement; var colouri = swatch['colouri']; if (swap) { var swapi = swap['colouri']; swap['colouri'] = colouri; s_swatches[colouri-1] = s_swatches[swapi-1]; s_motifs[colouri-1] = s_motifs[swapi-1]; s_logos[colouri-1] = s_logos[swapi-1]; s_swatches[swapi-1] = null; s_motifs[swapi-1] = null; s_logos[swapi-1] = null; s_swatches[colouri-1].style.backgroundColor = palate[colouri]; swap = null; make_PM_table(); make_MP_graph(); } else { alert("You must select a motif to set to this colour first."); } } /* * page_loaded * * Called when the page has loaded for the first time. */ function page_loaded() { first_load_setup(); post_load_setup(); } /* * page_loaded * * Called when a cached page is reshown. */ function page_shown(e) { if (e.persisted) post_load_setup(); } /* * union_nums * * Returns a union of two sorted lists of numbers. */ function union_nums(list1, list2) { "use strict"; var i, j, list_out; i = j = 0; list_out = []; while (i < list1.length && j < list2.length) { if (list1[i] < list2[j]) { list_out.push(list1[i]); i++; } else if (list1[i] === list2[j]) { list_out.push(list1[i]); i++; j++; } else { // list1[i] > list2[j] list_out.push(list2[j]); j++; } } if (i < list1.length) { for (; i < list1.length; i++) { list_out.push(list1[i]); } } else { for (; j < list2.length; j++) { list_out.push(list2[j]); } } return list_out; } /* * intersect_nums * * Removes numbers from the target_list which do not also appear in the * incoming_list. Both lists must be sorted. */ function intersect_nums(target_list, incoming_list) { "use strict"; var i, j, shift; shift = i = j = 0; while (i < target_list.length && j < incoming_list.length) { if (target_list[i] > incoming_list[j]) { j++; } else if (target_list[i] < incoming_list[j]) { i++; shift++; } else { if (shift > 0) target_list[i - shift] = target_list[i]; i++; j++; } } target_list.length = i - shift; } function calculate_seq_ids() { var i, motif; // calculate sequence id sets if (!data['options']['noseq']) { if (s_count == 0) { union_seq_ids = []; intersect_seq_ids = []; } else { for (i = 0; i < s_motifs.length; i++) { motif = s_motifs[i]; if (motif) { union_seq_ids = motif["seqs"].slice(0); intersect_seq_ids = union_seq_ids.slice(0); break; } } for (; i < s_motifs.length; i++) { motif = s_motifs[i]; if (motif === null) continue; union_seq_ids = union_nums(union_seq_ids, motif["seqs"]); intersect_nums(intersect_seq_ids, motif["seqs"]); } } } } function display_seq_ids() { var u_n_cont, u_p_cont, i_n_cont, i_p_cont, i_s_cont; var union_count, intersect_count, total_count; var union_percent, intersect_percent, intersect_seqs, i; var sequences; sequences = data["sequences"]; union_count = union_seq_ids.length; intersect_count = intersect_seq_ids.length; total_count = sequences.length; union_percent = Math.round((union_count / total_count) * 100); intersect_percent = Math.round((intersect_count / total_count) * 100); u_n_cont = $('matching_union_number'); u_p_cont = $('matching_union_percentage'); i_n_cont = $('matching_intersection_number'); i_p_cont = $('matching_intersection_percentage'); i_s_cont = $('matching_intersection_sequences'); u_n_cont.innerHTML = ""; u_n_cont.appendChild(document.createTextNode(union_count)); u_p_cont.innerHTML = ""; u_p_cont.appendChild(document.createTextNode(union_percent)); i_n_cont.innerHTML = ""; i_n_cont.appendChild(document.createTextNode(intersect_count)); i_p_cont.innerHTML = ""; i_p_cont.appendChild(document.createTextNode(intersect_percent)); intersect_seqs = []; for (i = 0; i < intersect_count; i++) { intersect_seqs.push(sequences[intersect_seq_ids[i]]); } i_s_cont.value = intersect_seqs.join("\n"); } /* * find_highest_peaks * * Locate highest peaks for every motifs * Compute every x position and keep the highest one */ /* function find_highest_peaks(smoothing_type) { var sequence_length=data['seqlen']; var windo=parseInt($("windo").value); var half_window = windo / 2; var weights = []; var tbl = $("motifs"); var tbody = tbl.tBodies[0]; if (smoothing_type==1) { // Only computed for weighted moving average var total_weight = 0; for (var i = 0; i < windo; i++) { var pos = i + 0.5; var weight = (pos < half_window ? pos / half_window : (windo - pos) / half_window); weights.push(weight); total_weight += weight; } } for (var i = 0; i < data['motifs'].length; i++) { // For each motif var motif = data['motifs'][i]; var sites = motif['sites']; var max_prob=-1; var index_max_prob=-1; var xpos = (motif.len / 2) - (sequence_length / 2) + half_window; var end = sites.length - windo; for (var j = 0; j < end; j++, xpos += 1) { var sum = 0; for (var k = 0; k < windo; k++) { sum += (smoothing_type==1) ? sites[j + k] * weights[k] : sites[j + k]; } var avg = (smoothing_type==1) ? sum / total_weight : sum / windo; var prob = avg / motif['total_sites']; if (prob>max_prob) { // If Y axis value is higher than saved one max_prob=prob; // Save it index_max_prob=Math.floor(xpos); // Save the location } } motif["highest_peak"]=index_max_prob; // Save highest peak location for this motif } }*/ /* * first_load_setup * * Setup state that is dependent on everything having been loaded already. * On browsers which cache state this is only run once. */ function first_load_setup() { if (data['options']['noseq']) { // no sequence ids to display $('seq_area').style.display='none'; } if (!data['options']['local']) { // bins are centered, there is only one peak $('show_blocation').checked = false; $('CB_show_blocation').style.display='none'; $('box_peak_sort').style.display = 'none'; toggle_class($('motifs'), 'hide_OEbins', true); } if (!data['options']['neg_sequences']) { $('show_fisherpv').checked = false; $('show_negtsites').checked = false; $('show_negbsites').checked = false; $('show_negative_binomial').checked = false; // no negative sites, so hide negative bin sites and total $('CB_show_plot_negative').style.display= 'none'; $('plot_negative').value = 0; $('CB_show_negbsites').style.display= 'none'; $('CB_show_negtsites').style.display= 'none'; $('CB_show_negative_binomial').style.display='none'; $('CB_filter_on_negbintest').style.display='none'; $('cb_show_fisherpv').style.display = 'none'; $('cb_filter_on_fisherpv').style.display = 'none'; } if (data['options']['disc']) { // negative data set was not used with a discriminative search $('cb_show_fisherpv').style.display = 'none'; } if (!data['options']['mcc']) { $('CB_show_MCC').style.display='none'; } if (!data['options']['optimize_score']) { // per motif score optimisation turned off, so hide column $('show_score').checked = false; } } /* * post_load_setup * * Setup state that is dependent on everything having been loaded already. */ function post_load_setup() { "use strict"; var tbl, i; if (data["options"]["norc"]) $("logo_popup_canvas_rc").style.display = "none"; $("filter_id").disabled = !($("filter_on_id").checked); $("filter_alt").disabled = !($("filter_on_alt").checked); $("filter_evalue").disabled = !($("filter_on_evalue").checked); $("filter_binwidth").disabled = !($("filter_on_binwidth").checked); $("filter_negbintest").disabled = !($("filter_on_negbintest").checked); tbl = $("motifs"); toggle_class(tbl, "hide_db", !$("show_db").checked); toggle_class(tbl, "hide_id", !$("show_id").checked); toggle_class(tbl, "hide_name", !$("show_name").checked); toggle_class(tbl, "hide_fisherpv", !$("show_fisherpv").checked); toggle_class(tbl, "hide_evalue", !$("show_evalue").checked); toggle_class(tbl, "hide_pvalue", !$("show_pvalue").checked); toggle_class(tbl, "hide_MCC", !$("show_MCC").checked); toggle_class(tbl, "hide_blocation", !$("show_blocation").checked); toggle_class(tbl, "hide_bwidth", !$("show_bwidth").checked); toggle_class(tbl, "hide_bsites", !$("show_bsites").checked); toggle_class(tbl, "hide_tsites", !$("show_tsites").checked); toggle_class(tbl, "hide_negbsites", !$("show_negbsites").checked); toggle_class(tbl, "hide_negtsites", !$("show_negtsites").checked); toggle_class(tbl, "hide_negative_binomial", !$("show_negative_binomial").checked); toggle_class(tbl, "hide_maxprob", !$("show_maxprob").checked); toggle_class(tbl, "hide_hpeak", !$("show_hpeak").checked); //max prob location toggle_class(tbl, "hide_nbinstested", !$("show_nbinstested").checked); toggle_class(tbl, "hide_score", !$("show_score").checked); make_PM_table(); make_CEM_table(); make_MP_graph(); add_MP_graph_listeners(); if (!data['options']['noseq']) display_seq_ids(); } /* * sort_motif_id * * Takes 2 motif objects and compares them based on id and database. */ function sort_motif_id(m1, m2) { var diff; diff = m1['id'].localeCompare(m2['id']); if (diff == 0) { diff = m1['db'] - m2['db']; } return diff; } /* * sort_motif_alt * * Takes 2 motif objects and compares them based on alternate id. */ function sort_motif_alt(m1, m2) { var diff; if (m1['alt'] && m2['alt']) { diff = m1['alt'].localeCompare(m2['alt']); if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } else { if (m1['alt']) { return -1; } else { return 1; } } } /* * sort_motif_fisherpv * * Takes 2 motif objects and compares them based on the Fisher pvalue */ function sort_motif_fisherpv(m1, m2) { var diff, p1, p2; p1 = m1['peaks'][0]; p2 = m2['peaks'][0]; diff = p1['fisher_log_adj_pvalue'] - p2['fisher_log_adj_pvalue']; if (diff != 0) return diff; diff = p2['pos_sites'] - p1['pos_sites']; if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } function sort_motif_neg_pvalue(m1, m2) { var diff, p1, p2; //return sort_motif_evalue(m1, m2); p1 = m1['peaks'][0]; p2 = m2['peaks'][0]; diff = p1['neg_log_adj_pvalue'] - p2['neg_log_adj_pvalue']; if (diff != 0) return diff; diff = p2['neg_sites'] - p1['neg_sites']; if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } function sort_motif_neg_sites(m1, m2) { var diff, p1, p2; p1 = m1['peaks'][0]; p2 = m2['peaks'][0]; diff = p1['neg_sites'] - p2['neg_sites']; if (diff != 0) return diff; diff = p1['neg_log_adj_pvalue'] - p2['neg_log_adj_pvalue']; if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } /* * sort_motif_evalue * * Takes 2 motif objects and compares them based on the log_adj_pvalue. */ function sort_motif_evalue(m1, m2) { var diff, p1, p2; p1 = m1['peaks'][0]; p2 = m2['peaks'][0]; diff = p1['log_adj_pvalue'] - p2['log_adj_pvalue']; if (diff != 0) return diff; diff = p1['spread'] - p2['spread']; if (diff != 0) return diff; return sort_motif_id(m1, m2); } /* * sort_motif_spread * * Takes 2 motif objects and compares them based on the bin_width. */ function sort_motif_spread(m1, m2) { var diff, p2, p2; p1 = m1['peaks'][0]; p2 = m2['peaks'][0]; diff = p1['spread'] - p2['spread']; if (diff != 0) return diff; diff = p1['log_adj_pvalue'] - p2['log_adj_pvalue']; if (diff != 0) return diff; return sort_motif_id(m1, m2); } /* * sort_motif_probability * * Takes 2 motif objects and compares them based on the maximum probability. */ function sort_motif_probability(m1, m2) { var diff; diff = m2['max_prob'] - m1['max_prob']; if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } /* * sort_motif_sites * * Takes 2 motif objects and compares them based on the bin sites. */ function sort_motif_sites(m1, m2) { var diff, p1, p2; p1 = m1['peaks'][0]; p2 = m2['peaks'][0]; diff = p2['sites'] - p1['sites']; if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } /* * sort_motif_center * * Takes 2 motif objects and compares them based on the abs(bin location). */ function sort_motif_center(m1, m2) { var diff, p1, p2; p1 = m1['peaks'][0]; p2 = m2['peaks'][0]; diff = Math.abs(p1['center']) - Math.abs(p2['center']); if (diff != 0) return diff; diff = p1['center'] - p2['center']; if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } /* * sort_motif_position * * Takes 2 motif objects and compares them based on the bin location. */ function sort_motif_position(m1, m2) { var diff, p1, p2; p1 = m1['peaks'][0]; p2 = m2['peaks'][0]; diff = p1['center'] - p2['center']; if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } /* * sort_motif_mcc * * Takes 2 motif objects and compares them based on the Matthews Correlation Coefficient. */ function sort_motif_mcc(m1, m2) { var diff, p1, p2; p1 = m1['peaks'][0]; p2 = m2['peaks'][0]; diff = p2['mcc'] - p1['mcc']; if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } /* * sort_motif_total_sites * * Takes 2 motif objects and compares them based on the total sites. */ function sort_motif_total_sites(m1, m2) { var diff; diff = m2['total_sites'] - m1['total_sites']; if (diff != 0) return diff; return sort_motif_evalue(m1, m2); } /* * get_sort_cmp * * Gets the sorting comparator by index. * */ function motif_sort_cmp(index) { "use strict"; if (index > 0 && index < sort_table["motif"].length) { return sort_table["motif"][index]["fn"]; } return sort_motif_evalue; } /* * sort_peak_fisherpv * * Takes 2 peak objects and compares them based on the Fisher pvalue */ function sort_peak_fisherpv(p1, p2) { var diff; if (p1['filtered'] != p2['filtered']) return (p1['filtered'] ? 1 : -1); diff = p1['fisher_log_adj_pvalue'] - p2['fisher_log_adj_pvalue']; if (diff != 0) return diff; diff = p2['pos_sites'] - p1['pos_sites']; if (diff != 0) return diff; return sort_peak_evalue(p1, p2); } function sort_peak_evalue(p1, p2) { var diff; if (p1['filtered'] != p2['filtered']) return (p1['filtered'] ? 1 : -1); diff = p1['log_adj_pvalue'] - p2['log_adj_pvalue']; if (diff != 0) return diff; diff = p1['spread'] - p2['spread']; if (diff != 0) return diff; return p1['center'] - p2['center']; } function sort_peak_mcc(p1, p2) { var diff; if (p1['filtered'] != p2['filtered']) return (p1['filtered'] ? 1 : -1); diff = p2['mcc'] - p1['mcc']; if (diff != 0) return diff; return sort_peak_evalue(p1, p2); } function sort_peak_center(p1, p2) { if (p1['filtered'] != p2['filtered']) return (p1['filtered'] ? 1 : -1); diff = Math.abs(p1['center']) - Math.abs(p2['center']); if (diff != 0) return diff; return p1['center'] - p2['center']; } function sort_peak_position(p1, p2) { if (p1['filtered'] != p2['filtered']) return (p1['filtered'] ? 1 : -1); return p1['center'] - p2['center']; } function sort_peak_spread(p1, p2) { var diff; if (p1['filtered'] != p2['filtered']) return (p1['filtered'] ? 1 : -1); diff = p1['spread'] - p2['spread']; if (diff != 0) return diff; diff = p1['log_adj_pvalue'] - p2['log_adj_pvalue']; if (diff != 0) return diff; return p1['center'] - p2['center']; } function sort_peak_sites(p1, p2) { var diff; if (p1['filtered'] != p2['filtered']) return (p1['filtered'] ? 1 : -1); diff = p2['sites'] - p1['sites']; if (diff != 0) return diff; return sort_peak_evalue(p1, p2); } function sort_peak_neg_pvalue(p1, p2) { var diff; if (p1['filtered'] != p2['filtered']) return (p1['filtered'] ? 1 : -1); diff = p1['neg_log_adj_pvalue'] - p2['neg_log_adj_pvalue']; if (diff != 0) return diff; diff = p2['neg_sites'] - p1['neg_sites']; if (diff != 0) return diff; return sort_peak_evalue(p1, p2); } function sort_peak_neg_sites(p1, p2) { var diff; if (p1['filtered'] != p2['filtered']) return (p1['filtered'] ? 1 : -1); diff = p1['neg_sites'] - p2['neg_sites']; if (diff != 0) return diff; diff = p1['neg_log_adj_pvalue'] - p2['neg_log_adj_pvalue']; if (diff != 0) return diff; return sort_peak_evalue(p1, p2); } function peak_sort_cmp(index) { "use strict"; if (index > 0 && index < sort_table["region"].length) { return sort_table["region"][index]["fn"]; } return sort_peak_evalue; } /* * log2str * * Converts a log value into scientific notation. */ function log2str(log_val, precision, max) { var log10_val, e, m; if (log_val < 0) { log10_val = log_val / Math.log(10); e = Math.floor(log10_val); m = Math.pow(10, log10_val - e); if (m + (0.5 * Math.pow(10, -precision)) >= 10) { m = 1; e += 1; } return "" + m.toFixed(precision) + "e" + e; } else if (typeof max !== "number" || Math.exp(log_val) < max) { return Math.exp(log_val).toFixed(precision); } else { return ">"+max; } } /* * str2log * * Converts a scientific notation number string to a log value. */ function str2log(str, default_value) { var sci_num_re, parts, m, e, log_num; if (typeof default_value === "undefined") { default_value = null; } sci_num_re = /^([+]?\d+(?:\.\d+)?)(?:[eE]([+-]\d+))?$/; parts = sci_num_re.exec(str); if (parts && parseFloat(parts[1]) != 0) { m = parseFloat(parts[1]); if (m === 0) return default_value; e = (parts.length == 3 && parts[2] != null ? parseInt(parts[2]) : 0); log_num = (((Math.log(m)/Math.log(10)) + e) * Math.log(10)); return log_num; } else { return default_value; } } /* * pvstr * * Gets the p-value of the motif in string form. */ function pvstr(peak) { return log2str(peak['log_adj_pvalue'], 1); } /* * evstr * * Gets the E-value of the motif in string form. */ function evstr(peak, type) { return log2str(peak[type] + Math.log(data['tested']), 1); } /* * make_swatch * * Make a swatch block. */ function make_swatch(colouri) { var swatch = document.createElement('div'); swatch.className = 'swatch'; swatch.style.backgroundColor = palate[colouri]; swatch.style.color = text_palate[colouri]; return swatch; } function make_CEM_main_row(tbody, motif) { "use strict"; var colouri, row, swatch, peak, expander; peak = motif['peaks'][0]; colouri = motif['colouri']; if (!colouri) colouri = 0; row = tbody.insertRow(tbody.rows.length); row['data_peak'] = peak; swatch = make_swatch(colouri); swatch.onclick = toggle_graph_motif; if (colouri != 0) { s_swatches[colouri -1] = swatch; } add_cell(row, swatch); add_text_cell(row, motif_dbs[motif['db']]['name'], 'col_db'); add_cell(row, make_link(motif['id'], motif['url']), 'col_id'); add_text_cell(row, motif['alt'], "col_name"); add_text_cell(row, evstr(peak, 'log_adj_pvalue'), 'col_evalue'); if (data['options']['neg_sequences']) { add_text_cell(row, evstr(peak, 'fisher_log_adj_pvalue'), "col_fisherpv"); } add_text_cell(row, pvstr(peak), 'col_pvalue'); if (data['options']['neg_sequences']) { add_text_cell(row, log2str(peak['neg_log_adj_pvalue'],1), "col_negative_binomial"); } else { add_text_cell(row, '', "col_negative_binomial"); } if (data['options']['mcc']) { add_text_cell(row, peak['mcc'].toFixed(3), "col_MCC"); } else { add_text_cell(row, '', "col_MCC"); } add_text_cell(row, peak['center'], "col_blocation"); add_text_cell(row, peak['spread'], 'col_bwidth'); add_text_cell(row, Math.round(peak['sites']), "col_bsites"); add_text_cell(row, motif['total_sites'], "col_tsites"); if (data['options']['neg_sequences']) { add_text_cell(row, Math.round(peak['neg_sites']), "col_negbsites"); add_text_cell(row, motif['neg_total_sites'], "col_negtsites"); } else { add_text_cell(row, '', "col_negbsites") add_text_cell(row, '', "col_negtsites"); } add_text_cell(row, motif["max_prob"].toFixed(4), "col_maxprob"); add_text_cell(row, motif["max_prob_loc"], "col_problocation"); add_text_cell(row, motif['n_tested'], "col_nbinstested"); add_text_cell(row, motif['score_threshold'].toFixed(2), "col_score"); if (motif['peaks'].length > 1) { expander = document.createElement('span'); expander.appendChild(document.createTextNode("\u21A7")); expander.className = "expander"; expander.addEventListener("click", toggle_peaks, false); add_cell(row, expander, "col_OEbins"); } else { add_text_cell(row, '-', "col_OEbins"); } row.addEventListener('mouseover', highlight_peak, false); row.addEventListener('mouseout', dehighlight_peak, false); } function make_CEM_sub_row(tbody, peak) { var row = tbody.insertRow(tbody.rows.length); row['data_peak'] = peak; row.className = "sub_peak"; add_text_cell(row,'\u2022', 'no_swatch'); add_text_cell(row, '', 'col_db'); add_text_cell(row, '', 'col_id'); add_text_cell(row, '', 'col_name'); add_text_cell(row, evstr(peak, 'log_adj_pvalue'), 'col_evalue'); if (data['options']['neg_sequences']) { add_text_cell(row, evstr(peak, 'fisher_log_adj_pvalue'), "col_fisherpv"); } add_text_cell(row, pvstr(peak), 'col_pvalue'); if (data['options']['neg_sequences']) { add_text_cell(row, log2str(peak['neg_log_adj_pvalue'],1), "col_negative_binomial"); } else { add_text_cell(row, '', "col_negative_binomial"); } if (data['options']['mcc']) { add_text_cell(row, peak['mcc'].toFixed(3), "col_MCC"); } else { add_text_cell(row, '', "col_MCC"); } add_text_cell(row, peak['center'], "col_blocation"); add_text_cell(row, peak['spread'], 'col_bwidth'); add_text_cell(row, Math.round(peak['sites']), "col_bsites"); add_text_cell(row, '', "col_tsites"); if (data['options']['neg_sequences']) { add_text_cell(row, Math.round(peak['neg_sites']), "col_negbsites"); } else { add_text_cell(row, '', "col_negbsites") } add_text_cell(row, '', "col_negtsites"); add_text_cell(row, '', "col_maxprob"); add_text_cell(row, '', "col_problocation"); add_text_cell(row, '', "col_nbinstested"); add_text_cell(row, '', "col_score"); add_text_cell(row, '', "col_OEbins"); row.addEventListener('mouseover', highlight_peak, false); row.addEventListener('mouseout', dehighlight_peak, false); } function make_CEM_skip_row(tbody, n_skipped) { var row, cell, desc; if (n_skipped === 0) return; row = tbody.insertRow(tbody.rows.length); row.className = "sub_peak"; if (n_skipped === 1) { desc = "1 peak hidden due to filters"; } else { desc = n_skipped + " peaks hidden due to filters"; } cell = row.insertCell(row.cells.length); cell.colSpan = 19; cell.style.textAlign = "center"; cell.style.fontWeight = "bold"; cell.appendChild(document.createTextNode(desc)); } /* * make_CEM_table * * Generate the table which lists centrally enriched motifs. */ function make_CEM_table() { var motif_sort, peak_sort; var filter, motifs, filtered, motif, peaks, motif_dbs; var tbl, tbody, row, cell, i, j, skipped; // get the filter and sort comparator motif_sort = motif_sort_cmp(parseInt($('motif_sort').value)); peak_sort = peak_sort_cmp(parseInt($('peak_sort').value)); filter = get_filter(); motifs = data['motifs']; // sort the motif peaks for (i = 0; i < motifs.length; i++) { motif = motifs[i]; peaks = motif['peaks']; for (j = 0; j < peaks.length; j++) { peaks[j]["filtered"] = filter_peak(filter, peaks[j]); } peaks.sort(peak_sort); } // filter the motifs filtered = []; for (i = 0; i < motifs.length; i++) { if (filter_motif(filter, motifs[i])) continue; if (motifs[i]["peaks"][0]["filtered"]) continue; filtered.push(motifs[i]); } // sort filtered.sort(motif_sort); // limit if (filter["on_count"]) { if (filtered.length > filter["count"]) filtered.length = filter["count"]; } // re-add any omitted s_motifs motifs outer_loop: for (i = 0; i < s_motifs.length; i++) { if (s_motifs[i] == null) continue; for (j =0; j < filtered.length; j++) { if (filtered[j] === s_motifs[i]) { continue outer_loop; } } filtered.push(s_motifs[i]); } // sort again filtered.sort(motif_sort); // clear the table tbl = $("motifs"); for (i = tbl.tBodies.length - 1; i >= 0; i--) { tbody = tbl.tBodies[i]; tbody.parentNode.removeChild(tbody); } motif_dbs = data['motif_dbs']; // add the new rows to the table for (i = 0; i < filtered.length; i++) { motif = filtered[i]; peaks = motif['peaks']; tbody = document.createElement('tbody'); tbody.className = "peak_group"; tbody["data_motif"] = motif; tbody.addEventListener('mouseover', hover_logo, false); tbody.addEventListener('mouseout', dehover_logo, false); make_CEM_main_row(tbody, motif); skipped = 0; for (j = 1; j < peaks.length; j++) { if (filter_peak(filter, peaks[j])) { skipped++; continue; } make_CEM_sub_row(tbody, peaks[j]); } make_CEM_skip_row(tbody, skipped); tbl.appendChild(tbody); } // note the count of filtered motifs if (filtered.length != motifs.length) { skipped = motifs.length - filtered.length; tbody = document.createElement('tbody'); row = tbody.insertRow(tbody.rows.length); if (skipped === 1) { desc = "1 motif hidden due to filters"; } else { desc = skipped + " motifs hidden due to filters"; } cell = row.insertCell(row.cells.length); cell.colSpan = 19; cell.style.textAlign = "center"; cell.style.fontWeight = "bold"; cell.appendChild(document.createTextNode(desc)); tbl.appendChild(tbody); } } function get_filter() { var filter, id_pat, alt_pat, alt_re, log_evalue_max, spread, count; var neg_log_pvalue_min; filter = {}; // get the db filter filter["on_db"] = $("filter_on_db").checked; filter["db"] = $("filter_db").value; // get the id filter filter["on_id"] = $("filter_on_id").checked; id_pat = $("filter_id").value; try { filter["id"] = new RegExp(id_pat, "i"); $("filter_id").className = ""; } catch (err) { $("filter_id").className = "error"; filter["on_id"] = false; } // get the name filter filter["on_alt"] = $("filter_on_alt").checked; alt_pat = $("filter_alt").value; try { filter["alt"] = new RegExp(alt_pat, "i"); $("filter_alt").className = ""; } catch (err) { filter["on_alt"] = false; $("filter_alt").className = "error"; } // get the evalue filter filter["on_pvalue"] = $("filter_on_evalue").checked; if ((log_evalue_max = str2log($("filter_evalue").value)) != null) { filter["log_pvalue"] = log_evalue_max - Math.log(data['tested']); $("filter_evalue").className = ""; } else { filter["on_pvalue"] = false; $("filter_evalue").className = "error"; } // get the Fisher pv filter filter["on_fisherpv"] = $("filter_on_fisherpv").checked; if ((log_fisherpv_max = str2log($("filter_fisherpv").value)) != null) { filter["log_fisherpv"] = log_fisherpv_max - Math.log(data['tested']); $("filter_fisherpv").className = ""; } else { filter["on_fisherpv"] = false; $("filter_fisherpv").className = "error"; } // get the spread filter filter["on_spread"] = $("filter_on_binwidth").checked; spread = parseInt($("filter_binwidth").value); if (isNaN(spread) || spread < 1) { filter["on_spread"] = false; $("filter_binwidth").className = "error"; } else { filter["spread"] = spread; $("filter_binwidth").className = ""; } // get the negative binomial test filter filter["on_neg"] = data['options']['neg_sequences'] && $("filter_on_negbintest").checked; if ((neg_log_pvalue_min = str2log($("filter_negbintest").value)) != null) { $("filter_negbintest").className = ""; filter["neg_log_pvalue"] = neg_log_pvalue_min - Math.log(data['tested']); } else { filter["on_neg"] = false; $("filter_negbintest").className = "error"; } // get the motif count limit filter["on_count"] = $("filter_on_top").checked; count = parseInt($("filter_top").value); if (isNaN(count) || count < 1) { filter["on_count"] = false; $("filter_top").className = "error"; } else { filter["count"] = count; $("filter_top").className = ""; } return filter; } function filter_motif(filter, motif) { if (filter["on_db"] && motif["db"] != filter["db"]) return true; if (filter["on_id"] && !filter["id"].test(motif["id"])) return true; if (filter["on_alt"] && !filter["alt"].test(motif["alt"])) return true; return false; } function filter_peak(filter, peak) { if (filter["on_fisherpv"] && peak["fisher_log_adj_pvalue"] > filter["log_fisherpv"]) return true; if (filter["on_pvalue"] && peak["log_adj_pvalue"] > filter["log_pvalue"]) return true; if (filter["on_spread"] && peak["spread"] > filter["spread"]) return true; if (filter["on_neg"] && peak["neg_log_adj_pvalue"] < filter["neg_log_pvalue"]) return true; return false; } function filter_CEM_table() { "use strict"; var tbl, tbody, tr, motif, peaks, i, j, filter; tbl = $("motifs"); filter = get_filter(); for (i = 0; i < tbl.tBodies.length; i++) { tbody = tbl.tBodies[i]; motif = tbody["data_motif"]; toggle_class(tbody, "filtered", filter_motif(filter, motif)); for (j = 0; j < tbody.rows.length; j++) { } } } /* * show_all_peaks * * Show or hide sub-peaks */ function show_all_peaks(param) { var tbl = $("motifs"); var tbody = tbl.tBodies[0]; var NValue=param.childNodes[0].nodeValue; // Catch the motif (based on argument value sent by clicking on arrow) var bin_number=0; for (var i=0; i<tbody.rows.length;i++) { // For each motif if (tbody.rows[i].className==param.className) { // For each sub-peaks bin_number++; if (must_be_display(param.className,bin_number)==false || NValue=="\u21A5") { // If it has to be hidden or arrow was up tbody.rows[i].style.display="none"; // Hide it } else { tbody.rows[i].style.display="table-row"; // Show it } } } param.childNodes[0].nodeValue= (NValue=="\u21A7") ? "\u21A5" : "\u21A7" ; // Change arrow orientation } function toggle_peaks(e) { var expander, group; if (!e) e = window.event; if (e.target) expander = e.target; else if (e.srcElement) expander = e.srcElement; group = find_parent(expander.parentNode, "peak_group"); toggle_class(group, "more"); } /* * must_be_display * * Check all sub-peaks and verify if they have to be displayed or not (based on filters) */ function must_be_display(ID, bin_number) { "use strict"; var motifs, i, motif, peak, log_pvalue_max, log_evalue_max, log_pvalue_min; motifs = data['motifs']; for (i = 0; i < motifs.length; i++) { motif = motifs[i]; if (motif['db'] + motif['id'] == ID) { // Catch the motif peak = motif['peaks'][bin_number]; // Catch the sub-peaks if ($("filter_on_evalue").checked) { if ((log_evalue_max = str2log($("filter_evalue").value)) != null) { log_pvalue_max = log_evalue_max - Math.log(data['tested']); } else { log_pvalue_max = 0; } if (log_pvalue_max < peak['log_adj_pvalue']) return false; } if ($("filter_on_fisherpv").checked) { if ((log_evalue_max = str2log($("filter_fisherpv").value)) != null) { log_pvalue_max = log_evalue_max - Math.log(data['tested']); } else { log_pvalue_max = 0; } if (log_pvalue_max < peak['fisher_log_adj_pv']) return false; } if ($("filter_on_negbintest").checked) { if ((log_pvalue_max = str2log($("filter_negbintest").value)) == null) { log_pvalue_min = Math.log(data['tested']); } if (log_pvalue_min > peak['neg_log_adj_pvalue']) return false; } if ($("filter_on_binwidth").checked && parseInt($("filter_binwidth").value) > peak['spread']) { return false; } } } return true; } /* * make_PM_table * * Generate the table which lists plotted motifs */ function make_PM_table() { swap = null; var graphed = []; var unused = []; for (var i = 1; i < palate.length; i++) { if (s_motifs[i-1]) graphed.push(s_motifs[i-1]); else unused.push(i); } graphed.sort(sort_motif_evalue); var tbl = $("graph_list"); var tbody = tbl.tBodies[0]; while (tbody.rows.length > 0) { tbody.deleteRow(0); } // add the new rows to the table for (var i = 0; i < graphed.length; i++) { var motif = graphed[i]; var colouri = motif['colouri']; if (!colouri) colouri = 0; var row = tbody.insertRow(tbody.rows.length); row['motif'] = motif; var swatch = make_swatch(colouri); swatch.onmousedown = swap_colour; add_cell(row, swatch); add_cell(row, make_link(motif['id'], motif['url'])); if (!s_logos[colouri-1]) { s_logos[colouri-1] = document.createElement("canvas"); var pspm = new Pspm(motif['pwm'], motif['id'], 0, 0, motif['motif_nsites'], motif['motif_evalue']); var logo = logo_1(alphabet, "", pspm); draw_logo_on_canvas(logo, s_logos[colouri-1], false, 0.3); } add_cell(row, s_logos[colouri-1]); } var div = $("unused_colours"); while (div.firstChild) div.removeChild(div.firstChild); $("unused_colours_section").style.display = (unused.length > 0 ? "block" : "none"); for (var i = 0; i < unused.length; i++) { var swatch = make_swatch(unused[i]); swatch['colouri'] = unused[i]; swatch.onclick = set_colour; div.appendChild(swatch); } } /* * make_MP_graph * * Create a motif probability graph on the canvas. */ function make_MP_graph() { var canvas = $("graph"); canvas.width = canvas.width; if (canvas.getContext) { var ctx = canvas.getContext('2d'); make_MP_graph2(ctx, canvas.width, canvas.height); } } function handle_MP_graph_mousemove(e) { "use strict"; var graph, start, stop, left, width, pop; graph = $("graph"); graph_click["stop"] = e.pageX - graph.getBoundingClientRect().left; // constrain stop and start to the graph start = graph_click["start"]; if (start < graph_metrics.left_mark) { start = graph_metrics.left_mark; } else if (start > graph_metrics.right_mark) { start = graph_metrics.right_mark; } stop = graph_click["stop"]; if (stop < graph_metrics.left_mark) { stop = graph_metrics.left_mark; } else if (stop > graph_metrics.right_mark) { stop = graph_metrics.right_mark; } // pick the smaller to be the left if (start < stop) { left = start; width = stop - start; } else { left = stop; width = start - stop; } // visualize the selected range pop = $("pop_peak"); if (width > 10) { pop.style.width = width + "px"; pop.style.left = left + "px"; pop.style.visibility = "visible"; } else { pop.style.visibility = "hidden"; } } function handle_MP_graph_mouseup(e) { "use strict"; var graph, start, stop, left, right, left_val, right_val, pop, l, w, d, unit; document.removeEventListener("mouseup", handle_MP_graph_mouseup, false); document.removeEventListener("mousemove", handle_MP_graph_mousemove, false); graph = $("graph"); graph_click["stop"] = e.pageX - graph.getBoundingClientRect().left; // hide the range preview pop = $("pop_peak"); pop.style.visibility = "hidden"; // constrain stop and start to the graph start = graph_click["start"]; if (start < graph_metrics.left_mark) { start = graph_metrics.left_mark; } else if (start > graph_metrics.right_mark) { start = graph_metrics.right_mark; } stop = graph_click["stop"]; if (stop < graph_metrics.left_mark) { stop = graph_metrics.left_mark; } else if (stop > graph_metrics.right_mark) { stop = graph_metrics.right_mark; } // pick the smaller to be the left if (start < stop) { left = start; right = stop; } else { left = stop; right = start; } l = graph_metrics.left_mark; w = graph_metrics.right_mark - graph_metrics.left_mark; d = graph_metrics.right_val - graph_metrics.left_val; unit = w / d; // convert into graph values left_val = graph_metrics.left_val + Math.round((left - l) / unit); right_val = graph_metrics.left_val + Math.round((right - l) / unit); // check if we're doing a legend move and not a zoom if ((right - left) < 10 || left_val == right_val) { move_legend(e); return; } // add a zoom to the stack zooms.push({"left_val": left_val, "right_val": right_val}); make_MP_graph(); $("zoom_out").disabled = false; $("zoom_center").disabled = false; } function handle_MP_graph_mousedown(e) { "use strict"; var graph; document.addEventListener("mouseup", handle_MP_graph_mouseup, false); document.addEventListener("mousemove", handle_MP_graph_mousemove, false); graph = $("graph"); graph_click["start"] = e.pageX - graph.getBoundingClientRect().left; } function handle_zoom_out_click() { if (zooms.length > 0) { zooms.pop(); make_MP_graph(); if (zooms.length == 0) { $("zoom_out").disabled = true; $("zoom_center").disabled = true; } } } function handle_zoom_center_click() { var zoom, reach; if (zooms.length > 0) { zoom = zooms.pop(); reach = Math.max(1, Math.round((zoom["right_val"] - zoom["left_val"]) / 2)); zooms.push({"left_val": -reach, "right_val": reach}); make_MP_graph(); } } function add_MP_graph_listeners() { "use strict"; var graph, zoom_out, zoom_center; graph = $("graph"); graph.addEventListener("mousedown", handle_MP_graph_mousedown, false); zoom_out = $("zoom_out"); zoom_out.disabled = true; zoom_out.addEventListener("click", handle_zoom_out_click, false); zoom_center = $("zoom_center"); zoom_center.addEventListener("click", handle_zoom_center_click, false); zoom_center.disabled = true; } function download_eps() { var canvas = $("graph"); canvas.width = canvas.width; if (canvas.getContext) { var ctx = canvas.getContext('2d'); var eps_ctx = new EpsContext(ctx, canvas.width, canvas.height); eps_ctx.register_font("14pt Helvetica", "Helvetica", 14 / 3 * 4); eps_ctx.register_font("16px Helvetica", "Helvetica", 16); eps_ctx.register_font("9px Helvetica", "Helvetica", 9); make_MP_graph2(ctx, canvas.width, canvas.height); $("eps_content").value = eps_ctx.eps(); } } function make_MP_graph2(ctx, width, height) { "use strict"; var windo, type, legend, plot_negative, plot_distance, motifs, rset, i, motif; var name, sig, colour, weights, graph, peak_highlight; // get the graph settings windo = parseInt($("windo").value); if (isNaN(windo) || windo < 1) { windo = 20; $("windo").value = 20; } type = parseInt($("plot_type").value); legend = parseInt($("legend").value); plot_negative = parseInt($("plot_negative").value); plot_distance = parseInt($("plot_distance").value) != 0; // get the selected motifs motifs = []; for (i = 0; i < s_motifs.length; i++) { if (s_motifs[i] != null) motifs.push(s_motifs[i]); } // sort the motifs motifs.sort(sort_motif_evalue); // create a result set with all the selected motifs rset = new CentrimoRSet(data["seqlen"]); for (i = 0; i < motifs.length; i++) { motif = motifs[i]; name = motif["id"]; if (motif["alt"]) name = motif["alt"] + " " + motif["id"]; sig = "p=" + log2str(motif["best_log_adj_pvalue"], 1); colour = palate[motif["colouri"]]; if (plot_negative) { rset.add(name, sig, colour, motif["len"], motif["total_sites"], motif["sites"], motif["neg_total_sites"], motif["neg_sites"]); } else { rset.add(name, sig, colour, motif["len"], motif["total_sites"], motif["sites"], 0, 0); } } // get the smoothing weights weights = (type == 1 ? triangular_weights(windo) : uniform_weights(windo)); // get the zoom var range_left = null; var range_right = null; if (zooms.length > 0) { var zoom = zooms[zooms.length - 1]; range_left = zoom["left_val"]; range_right = zoom["right_val"]; } // now make a new graph from the result set and smoothing weights graph = new CentrimoGraph(rset, weights, "CentriMo " + data["version"], range_left, range_right, plot_distance); graph_metrics = graph.draw_graph(ctx, width, height, legend, legend_x, legend_y); peak_highlight = $("pop_peak"); peak_highlight.style.top = graph_metrics.top_edge + "px"; peak_highlight.style.height = (graph_metrics.bottom_edge - graph_metrics.top_edge) + "px"; } function sync_sort_selection () { "use strict"; var i, mapper, motif_sort, region_sort; motif_sort = $("motif_sort"); region_sort = $("peak_sort"); if (typeof sync_sort_selection.mapper === "undefined") { var id2idx; // first map region id to index id2idx = {}; for (i = 0; i < region_sort.options.length; i++) { id2idx[sort_table["region"][parseInt(region_sort.options[i].value, 10)]["id"]] = i; } // now generate a mapping of index in motif sort to index in region sort mapper = []; for (i = 0; i < motif_sort.options.length; i++) { mapper[i] = id2idx[sort_table["motif"][parseInt(motif_sort.options[i].value, 10)]["pair"]]; } sync_sort_selection.mapper = mapper; } else { mapper = sync_sort_selection.mapper; } if (!$('allow_peak_sort').checked) { region_sort.selectedIndex = mapper[motif_sort.selectedIndex]; } } function populate_sort_list (sellist, items) { var i, j, item, opt, priority, selected; priority = 0; selected = 0; for (i = 0, j = 0; i < items.length; i++) { item = items[i]; if (typeof item["show"] === 'undefined' || item["show"]) { opt = document.createElement("option"); opt.innerHTML = item["name"]; opt.value = i; sellist.add(opt, null); if (typeof item["priority"] !== 'undefined' && item["priority"] > priority) { selected = j; priority = item["priority"]; } j++; } } sellist.selectedIndex = selected; } function populate_sort_lists() { "use strict"; var i, motif_sort, region_sort, motif_sort_list, region_sort_list; motif_sort = $("motif_sort"); region_sort = $("peak_sort"); try {motif_sort.removeEventListener("click", sync_sort_selection, false);} catch (e) {} try {motif_sort.removeEventListener("change", sync_sort_selection, false);} catch (e) {} for (i = motif_sort.options.length-1; i >= 0; i--) motif_sort.remove(i); for (i = region_sort.options.length-1; i >= 0; i--) region_sort.remove(i); motif_sort_list = sort_table["motif"]; region_sort_list = sort_table["region"]; populate_sort_list(motif_sort, motif_sort_list); populate_sort_list(region_sort, region_sort_list); sync_sort_selection(); motif_sort.addEventListener("click", sync_sort_selection, false); motif_sort.addEventListener("change", sync_sort_selection, false); } </script> <style type="text/css"> div.graph_box { position: relative; } div.pop_graph_peak { position:absolute; left: 0; top: 0; z-index: 5; width: 10px; height: 10px; opacity: 0.2; background-color: #3333ff; visibility: hidden; } 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; } table.motifs { margin-top: 20px; border-collapse:collapse; } table.motifs * td, table.motifs * th { padding-left: 15px; padding-right: 15px; 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border: 3px outset black; } div.swatch:active { width: 16px; height: 16px; font-size: 16px; border: 3px inset black; } span.expander { cursor: pointer; font-size: larger; } div.pop_logo { position:absolute; z-index:1; top:0px; left:0px; border: 3px outset black; background-color: white; display:none; } div.pop_colour { position:absolute; z-index:1; top:0px; left:0px; margin-left: -13px; margin-top: -13px; display:none; } div.pop_content { position:absolute; z-index:1; width:300px; padding: 5px; background: #E4ECEC; font-size: 12px; font-family: Arial; border-style: double; border-width: 3px; border-color: #AA2244; display:none; } span.arrow { font-size: larger; color: red; } #unused_colours div.swatch { display: inline-block; margin-right: 5px; } .no_swatch { text-align: center; font-size: larger; } input.error:enabled { background: #FF5555; } tr.sub_peak { display: none; } tbody.more > tr.sub_peak { display: table-row; } </style> <style type="text/css"> /* The following is the content of meme.css */ body { background-color:white; font-size: 12px; font-family: Verdana, Arial, Helvetica, sans-serif;} div.help { display: inline-block; margin: 0px; padding: 0px; width: 12px; height: 13px; cursor: pointer; background-image: url(data:image/gif;base64,R0lGODlhDAANAIABANR0AP///yH5BAEAAAEALAAAAAAMAA0AAAIdhI8Xy22MIFgv1DttrrJ7mlGNNo4c+aFg6SQuUAAAOw==); } div.help:hover { background-image: url(data:image/gif;base64,R0lGODlhDAANAKEAANR0AP///9R0ANR0ACH+EUNyZWF0ZWQgd2l0aCBHSU1QACH5BAEAAAIALAAAAAAMAA0AAAIdDGynCe3PgoxONntvwqz2/z2K2ImjR0KhmSIZUgAAOw==); } p.spaced { line-height: 1.8em;} span.citation { font-family: "Book Antiqua", "Palatino Linotype", serif; color: #004a4d;} p.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;} td.jump { font-size: 13px; color: #ffffff; background-color: #00666a; font-family: Georgia, "Times New Roman", Times, serif;} a.jump { margin: 15px 0 0; font-style: normal; font-variant: small-caps; font-weight: bolder; font-family: Georgia, "Times New Roman", Times, serif;} h2.mainh {font-size: 1.5em; 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text-align:left; width:8em; padding: 3px 0px;} th.actionth {font-weight:normal; text-align:left;} .explain h5 {font-size:1em; margin-left: 1em;} div.doc {margin-left: 2em; margin-bottom: 3em;} th.trainingset { border-bottom: thin dashed black; font-weight:normal; padding:0px 10px; } div.pop_content { position:absolute; z-index:50; width:300px; padding: 5px; background: #E4ECEC; font-size: 12px; font-family: Arial; border-style: double; border-width: 3px; border-color: #AA2244; display:none; } div.pop_content > *:first-child { margin-top: 0px; } div.pop_content h1, div.pop_content h2, div.pop_content h3, div.pop_content h4, div.pop_content h5, div.pop_content h6, div.pop_content p { margin: 0px; } div.pop_content p + h1, div.pop_content p + h2, div.pop_content p + h3, div.pop_content p + h4, div.pop_content p + h5, div.pop_content p + h6 { margin-top: 5px; } div.pop_content p + p { margin-top: 5px; } div.pop_content > *:last-child { margin-bottom: 0px; } div.pop_content div.pop_close { /* old definition */ float:right; bottom: 0; } div.pop_content span.pop_close, div.pop_content span.pop_back { display: inline-block; border: 2px outset #661429; background-color: #CCC; padding-left: 1px; padding-right: 1px; padding-top: 0px; padding-bottom: 0px; cursor: pointer; color: #AA2244; /*#661429;*/ font-weight: bold; } div.pop_content span.pop_close:active, div.pop_content span.pop_back:active { border-style: inset; } div.pop_content span.pop_close { float:right; /*border: 2px outset #AA002B;*/ /*color: #AA2244;*/ } div.pop_content:not(.nested) .nested_only { display: none; } div.pop_back_sec { margin-bottom: 5px; } div.pop_close_sec { margin-top: 5px; } table.hide_advanced tr.advanced { display: none; } span.show_more { display: none; } table.hide_advanced span.show_more { display: inline; } table.hide_advanced span.show_less { display: none; } /***************************************************************************** * Program logo styling ****************************************************************************/ div.prog_logo { border-bottom: 0.25em solid #0f5f60; height: 4.5em; width: 24em; display:inline-block; } div.prog_logo img { float:left; width: 4em; border-style: none; margin-right: 0.2em; } div.prog_logo h1, div.prog_logo h1:hover, div.prog_logo h1:active, div.prog_logo h1:visited { margin:0; padding:0; font-family: Arial, Helvetica, sans-serif; font-size: 3.2em; line-height: 1em; vertical-align: top; display: block; color: #026666; letter-spacing: -0.06em; text-shadow: 0.04em 0.06em 0.05em #666; } div.prog_logo h2, div.prog_logo h2:hover, div.prog_logo h2:active, div.prog_logo h2:visited { display: block; margin:0; padding:0; font-family: Helvetica, sans-serif; font-size: 0.9em; line-height: 1em; letter-spacing: -0.06em; color: black; } div.big.prog_logo { font-size: 18px; } </style> </head> <body onload="page_loaded()" onpageshow="page_shown(event)"> <!-- Popups --> <div id="logo_popup" class="pop_logo"> <canvas id="logo_popup_canvas" width="200" height="50"></canvas> <canvas id="logo_popup_canvas_rc" width="200" height="50"></canvas> </div> <!-- Help popups --> <div class="pop_content" style="width:400px" id="pop_prob_graph"> <p>Each "motif probability curve" shows the (estimated) probability of the <b>best</b> match to a given motif occurring at a given position in the input sequences. This estimated probability is based only on sequences that contain at least one match with score greater than the minimum score defined for this motif, and is the maximum likelihood estimate of the conditional probability shown below.</p> <p>Points (X,Y) on the plot are:<br> Y = Pr(best match occurs at position X | sequence contains a match)</p> <p><b>Note:</b> The plots are smoothed according to the function selected from the "Smoothing" menu on the right. Setting the smoothing window size to 1 turns off smoothing.</p> <p>If a negative dataset has been supplied then two lines are drawn for each motif representing both datasets. The normal dataset is plotted with a single unbroken line whereas the negative dataset is plotted with a dashed line.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_plotting"> <p>This shows a listing of all motifs currently plotted on the graph.</p> <p>The color used to plot a motif can be changed by clicking on the color swatch next to the motif you want to change, followed by clicking on the color swatch you wish to swap it with.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_unused_colours"> <p>These are extra colors you may use for plotting motifs.</p> <p>Click on the color swatch next to one of the above motifs, then click on one of these "unused color" swatches to change the color of the motif's plot.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" style="width: 500px" id="pop_graph"> <p>These options change the display of the graph.</p> <dl> <dt>Smoothing:</dt> <dd><p>Allows selection of the smoothing function applied to the graph.</p> <p>The weighted moving average option uses weights shaped as an isosceles triangle where the central point (or points in an even sized window) get the maximum weight.</p> <p>The moving average simply weights all points in the smoothing window equally.</p> <p><b>Note:</b> Setting the smoothing window size to 1 turns off smoothing.</dd></p> <dt>Window</dt> <dd><p>The window size used to smooth the graph. The larger the smoothing window size, the smoother the graph, at the cost of hiding detail.</p> <p>Below a smoothing window size of 10, thinner lines are used on the graph to allow more detail to be visible.</p> <p><b>Note:</b> Remember to press "return" or "enter" after changing the number in the input box in order to see the effect of the new smoothing window size.</p></dd> <dt>Legend</dt> <dd><p>Choose to display/disable the on-graph legend. The legend can be moved by clicking on the graph.</p></dd> <dt>Negative Sequences</dt> <dd><p>Choose whether to plot the motif probability curve(s) for the negative sequences (if provided). The curve(s) are plotted as dashed lines, using the same color as the corresponding curve for the positive sequences.</p></dd> <dt>Zoom</dt> <dd>Drag a range on the graph to zoom into that section. Clicking "Undo Zoom" will return the view to the preiously displayed part of the graph and clicking "Center on 0" will move the view so 0 is in the center.</dd> <dt>Download EPS</dt> <dd><p>Download the graph that you are currently viewing as an encapsulated postscript (EPS) image. EPS images are scalable making them suitable for publication.</p></dd> </dl> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_filtering"> <p>List only enriched motifs that meet the selected filter criteria below.</p> <p><b>Selected motifs are always listed</b>; deselect all motifs first by clicking on the "X" above the color swatches if you wish to filter all motifs.</p> <p>To filter on "ID" or "Name", you can enter any Javascript regular expression pattern. See <a href="http://www.w3schools.com/jsref/jsref_obj_regexp.asp">here</a> for documentation on Javascript regular expression patterns.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_sorting"> <p>Sorting is applied after filtering where possible (the exception being the "Top" filter) so the filters applied will affect the sort. You can choose the motif sorting feature using the "Motifs:" menu.</p> <p>If CentriMo is searching for locally enriched regions (not just centrally enriched regions), then multiple regions may be found per motif, and the "Regions:" menu will also be displayed. In this case, CentriMo first sorts all regions using the feature shown in the "Regions:" menu, and then it sorts the highest-ranked region of each motif according to the feature shown in the "Motifs:" menu. </p> <p> Unless you check the box next to the "Regions:" menu, it will automatically show the same feature as the "Motifs:" menu (or "<i>E</i>-value" if a motif-only feature is chosen in the "Motifs:" menu). </p> <p> <b>Note:</b>The motif <i>p</i>-value shown in the plot legend will always be for the region with the lowest <i>p</i>-value, and therefore may not match the value shown in the table "<i>p</i>-value" column when the "Regions:" menu is not set to "<i>p</i>-value". </p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_db"> <p>The name of the database (file name) that contains the motif.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_id"> <p>A name for the motif that is unique in the motif database file.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_name"> <p>An alternate name of the motif that may be provided in the motif database file.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_fisherpv"> <p>The expected number motifs that would have least one region as <b>comparatively</b> enriched for best matches to the motif as the reported region in the <b>positive</b> sequences compared with the <b>negative</b> sequences. </p> <p> The Fisher <i>E</i>-value is the (one-sided) <i>p</i>-value of the one-sided Fisher's exact test that <b>at least</b> as many best matches in the region in the positive sequences that contain at least one match, multiplied by the number of motifs in the input database(s). The Fisher's exact test <i>p</i>-value is corrected for the number of regions and score thresholds tested ("Multiple Tests"). </p> <p> Fisher's exact test assumes that the probability that the best match (if any) falls into a given region is the same for all positive and negative sequences. </p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_pvalue"> <p>The probability that any tested region would be as enriched for best matches to this motif as the reported region is.</p> <p>By default the <i>p</i>-value is calculated by using the one-tailed binomial test on the number of sequences with a match to the motif ("Total Matches") that have their best match in the reported region ("Region Matches"), corrected for the number of regions and score thresholds tested ("Multiple Tests"). The test assumes that the probability that the best match in a sequence falls in the region is the region width divided by the number of places a motif can align in the sequence (sequence length minus motif width plus 1).</p> <p>When CentriMo is run in discriminative mode with a negative set of sequences, the <i>p</i>-value of a region is calculated using Fisher's exact test on the enrichment of best matches in the positive sequences ("Region Matches") relative to the negative sequences ("Negative Region Matches"), corrected for the number of regions and score thresholds tested ("Multiple Tests"). The test assumes that the probability that the best match (if any) falls into a given region is the same for all positive and negative sequences. <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_evalue"> <p>The expected number motifs that would have least one region as enriched for best matches to the motif as the reported region. The <i>E</i>-value is the <i>p</i>-value multiplied by the number of motifs in the input database(s).</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_MCC"> <p>The Matthew's Correlation Coefficient (MCC) gives a measure of the ability of the motif to discriminate the positive sequences from the negative sequences: <dl> <dt> MCC = [TP*TN - FP*FN] / [(TP + FP) * (TP + FN) * (TN + FP) * (TN + FN)]</dt> </dl> where <dl> <dd>TP is the number of positive sequences with a best match in the reported region,</dd> <dd>FP is the number of negative sequences with a best match in the reported region,</dd> <dd>TN is the number of negative sequences without a best match in the reported region, and</dd> <dd>FN is the number of positive sequences without a best match in the reported region.</dd> </dl> <p>MCC ranges from -1 to +1, where a +1 result indicates that the occurrence of the best match to the motif in the reported region perfectly discriminates positive sequences from negative sequences. <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_score"> <p>This is the score threshold (in bits) for determining if a sequence contains a match to this motif.</p> <p>When score optimization is enabled, this column lists the score threshold that gives the best <i>p</i>-value. Otherwise it shows the smallest score found that was above the minimum score threshold specified to CentriMo.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_binw"> <p>The width (in sequence positions) of the most enriched region. A best match to the motif is counted as being in the region if the center of the motif falls in the region.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_bin_sites"> <p>The number of (positive) sequences whose <b>best</b> match to the motif falls in the reported region.</p> <p><b>Note:</b> This number may be less than the number of (positive) sequences that have a best match in the region. The reason for this is that a sequence may have many matches that score equally best. If <i>n</i> matches have the best score in a sequence, 1/<i>n</i> is added to the appropriate bin for each match.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_neg_bin_sites"> <p>The number of <b>negative</b> sequences where the <b>best</b> match to the motif falls in the reported region. This value is rounded but the underlying value may contain fractional counts.</p> <p><b>Note:</b> This number may be less than the number of <b>negative</b> have a best match in the region. The reason for this is that a sequence may have many matches that score equally best. If <i>n</i> matches have the best score in a sequence, 1/<i>n</i> is added to the appropriate bin for each match.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_total_sites"> <p>The number of sequences containing a match to the motif above the score threshold ("Score Threshold").</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_neg_total_sites"> <p>The number of <b>negative</b> sequences containing a match to the motif above the minimum score threshold. When score optimization is enabled the score threshold may be raised higher than the minimum.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_negative_binomial"> <p>The probability that any tested region in the <b>negative</b> sequences would be as enriched for best matches to this motif according to the Binomial test.</p> <p>Use the filter to display only motifs differentially enriched in both datasets (low <i>p</i>-value and high negative <i>p</i>-value).</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_prob"> <p>The maximum probability that the best match occurs at any single sequence position. If the smoothing window size ("Window:", to right of graph) is set to "1", then this is value is the maximum value of the match-probability curve.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_nbinstested"> <p>This is the number of multiple tests (<i>n</i>) done for this motif. It was used to correct the original <i>p</i>-value of a region for multiple tests using the formula </p> <dl> <dd>p' = 1 - (1-p)^n</dd> </dl> <p>where <i>p</i> is the uncorrected <i>p</i>-value. The number of multiple tests is the number of regions considered times the number of score thresholds considered. It depends on the motif length, sequence length, and the type of optimizations being done (central enrichment, local enrichement, score optimization).</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_bin_location"> <p>Location of the center of the most enriched region.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_SMmotifs"> <p>The text box lists the sequence identifiers for sequences which have at least one of their best matches in the most significant region of <b>all</b> the selected motifs.</p> <p>The "Intersection" subheading gives the number of identifiers in the text box and their percentage out of the total number of input sequences.</p> <p>The "Union" subheading lists the number and percentage of sequences that have at least one of their best matches in the most significant region of <b>any</b> of the selected motifs and their percentage out of the total number of input sequences.</p> <p>Note that the number of sequences with a match to a given motif in its best region may be larger than the value of "Region Matches". This is because a sequence may have multiple equally best matches and in that case a fractional match count is assigned to each of them when "Region Matches" is computed.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_OEbins"> <p>When more than one significant, non-overlapping region is found, they can be shown (and hidden again) by clicking the arrow.</p> <p>By default the regions are sorted by <i>E</i>-value, but this can be changed by the menu on the right of the page.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <div class="pop_content" id="pop_problocation"> <p>Sequence position where the (unsmoothed) match-probability curve for this motif attains its maximum. Set the smoothing window size ("Window:", to right of graph) to "1" to see the unsmoothed match probability curve.</p> <div style="float:right; bottom:0px;">[ <a href="javascript:help_popup()">close</a> ]</div> </div> <!-- Page starts here --> <div id="top" class="pad1"> <div class="prog_logo big"> <img 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uwI4cGMlQx9YgUPehfRKdgFVZCRvD5KLn+Qj53TCV/SzMY3jyCPGkfCfcuIXbaNP92g4BfspP1pFcETlUxeegvGla/jGTeGqCvnIuzYieud13Ff23rKVzpZT8iKNTinTSQYH/sf86UFBKSiEszb0jF/8BGUlSGIAogqamISvpHDMX2wFDnSTsub77LCPRx3vY6YWD+NTUH+enwVl4xv4KqmG7hiLOQ6K3i1w5NUCw70HxaT9s3nXNOUzaplC5kUOpnwQCLeRU9y5ywT5VUSU2e4ECVIM6SRKWTyW99vf1QE30sX/z9tAnjjbQcDLgnQrefZLXB89ZmVcZP8mEwKJsspU9TshFufKabPwm9J6ubmLs+CU/7s7izCrpnLopR16Hr2ZGfNF/jfeB9dbICls90k+uLRpaXju/NOxOoq9Bs2Ut9QgazKmIsrsA0cStO+XacSPf5zG8/P7Br9++pXIRD4LqnUd99JFMGgR19YQsTEK1sbe9JEXq+eTXWtgP2OSaTctIOBxl4YldM9FvNLL2F46jnq0jKQKiux3ziHPa/dwNI7bGwpy2H8+ucZG5PCsrdsTHhzLU8l3c0oZTTPu5/HivW0upqkJp4y/DdxB6bzt8Ft3sn/tLmB+yx7qG0QCJGiiJDDKc61UVWhZ/R4Z1v7+pQgLn+AwsM2tmXIHM6xMnKEyvE8gWkzXIQmFPHi6t1Iccm4u+3nLs/Lp/ucWXsRvH6mP96TpR9KPLz5EOVf1LHnpu50TT+A88MnkDp3xrRkCaqqol51JbLaKi5P53j0f3iUYJfOtL3k5Fzp+O9P3w1ndjsDXZJo2LaOsNk3wKZN3Cutw18voyzugWfUqwRT2t9nOngcnSxiGdAdtWsMeoOFEZ9WET93Kclx/+CrO++m6vBUDPN78O6OWq5OmM02cRt7TbsoeHE2o8f4iepdzXLzcg5KB8hUM0mo6X/mOIDX3MDnNUfZGdjPDPMoWtb8hp17BAYMdhMWrtCktrC9Lp8lSyQUXQDTb9ZjcvRBFcYyREzk7xtryFV3UetQeHCWibmel0+LdAkuF8aNWwmOHIm9l55uqRYi9rQw47MYmgYtBPPd+Pv1xj+gH/ZvViM0NNBy582nfVnHw785J+PpZ0sgMZ7G9A0ITlerS7nvALb/egTz5Om4nvgjrpuv+557JiAUFCKkpBCQA2A2IfTqDQf3Eerycjt30kvXh419VrOqvI4Rzmu48dBdjOy3jE8PltCyQ6HM56B+yJ8JF+z0Dw7ggfJn+a+N1Wd2Ax8eOowrch5hiDKYJV8KHI/JYPoUH888FoEiuniy6mOefjHAkF4W7rnXy+xePdh36WtsH/4Cn8y4hxXDniU0ez/zPrEyTe7YNja24Xajz9pD4Pp5REcGmDu/hYGjTKhHsgn94DMCnRMI2qwEOkQSmHoFxMbiG3r64o16AbzeSDYZCUZFEIyKwDNpHE0Z30JiIpann0f/vUwkQkUlYn0DwZHDTzXhnbcg1ddjXLkKgBHBETzs+QPLx9xKbO5EasolbEdHUVgaILqThxOG45TmWVjgWsAdnrvY+UUCd13S58wC6BCqp3t3mcaHH8ZbFca+zl9xdOprSPO+IvmBnWz6OJprh8fyu4m9uUI/mmu9c9ji3EaFUEm9oYnHK/fz6hcZPFG4gI7Hs9o9uG3rTrBYcA8ZiE4Cm05FN6h369HrZV+gjhgOoaGg0+GeOQ153BhU6cI7iNHOKoRYcbz1CmJVFebPl5/yz2tqERsa8Q44tXfBNXcWakICpi+/RnS521YyO8vduHV+A8s+DqHy2+5E7ZvI5892o653Ov2+/gN2TwzLPwlBb1QZPkI5swBECS5PrUPK3Ml/p8zlkpFumrvsparbDuYOS+bJrtfzyMwkBMPpiZMXO99nQc2VPLCglJQUH8LYkVjeeb/9gsY77xHs2welQ3Tb37yDB4IkgdGI95IBqGKrxQgMHYxj0W/OvTH+F8LTqzvyvHmY/v4PpNq6NgEgy6gjT09w4Xzij+j2HUB//PQtafEJMtOudpCbp7JwdjxxoUam945gkD2OPz8agSCJjJjspEOs/4cjgXEFO3mleh6p4h4eEe7nLvd9vBA/n+dm92LW1f4fWj9h4gd1iE3NeN54Hfc1MxH27sNYXnUqfNrYgnjwEIHhQ057O5c8oH/rrNlkItivz2k+tq9b54tGAEDrq2ocDqzvLW3tmPoGBJ0Ob9fTU9v7JoxBtVoJff2ddnVMnOLhnodbGBus49kba3n0nk+RdmWRUyQxLTaTAV+9jCn74A8sBgWDWLZtRzpZTdJ9t1OXk0mUEolO1BE5ajTuBXfhuO369rHkhkbMy5ahjh+Pc/glGEKsYDRifuMdfM/8d6uZ+nw5KAqBy0edPh5KAq5nn0INBpB797ygkzL/FP6e3fFdOwvzcy9gWrEKtbISevVC/Zfj7XJ4KL47bsH0xNPonnmcYMeo08qj7Cqhtz3CDVtAiDjODZun0FMYSmLaTlAU5Icf/IEhwOFEt3I1crduCEVFWF98HQD7xKsgNxfzQ48S/sifEevqT/dVt6Yj5uXjfPg3rQ/SpwfBgf0xvL8EndCqL/0HS1FjY/CPap+vx7XwTtwPLEC5iDu/1eaLeG69kcDgSwjqROROcXh/ILrpmTIBwsMI+c3D7crMOzMR0nYQvOsOakpyke65keHDnAT+6wGCvXpgKyg9swUwZh9AdLtp/vJjbIt+j/HNt9FnZSPu2oXrb38FfwDr088RsWMXjrdexde/N8aCYqz3Pkhg/Fjcg08tx/pvuA7dtm8Jvete/JMnIOTlE7x+LrKIxo9ZgaGpNGz+5qcnjr164L9qOsYPlmLO3ItnWOteCMHnx7h4CWJ0NA1P/aE1APS3v7TdZ6+oQN2V2W4IVwGCl41G9XpoXPEpereX8MGjUJubkZ96gvoH54OqYjici/3Ka1GNRlxffIzltrtRT56kees6At2ST6s48vHn0L31DorXiyDLONM24x7UV+vlnwmd20tEcm/ky0bRuGwJigCGvELsQ0bhfe1lmm+e094Te/wZrK+8gXDqDSj/c2oISEvHN34MSmgIvphoPA8sRLlyOvX339kW5fL3601D2kYArCPHIuTl4/nL4+06H6D+8UdpPH6QwNxrELp21Tr/ZyZoMeF/dBG6jCz06bvQF5YQftd9qD174ph25sxoQlJSq9d1Jgsg22y0bF6Dr0/rGzVEtwdBVpBDrO0qMhw5RvjsG5CHD6Xhg7d+MkCjb3YSCLNpvfZzTxuCClEDhiPbw5Hy8pE7RON66Tk8E8ee8XrL1nSs825BcrvbrwUIyZ3bOh9AsfzwDlp/n540fv0pcmLCWUXntM7/haKKOhH3ow9hfuC3BOfOoelPDyN3ivvRULRq0IP7DBagvjSPgD1Ua9XzzQrU1qEvLcc7sC/ofnyLpz4gE5YyAF1dXXsLoHX+eWoFOkQhd4g6q2sDegk1PAxOCQDNMbvIEPr1O3MgSOMi8R5SumkCuJjx9eutCeBiRu2jCeDitgDJiZoALmoL8C+ri5oALnI0AWgC0NAEoKEJQEMTwK+Kx+OhqrKK5sZm1q9eT0Z6Bk0NTWxYvYGKsgr8Pj8b126kuKCY+pP1bFi9AUeLg/qT9axbtQ6P23PGeutP1rNp3SYEBERBZNPaTdT/yza2qsoqcg/nosoqu9J2AVBe/OPvBDqQfYCW5hYydmRQmHfmNLGCKrDum3U0NTRRW1MLwJGcIzTUN5C1O4uc/TnnnAD+Y0mimuqbWPXFKm6/73aGXTqM2upa1q9az3W3XkdxQTEbvtnAtKunsS9rHy0NLUycOpHtm7Zjs9mYPH0y+zL2MWjYILJ2ZiEKIsNGDwNgd9pups+eTnZWNo4WBxOnTmT9yvWYrCa6dO1CXEIc1RXV1NXUUV5STr+B/cjYkcHK5St55qVnqK2qpbKykpiYGFxOF117dAWgIK+AohNFjJkwhqyMLLqkdGHrxq04WhzMuGYGAEdzjpI6OJXCvEKWf76cp196msqSSvSSnrUr13LH/Dvant+6ah3qWb6V3P27315YAlBVldwjuZSXl1NbWYstzIaiKIRHhHMg+wB5x/KIT4gnNyeXDas3MOeGOTTUNWAxWdAb9aRvSae6uprO3Ttjtpg5cugIiqJQXV2NoAosfWcp8cnx9O3XlyVvL6HwRCFxCXHU1dYRciQEi8UCIugkHau+WsWU6VMYMWoEABXlFeTn5rNpzSYGpA4g/dt0xk4YS+buTCZNncT6b9azf+9+Jk+fTDAQxOVykXs4l11pu5g1ZxY5B3MoPF6IyWIiOyObupo6GhsamXXtLDJ2ZJCQnACAZdsO+OqrHzxL+GsJoG0/QLWj+lcVQUVpBfEJ8ZQUl5CUnERjQyNetxeH04HJaCIkJIT6+noUWSEiKoKa6hr0ej2hYaG4HC4UFEJCQyjMKyQyKhJ7hB2vz4vJYKKhsYG4TnEoQYXqqmpCw0LxeDyEhoYSHRNNTVUNzY3NhIaH4mhxEBsfS211LZ0SO5GXm4fZYqa2ppbUoalUlFUQ3TGaksISOsZ2pLmpGVEUkSQJWZaRFZmo6Cjq6+oxGAz4vX6iO0bj9XrpENOBkoISwuxhVJZXEhIWQkJSqwB09Y3gcp3V2YdgQvzP2vbfPx7+q1mAuto60ramMW3WNDat3YTRaCTcHk7+sXzKS8sZedlIDhUfov8l/Sk4XsD2LduZNXcWJ46fYG/WXsZNHode3z4NTFlxGW6Xmx59elBcWMzRI0cZM3FMW3l4ZDiH9h/CarMSHRPN4UOHiYiIwOV2kdI7hZjvXgxp++7ASp/+fWhpaWH/3v306deHE/knSEhIIPdoLm6Pm9ShqYhi+6mT3+cnLCyMNavWMHTEUOTvcrjU1ddhNBsxGow01je2CSAYaYdI+8UzB9ixaQdXzrmS+tp6PG4PqUNT2bhmI4OHDEZn0pGRnsHuHbvp1bcXNRU1jJs8jvxj+Zw4doI+A/qgyApe2cuqL1Yxetxo7JF26mrrsNvtHDpwiEFDB2E2mqmprsHV7GL9mvVcNv4y7BF2SgpK6JrSlU8Xf4ov6GPwkMFUlVUxaPAgyovLKSwoxGwx069/P0xWE2UFZVx19VV8tuQzRl42kq2btjL1qqkU5hUiiiKfL/mcjnEdGTJ8CJJOoqW5hXWr19Gvbz8C3gAmo4lnH3+Wv77yV+qq6zAajGxev5nUwadS2S03LqdRbUREJJJIDnCAoQxlN7sZwhAqqMCMmTDCmOmfef4LQG/Sk3s4l4iICMpKyji07xDxneLZv28/zhYnOr2OpK5JrFmxhsjISLZv2o4kSQiCQGV5JRGREaio+Pw+9mfup76xnqioKFRZJSM9g/FXjKeosIigP0ja9jRqKmsoLiimoa6BQDDAyZqTmGwmSo6W4HA48Pq8NNQ30NTYRNrmNGwhNvQGPUdzjhIfH8/iNxczcsxIqiqrMFvN7Nm5h0HDBuFyupCDMik9U/h86efo9DqunXct/Qb0w2a10aVbF9atXEdcQhwFeQV4fV58fh82q42qylPH5UrFUqqEKiQk3LjZz37iiGMf+4ghhnzysWEjmmj4BZOS/2pzgObGZhwOBxGREQSCAcLCwtrcM1FoNan2SDulxaWEhYW1JohQ1dZO9/roENMBr8fLpnWbGD95PF6PF71ej6RrHYsFQSAYDKKqKmazGWeLk4joCPR6PSerT2I0GwkNC6W5qRmdXofX7cXv8+P3+7HZbHi8ntZ5hNeLs8VJaHgoer0el8tFZGQkLc0tREVHcXDvQeKT4rHarDQ3NiMIAhFREXi9XgQEHC0Owu3hyIqMxWLhZM1JbCE2fF4fKir2iFaz7xbcKCjf+eIifvwYMeLDhwEDMnKrK4uIRbX8YnOAX1QAjQ2NbFq7ialXTqWqqoqIqAjCwsPITM+kxdHC2PFj2bJpC1arldFjR7Nn9x6Gjx7O0ZyjHNp/iOtuvo4jB49QeKKQSdMnYTS2f8dfdmY2HqeH0eNHk388n+ITxUycNvG0a7J2ZREZHUlpUSlms7nt8/gp43/wux87coy4TnFsWL2B6TOms3vnbrr36E5C54T2Xo2iUlZSRqekTuQfz6djx46kb0tH0klYrVbiYuPIPZZLIBBg2lXTMFlM/9Fx//sC+GXSxH3Hzu07mXHNDMpKy8ja3eqvHz9ynJQez1wLzgAAAv1JREFUKcQlxJGdmU3Pnj0Jt4eTsz+H9G3ppA5JpaSghKGXDqXoRBFlJWWkDkvFZDIRCAZY9cUqTGYTsizjcXsw6UwcOXyEvgP7IqgCB/cepGPHjnyz/BvC7eGtnZlzDLPZTHh4OAf2HiAqMoqq0ip6DehFWVEZ6dvSqa6qxh5ux+V24ff5+ccb/2DCpAmEhISQeziXkuIS7HY7HWM78sn7n9DS3ILBYMDr9eLxeNiyYQs9e/bkjZffYMpVU7CYLZjNZqrLqhF1ImMnjqW8qJye/XoC8OE7ocgBicMHdez61srxowa8bj3794nsTrNRUqjD1WwiO1ugRy/5Z+2X72cJ+0XnABaLhQ1rNhCfGI/T4aSxsRF7uJ3jx45TUlxCYlIiWRlZ+L1+zBYzYyeN5ctPvqRTQie2btja1tHZGdmMmTAGFZXq6mryjuRxsu4kEREROFuciKJIWWkZzmYn5eXlHD18lOaGZpobW1225uZmbI02nA4ndSfrcLQ4aGxspLK8ktraWo7lHEOQBELDQjm07xBzbppD3/59cbvdpG1NI3VIKmu/WUvnLp05efIkgiDQuUtn1q5c2zYHSOmVgmSQGDR4EACZOzO55sZryPg2gxB7CCuXrWTC1AnfG3slQD4tICsAAiKCKiIgAiKq8ssekf9Fh4BgIIjX68VkMiErMjqdDkEQ8Lg9CGJrqFZRFARBQBRFjCYjTocTvV6PoiiIooiqqgSDQSxWC16vl+yMbC697FKCgWDbuC9KrX65qrReazQaCQQCGI1GREnE7XIjSRLBYOs9Or0ORVZwOVwEg0HCI8Lb7gsGgxhNRnxeH3q9Hq/Xi9FoxOvzYtQbKcwvpHP3zuh0Ovw+P4IgtN4nB1uv93gxmU1tz+1xe5B0EsFA6zOcapvWBGKq+l2yM6E1JKCq3/XId/9GBUn3yw0BujP8UUNbDNLQBKBxMWAVAJPWDhclAhDQmkFDQ0NDQ0NDQ0NDQ0NDQ0NDQ0NDQ0NDQ0NDQ0NDQ0ND4wLjfwE9VJhuBfJALAAAAABJRU5ErkJggg==" alt="CentriMo Logo"> <h1>CentriMo</h1> <h2>Local Motif Enrichment Analysis</h2> </div> <p> For further information on how to interpret these results or to get a copy of the MEME software please access <a href="http://meme-suite.org/">http://meme-suite.org</a>. </p> <p>If you use CentriMo in your research, please cite the following paper:<br /> <span class="citation"> Timothy L. Bailey and Philip Machanick, "Inferring direct DNA binding from ChIP-seq", <i>Nucleic Acids Research</i>, <b>40</b>:e128, 2012. <a href="http://nar.oxfordjournals.org/content/40/17/e128">[full text]</a> </span> </p> </div> <!-- navigation --> <div class="pad2"> <a class="jump" href="#graph_sec">Motif Probability Graph</a> | <a class="jump" href="#data_sec">Enriched Motifs</a> | <a class="jump" href="#inputs">Input Files</a> | <a class="jump" href="#info_sec">Program information</a> </div> <!-- alert the user when their browser is not up to the task --> <noscript><h1 style="color:red">Javascript is required to view these results!</h1></noscript> <h1 id="html5_warning" style="color:red; display:none;">Your browser does not support canvas!</h1> <script> if (!window.HTMLCanvasElement) $("html5_warning").style.display = "block"; </script> <h2 class="mainh pad2">Results</h2> <div class="box"> <span id="ins_desc"></span> <!-- write out the job description --> <script> if (data['job_description']) { var node = $("ins_desc"); while (node.firstChild) node.removeChild(node.firstChild); var header = document.createElement("h4"); header.id = "description"; header.appendChild(document.createTextNode("Description")); node.appendChild(header); var paragraphs = data['job_description'].split("\n\n"); for (var i = 0; i < paragraphs.length; i++) { var p = document.createElement("p"); var lines = paragraphs[i].split("\n"); for (var j = 0; j < lines.length; j++) { if (j != 0) p.appendChild(document.createElement('br')); p.appendChild(document.createTextNode(lines[j])); } node.appendChild(p); } } </script> <div> <div style="float:left; width:70%"> <h4 id="graph_sec">Motif Probability Graph (score ≥ <span id="ins_score2"></span>) <div class="help" onclick="help_popup(this, 'pop_prob_graph')"></div></h4> <script> $("ins_score2").innerHTML = (data['options']['optimize_score']) ? "optimal score threshold (bits) for given motif" : data['options']['score'] + " bits"; </script> <div class="graph_box"> <div id="pop_peak" class="pop_graph_peak"></div> <canvas id="graph" width="700" height="400"></canvas> </div> </div> <div class="graph_options_section"> <h4 id="graph_sec">Options</h4> <h5>Plotting <div class="help" onclick="help_popup(this, 'pop_plotting')"></div></h5> <div style="max-height:200px; min-height:100px; overflow-y: auto;"> <table class="graph_list" id="graph_list"><tbody></tbody></table> </div> <div id="unused_colours_section"> <h5>Unused Colours <div class="help" onclick="help_popup(this, 'pop_unused_colours')"></div></h5> <span id="unused_colours"></span> </div> <h5>Graph <div class="help" onclick="help_popup(this, 'pop_graph')"></div></h5> <div> <label for="plot_type">Smoothing:</label> <select id="plot_type" onchange="recreate_table=true; make_MP_graph(); recreate_table=false"> <option value="0">Moving Average</option> <option value="1" selected>Weighted Moving Average</option> </select> </div> <div> <label for="windo">Window:</label> <input type="number" style="min-width:40px;" id="windo" onkeypress="num_keys(event)" onchange="recreate_table=true; make_MP_graph(); recreate_table=false" value="20" size="2" step="1" min="1"> </div> <div> <label for="legend">Legend:</label> <select id="legend" onchange="make_MP_graph()"> <option value="0">Disabled</option> <option value="1" selected>Enabled (click on graph to move)</option> </select> </div> <div> <label for="plot_distance">X-axis:</label> <select id="plot_distance" onchange="make_MP_graph()"> <option value="0">Position of Best Site in Sequence</option> <option value="1">Distance of Best Site from Sequence Center</option> </select> </div> <div id="CB_show_plot_negative"> <label for="plot_negative">Negative sequences:</label> <select id="plot_negative" onchange="make_MP_graph()"> <option value="0">Not plotted</option> <option value="1" selected>Plotted as dashed line</option> </select> </div> <div> <label>Zoom:</label> <input type="button" id="zoom_out" value="Undo Zoom"/> <input type="button" id="zoom_center" value="Center on 0"/> </div> <div style="margin-top:10px;"> <form id="eps_form" method="post" action=""> <script>$("eps_form").action = site_url + "/utilities/save_generated_file";</script> <input type="hidden" name="name" value="centrimo.eps"> <input type="hidden" name="mime_type" value="application/postscript"> <input type="hidden" id="eps_content" name="content" value=""> <input type="submit" onclick="download_eps()" value="Download EPS (for publication)"> </form> </div> </div> </div> <div> <div style="float:left; width:70%"> <h4 id="data_sec">Enriched motifs (<i>E</i>-value ≤ <span id="ins_ethresh"></span> using <span id="ins_test"></span> test) </h4> <script> $("ins_ethresh").innerHTML = data['options']["ethresh"]; $("ins_test").innerHTML = ((data['options']['disc']) ? "Fisher's exact" : "the binomial"); </script> <table class="motifs hide_db hide_maxprob hide_tsites" id="motifs"> <thead> <tr align="center"> <th class="deselect" onclick="clear_selection()" title="clear selection">☒</th> <th class="col_db">Database <div class="help" onclick="help_popup(this, 'pop_db')"></div></th> <th class='col_id'>ID <div class="help" onclick="help_popup(this, 'pop_id')"></div></th> <th class="col_name">Name <div class="help" onclick="help_popup(this, 'pop_name')"></div></th> <th class='col_evalue'><i>E</i>-value <div class="help" onclick="help_popup(this, 'pop_evalue')"></div></th> <th class='col_fisherpv'>Fisher <i>E</i>-value <div class="help" onclick="help_popup(this, 'pop_fisherpv')"></div></th> <th class="col_pvalue"><i>p</i>-value <div class="help" onclick="help_popup(this, 'pop_pvalue')"></div></th> <th class="col_negative_binomial">Negative <i>p</i>-value <div class="help" onclick="help_popup(this, 'pop_negative_binomial')"></div></th> <th class="col_MCC">MCC <div class="help" onclick="help_popup(this, 'pop_MCC')"></div></th> <th class="col_blocation">Region Center <div class="help" onclick="help_popup(this, 'pop_bin_location')"></div></th> <th class='col_bwidth'>Region Width <div class="help" onclick="help_popup(this, 'pop_binw')"></div></th> <th class="col_bsites">Region Matches <div class="help" onclick="help_popup(this, 'pop_bin_sites')"></div></th> <th class="col_tsites">Total Matches <div class="help" onclick="help_popup(this, 'pop_total_sites')"></div></th> <th class="col_negbsites">Negative Region Matches <div class="help" onclick="help_popup(this, 'pop_neg_bin_sites')"></div></th> <th class="col_negtsites">Negative Total Matches <div class="help" onclick="help_popup(this, 'pop_neg_total_sites')"></div></th> <th class="col_maxprob">Max Probability <div class="help" onclick="help_popup(this, 'pop_prob')"></div></th> <th class="col_problocation">Max Probability Location <div class="help" onclick="help_popup(this, 'pop_problocation')"></div></th> <th class="col_nbinstested">Multiple Tests <div class="help" onclick="help_popup(this, 'pop_nbinstested')"></div></th> <th class="col_score">Score Threshold <div class="help" onclick="help_popup(this, 'pop_score')"></div></th> <th class="col_OEbins">Other Regions <div class="help" onclick="help_popup(this, 'pop_OEbins')"></div></th> </tr> </thead> <tbody> </tbody> </table> </div> <div style="float:right; width:30%"> <div id="seq_area"> <h4>Matching sequences (out of <span id="ins_seqN"></span>) <div class="help" onclick="help_popup(this, 'pop_SMmotifs')"></div></h4> <script>$("ins_seqN").innerHTML = data['sequence_db']['count'];</script> <h5>Union: <span id="matching_union_number">0</span> sequences (<span id="matching_union_percentage">0</span>%).</h5> <h5>Intersection: <span id="matching_intersection_number">0</span> sequences (<span id="matching_intersection_percentage">0</span>%).</h5> <textarea id="matching_intersection_sequences" rows="10" cols="50" readonly></textarea> </div> <h4>Filter & Sort</h4> <h5>Filters <div style="margin-top:5px;" class="help" onclick="help_popup(this, 'pop_filtering')" ></div></h5> <div id="filters"> <div > <input type="checkbox" id="filter_on_top" value="1" onclick="toggle_filter(this, 'filter_top')"> <label for="filter_top" onclick="enable_filter('filter_on_top', 'filter_top')">Top</label> <input type="number" id="filter_top" value="10" size="4" min="1" step="1" onkeypress="num_keys(event); update_filter(event)" disabled> </div> <div > <input type="checkbox" id="filter_on_db" value="1" onclick="toggle_filter(this, 'filter_db')"> <label for="filter_db" onclick="enable_filter('filter_on_db', 'filter_db')" >Database is</label> <select id="filter_db" disabled> <script> var filter_db = $("filter_db"); filter_db.options.length = 0; for (var i = 0; i < data['motif_dbs'].length; i++) { var db = data['motif_dbs'][i]; filter_db.add(new Option(db['name'], i)); } </script> </select> </div> <div > <input type="checkbox" id="filter_on_id" value="1" onclick="toggle_filter(this, 'filter_id')"> <label for="filter_id" onclick="enable_filter('filter_on_id', 'filter_id')" >ID matches</label> <input type="text" id="filter_id" value=".*" size="12" onkeypress="update_filter(event)" disabled> </div> <div > <input type="checkbox" id="filter_on_alt" value="1" onclick="toggle_filter(this, 'filter_alt')"> <label for="filter_alt" onclick="enable_filter('filter_on_alt', 'filter_alt')" >Name matches</label> <input type="text" id="filter_alt" value=".*" size="12" onkeypress="update_filter(event)" disabled> </div> <div > <input type="checkbox" id="filter_on_evalue" value="1" onclick="toggle_filter(this, 'filter_evalue')"> <label for="filter_evalue" onclick="enable_filter('filter_on_evalue', 'filter_evalue')" ><i>E</i>-value ≤</label> <input type="text" id="filter_evalue" value="1" size="7" onkeypress="update_filter(event)" disabled> </div> <div id='cb_filter_on_fisherpv' > <input type="checkbox" id="filter_on_fisherpv" value="1" onclick="toggle_filter(this, 'filter_fisherpv')"> <label for="filter_fisherpv" onclick="enable_filter('filter_on_fisherpv', 'filter_fisherpv')" >Fisher <i>E</i>-value≤</label> <input type="text" id="filter_fisherpv" value="1" size="7" onkeypress="update_filter(event)" disabled> </div> <div > <input type="checkbox" id="filter_on_binwidth" value="1" onclick="toggle_filter(this, 'filter_binwidth')"> <label for="filter_binwidth" onclick="enable_filter('filter_on_binwidth', 'filter_binwidth')" >Region Width ≤</label> <input type="number" id="filter_binwidth" value="200" size="7" min="1" onkeypress="num_keys(event); update_filter(event)" disabled> </div> <div id='CB_filter_on_negbintest'> <input type="checkbox" id="filter_on_negbintest" value="1" onclick="toggle_filter(this, 'filter_negbintest')"> <label for="filter_negbintest" onclick="enable_filter('filter_on_negbintest', 'filter_negbintest')" >Negative set <i>E</i>-value ≥</label> <input type="text" id="filter_negbintest" value="1" size="7" onkeypress="update_filter(event)" disabled> </div> </div> <div style="margin: 5px 0;"> <h5>Sort <div class="help" onclick="help_popup(this, 'pop_sorting')"></div></h5> <div> <label for="motif_sort">Motifs: </label> <select id="motif_sort"></select> </div> <div id="box_peak_sort"> <input type="checkbox" id="allow_peak_sort" value="1" onclick="toggle_filter(this, 'peak_sort')"> <label for="peak_sort" onclick="enable_filter('allow_peak_sort', 'peak_sort')" >Regions: </label> <select id="peak_sort" disabled></select> </div> <script>populate_sort_lists();</script> </div> <div> <input type="button" value="Update" onclick="make_CEM_table()"> </div> <h4>Columns to display</h4> <div > <input type="checkbox" id="show_db" value="1" onclick="toggle_column('hide_db')"> <label for="show_db">Show Database</label> </div> <div > <input type="checkbox" id="show_id" value="1" onclick="toggle_column('hide_id')" checked> <label for="show_id">Show ID</label> </div> <div > <input type="checkbox" id="show_name" value="1" onclick="toggle_column('hide_name')" checked> <label for="show_name">Show Name</label> </div> <div > <input type="checkbox" id="show_evalue" value="1" onclick="toggle_column('hide_evalue')" checked> <label for="show_evalue">Show <i>E</i>-value</label> </div> <div > <input type="checkbox" id="show_pvalue" value="1" onclick="toggle_column('hide_pvalue')"> <label for="show_pvalue">Show <i>p</i>-value</label> </div> <div id='cb_show_fisherpv'> <input type="checkbox" id="show_fisherpv" value="1" onclick="toggle_column('hide_fisherpv')" checked> <label for="show_fisherpv">Show Fisher <i>E</i>-value</label> </div> <div id='CB_show_MCC'> <input type="checkbox" id="show_MCC" value="1" onclick="toggle_column('hide_MCC')"> <label for="show_MCC">Show Matthew's Correlation Coefficient</label> </div> <div id='CB_show_blocation'> <input type="checkbox" id="show_blocation" value="1" onclick="toggle_column('hide_blocation')" checked> <label for="show_blocation">Show Region Center</label> </div> <div > <input type="checkbox" id="show_bwidth" value="1" onclick="toggle_column('hide_bwidth')" checked> <label for="show_bwidth">Show Region Width</label> </div> <div > <input type="checkbox" id="show_bsites" value="1" onclick="toggle_column('hide_bsites')" checked> <label for="show_bsites">Show Region Matches</label> </div> <div > <input type="checkbox" id="show_tsites" value="1" onclick="toggle_column('hide_tsites')"> <label for="show_tsites">Show Total Matches</label> </div> <div id='CB_show_negative_binomial'> <input type="checkbox" id="show_negative_binomial" value="1" onclick="toggle_column('hide_negative_binomial')"> <label for="show_negative_binomial">Show Negative <i>p</i>-value</label> </div> <div id='CB_show_negbsites'> <input type="checkbox" id="show_negbsites" value="1" onclick="toggle_column('hide_negbsites')" checked> <label for="show_negbsites">Show Negative Region Matches</label> </div> <div id='CB_show_negtsites'> <input type="checkbox" id="show_negtsites" value="1" onclick="toggle_column('hide_negtsites')"> <label for="show_negtsites">Show Negative Total Matches</label> </div> <div > <input type="checkbox" id="show_maxprob" value="1" onclick="toggle_column('hide_maxprob')"> <label for="show_maxprob">Show Max Probability</label> </div> <div > <input type="checkbox" id="show_hpeak" value="1" onclick="toggle_column('hide_hpeak')"> <label for="show_hpeak">Show Max Probability Location</label> </div> <div > <input type="checkbox" id="show_nbinstested" value="1" onclick="toggle_column('hide_nbinstested')"> <label for="show_nbinstested">Show Multiple Tests</label> </div> <div> <input type="checkbox" id="show_score" value="1" onclick="toggle_column('hide_score')"> <label for="show_score">Show Score Threshold</label> </div> </div> <div style="clear:both"></div> </div> </div> <h2 id="inputs" class="mainh pad2">Input Files</h2> <div class="box"> <h4>Sequences</h4> <table class="inputs"> <tr><th>Database</th><th>Source</th><th>Sequence Count</th></tr> <tr> <td id="ins_seq_name"></td> <td id="ins_seq_source"></td> <td id="ins_seq_count"></td> </tr> </table> <script> { var db = data['sequence_db']; $("ins_seq_name").innerHTML = db['name']; $("ins_seq_source").innerHTML = db['source']; $("ins_seq_count").innerHTML = db['count']; } </script> <div id='neg_seq_input'> <h4>Negative sequences</h4> <table class="inputs"> <tr><th>Database</th><th>Source</th><th>Sequence Count</th></tr> <tr> <td id="ins_negseq_name"></td> <td id="ins_negseq_source"></td> <td id="ins_negseq_count"></td> </tr> </table> </div> <script> { if (data['options']['neg_sequences']) { var db = data['negative_sequence_db']; if (!db['name']) db['name'] = name_from_source(db['source']); $("ins_negseq_name").innerHTML = db['name']; $("ins_negseq_source").innerHTML = db['source']; $("ins_negseq_count").innerHTML = db['count']; } else { $('neg_seq_input').style.display='none'; } } </script> <h4>Motifs</h4> <table id="motif_dbs" class="inputs"> <thead> <tr><th>Database</th><th>Source</th><th>Motif Count</th></tr> </thead> <tbody></tbody> </table> <script> { var tbl = $('motif_dbs'); var tbody = tbl.tBodies[0]; while (tbody.rows.length > 0) { tbody.deleteRow(0); } var motif_dbs = data['motif_dbs']; for (var i = 0; i < motif_dbs.length; i++) { var db = motif_dbs[i]; var row = tbody.insertRow(tbody.rows.length); add_text_cell(row, db['name']); add_text_cell(row, db['source']); add_text_cell(row, db['count']); } } </script> </div> <div id="info_sec" class="bar"> <div class="subsection"> <a name="version"/> <h5>CentriMo version</h5> <span id="ins_version"></span> (Release date: <span id="ins_release"></span>) <script> $("ins_version").innerHTML = data["version"]; $("ins_release").innerHTML = data["release"]; </script> </div> <div class="subsection"> <a name="command" /> <h5>Command line summary</h5> <textarea id="cmd" rows="5" style="width:100%;" readonly="readonly"> </textarea> <script>$("cmd").value = data["cmd"].join(" ");</script> </div> </div> </body> </html>