comparison test-data/dreme_output_test1.html @ 2:3e5c80594237 draft

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

1:cb8a2242bf03

    <title>DREME</title>
    <script>
      // @JSON_VAR data
      var data = {
        "program": "dreme",
        "version": "4.12.0",
        "release": "Tue Jun 27 16:22:50 2017 -0700",
        "cmd": [
          "dreme", "-o", "./dreme_test1_out", "-p", "dreme_test_sites.fa",
          "-norc", "-rna", "-s", "1"
        ],
        "options": {
          "revcomp": false,
          "ngen": 100,
          "add_pv_thresh": 0.01,
          "seed": 1,
          "stop": {
            "evalue": "0.05"
          }
        },
        "alphabet": {
          "name": "RNA",
          "like": "rna",
          "ncore": 4,
          "symbols": [
            {
              "symbol": "A",
              "name": "Adenine",
              "colour": "CC0000"
            }, {
              "symbol": "C",
              "name": "Cytosine",
              "colour": "0000CC"
            }, {
              "symbol": "G",
              "name": "Guanine",
              "colour": "FFB300"
            }, {
              "symbol": "U",
              "aliases": "T",
              "name": "Uracil",
              "colour": "008000"
            }, {
              "symbol": "N",
              "aliases": "X.",
              "name": "Any base",
              "equals": "ACGU"
            }, {
              "symbol": "V",
              "name": "Not U",
              "equals": "ACG"
            }, {
              "symbol": "H",
              "name": "Not G",
              "equals": "ACU"
            }, {
              "symbol": "D",
              "name": "Not C",
              "equals": "AGU"
            }, {
              "symbol": "B",
              "name": "Not A",
              "equals": "CGU"
            }, {
              "symbol": "M",
              "name": "Amino",
              "equals": "AC"
            }, {
              "symbol": "R",
              "name": "Purine",
              "equals": "AG"
            }, {
              "symbol": "W",
              "name": "Weak",
              "equals": "AU"
            }, {
              "symbol": "S",
              "name": "Strong",
              "equals": "CG"
            }, {
              "symbol": "Y",
              "name": "Pyrimidine",
              "equals": "CU"
            }, {
              "symbol": "K",
              "name": "Keto",
              "equals": "GU"
            }
          ]
        },
        "background": {
          "freqs": [0.221, 0.245, 0.221, 0.312]
        },
        "sequence_db": {
          "name": "dreme test sites",
          "file": "dreme_test_sites.fa",
          "lmod": "Thu Apr 26 15:09:03 CEST 2018",
          "count": 1000
        },
        "control_db": {
          "name": "shuffled positive sequences",
          "from": "shuffled",
          "count": 1000,
          "freqs": [0.221, 0.245, 0.221, 0.312]
        },
        "motifs": [
          {
            "db": 0,
            "id": "UUYUCY",
            "alt": "DREME-1",
            "len": 6,
            "nsites": 459,

              [0.000000, 0.000000, 0.000000, 1.000000], 
              [0.000000, 0.294118, 0.000000, 0.705882], 
              [0.000000, 0.000000, 0.000000, 1.000000], 
              [0.000000, 1.000000, 0.000000, 0.000000], 
              [0.000000, 0.474946, 0.000000, 0.525054]
            ],
            "matches": [
              {
                "seq": "UUUUCC",
                "p": 147,
                "n": 75,
                "pvalue": "1.8e-007",
                "evalue": "8.1e-003"

                "seq": "UUUUCU",
                "p": 155,
                "n": 94,
                "pvalue": "2.2e-005",
                "evalue": "1.0e+000"
              }, {
                "seq": "UUCUCU",
                "p": 94,
                "n": 51,
                "pvalue": "1.3e-004",
                "evalue": "6.1e+000"
              }, {
                "seq": "UUCUCC",
                "p": 75,
                "n": 42,
                "pvalue": "1.1e-003",
                "evalue": "5.0e+001"
              }
            ]
          }, {
            "db": 0,
            "id": "YAGG",
            "alt": "DREME-2",
            "len": 4,
            "nsites": 793,
            "evalue": "5.1e-012",
            "p": 600,
            "n": 416,
            "pvalue": "1.1e-016",
            "unerased_evalue": "2.4e-012",
            "pwm": [
              [0.000000, 0.692308, 0.000000, 0.307692], 
              [1.000000, 0.000000, 0.000000, 0.000000], 
              [0.000000, 0.000000, 1.000000, 0.000000], 
              [0.000000, 0.000000, 1.000000, 0.000000]
            ],
            "matches": [
              {
                "seq": "CAGG",
                "p": 441,
                "n": 304,
                "pvalue": "1.5e-010",
                "evalue": "6.6e-006"
              }, {
                "seq": "UAGG",
                "p": 232,
                "n": 165,
                "pvalue": "1.1e-004",
                "evalue": "4.7e+000"
              }
            ]
          }, {
            "db": 0,
            "id": "GAAGAW",
            "alt": "DREME-3",
            "len": 6,
            "nsites": 89,
            "evalue": "3.4e-005",
            "p": 81,
            "n": 22,
            "pvalue": "8.2e-010",
            "unerased_evalue": "3.5e-004",
            "pwm": [
              [0.000000, 0.000000, 1.000000, 0.000000], 
              [1.000000, 0.000000, 0.000000, 0.000000], 
              [1.000000, 0.000000, 0.000000, 0.000000], 
              [0.000000, 0.000000, 1.000000, 0.000000], 
              [1.000000, 0.000000, 0.000000, 0.000000], 
              [0.494382, 0.000000, 0.000000, 0.505618]
            ],
            "matches": [
              {
                "seq": "GAAGAU",
                "p": 45,
                "n": 7,
                "pvalue": "2.4e-008",
                "evalue": "9.9e-004"
              }, {
                "seq": "GAAGAA",
                "p": 40,
                "n": 16,
                "pvalue": "7.9e-004",
                "evalue": "3.3e+001"
              }
            ]
          }, {
            "db": 0,
            "id": "SMUGGA",
            "alt": "DREME-4",
            "len": 6,
            "nsites": 119,
            "evalue": "3.7e-003",
            "p": 110,
            "n": 47,
            "pvalue": "9.1e-008",
            "unerased_evalue": "2.6e-005",
            "pwm": [
              [0.000000, 0.529412, 0.470588, 0.000000], 
              [0.428571, 0.571429, 0.000000, 0.000000], 
              [0.000000, 0.000000, 0.000000, 1.000000], 
              [0.000000, 0.000000, 1.000000, 0.000000], 
              [0.000000, 0.000000, 1.000000, 0.000000], 
              [1.000000, 0.000000, 0.000000, 0.000000]
            ],
            "matches": [
              {
                "seq": "GAUGGA",
                "p": 22,
                "n": 6,
                "pvalue": "1.7e-003",
                "evalue": "7.1e+001"
              }, {
                "seq": "GCUGGA",
                "p": 33,
                "n": 14,
                "pvalue": "3.6e-003",
                "evalue": "1.5e+002"
              }, {
                "seq": "CCUGGA",
                "p": 32,
                "n": 15,
                "pvalue": "8.6e-003",
                "evalue": "3.5e+002"
              }, {
                "seq": "CAUGGA",
                "p": 29,
                "n": 13,
                "pvalue": "9.1e-003",
                "evalue": "3.7e+002"
              }
            ]
          }
        ],
        "runtime": {
          "host": "ThinkPad-T450s",
          "when": "Thu May 03 13:22:29 CEST 2018",
          "cpu": 13.95,
          "real": 13.95,
          "stop": "evalue"
        }
      };
    </script>
    <script>
var site_url = "http://meme-suite.org";
</script>
    <script>

/*
 * $
 *
 * Shorthand function for getElementById
 */
function $(el) {
  return document.getElementById(el);
}


/*
 * See http://stackoverflow.com/a/5450113/66387
 * Does string multiplication like the perl x operator.
 */
function string_mult(pattern, count) {
    if (count < 1) return '';
    var result = '';
    while (count > 1) {
        if (count & 1) result += pattern;
        count >>= 1, pattern += pattern;
    }
    return result + pattern;
}

/*
 * See http://stackoverflow.com/questions/814613/how-to-read-get-data-from-a-url-using-javascript
 * Slightly modified with information from
 * https://developer.mozilla.org/en/DOM/window.location
 */
function parse_params() {
  "use strict";
  var search, queryStart, queryEnd, query, params, nvPairs, i, nv, n, v;
  search = window.location.search;
  queryStart = search.indexOf("?") + 1;
  queryEnd   = search.indexOf("#") + 1 || search.length + 1;
  query      = search.slice(queryStart, queryEnd - 1);

  if (query === search || query === "") return {};

  params  = {};
  nvPairs = query.replace(/\+/g, " ").split("&");

  for (i = 0; i < nvPairs.length; i++) {
    nv = nvPairs[i].split("=");
    n  = decodeURIComponent(nv[0]);
    v  = decodeURIComponent(nv[1]);
    // allow a name to be used multiple times
    // storing each value in the array
    if (!(n in params)) {
      params[n] = [];
    }
    params[n].push(nv.length === 2 ? v : null);
  }
  return params;
}

/*
 * coords
 *
 * Calculates the x and y offset of an element.
 * From http://www.quirksmode.org/js/findpos.html
 * with alterations to take into account scrolling regions
 */
function coords(elem) {
  var myX = myY = 0;
  if (elem.getBoundingClientRect) {
    var rect;
    rect = elem.getBoundingClientRect();
    myX = rect.left + ((typeof window.pageXOffset !== "undefined") ?
        window.pageXOffset : document.body.scrollLeft);
    myY = rect.top + ((typeof window.pageYOffset !== "undefined") ?
        window.pageYOffset : document.body.scrollTop);
  } else {
    // this fall back doesn't properly handle absolutely positioned elements
    // inside a scrollable box
    var node;
    if (elem.offsetParent) {
      // subtract all scrolling
      node = elem;
      do {
        myX -= node.scrollLeft ? node.scrollLeft : 0;
        myY -= node.scrollTop ? node.scrollTop : 0;
      } while (node = node.parentNode);
      // this will include the page scrolling (which is unwanted) so add it back on
      myX += (typeof window.pageXOffset !== "undefined") ? window.pageXOffset : document.body.scrollLeft;
      myY += (typeof window.pageYOffset !== "undefined") ? window.pageYOffset : document.body.scrollTop;
      // sum up offsets
      node = elem;
      do {
        myX += node.offsetLeft;
        myY += node.offsetTop;
      } while (node = node.offsetParent);
    }
  }
  return [myX, myY];
}

/*
 * position_popup
 *
 * Positions a popup relative to an anchor element.
 *
 * The avaliable positions are:
 * 0 - Centered below the anchor.
 */
function position_popup(anchor, popup, position) {
  "use strict";
  var a_x, a_y, a_w, a_h, p_x, p_y, p_w, p_h;
  var a_xy, spacer, margin, scrollbar, page_w;
  // define constants
  spacer = 5;
  margin = 15;
  scrollbar = 15;
  // define the positions and widths
  a_xy = coords(anchor);
  a_x = a_xy[0];
  a_y = a_xy[1];
  a_w = anchor.offsetWidth;
  a_h = anchor.offsetHeight;
  p_w = popup.offsetWidth;
  p_h = popup.offsetHeight;
  page_w = null;
  if (window.innerWidth) {
    page_w = window.innerWidth;
  } else if (document.body) {
    page_w = document.body.clientWidth;
  }
  // check the position type is defined
  if (typeof position !== "number") {
    position = 0;
  }
  // calculate the popup position
  switch (position) {
    case 1:
      p_x = a_x + a_w + spacer;
      p_y = a_y + (a_h / 2) - (p_h / 2);
      break;
    case 0:
    default:
      p_x = a_x + (a_w / 2) - (p_w / 2);
      p_y = a_y + a_h + spacer;
      break;
  }
  // constrain the popup position
  if (p_x < margin) {
    p_x = margin;
  } else if (page_w != null && (p_x + p_w) > (page_w - margin - scrollbar)) {
    p_x = page_w - margin - scrollbar - p_w;
  }
  if (p_y < margin) {
    p_y = margin;
  }
  // position the popup
  popup.style.left = p_x + "px";
  popup.style.top = p_y + "px";
}

function lookup_help_popup(popup_id) {
  var _body, pop, info;
  pop = document.getElementById(popup_id);
  if (pop == null) {
    _body = document.getElementsByTagName("body")[0];
    pop = document.createElement("div");
    pop.className = "pop_content";
    pop.id = popup_id;
    pop.style.backgroundColor = "#FFC";
    pop.style.borderColor = "black";
    info = document.createElement("p");
    info.style.fontWeight = "bold";
    info.appendChild(document.createTextNode("Error: No popup for topic \"" + popup_id + "\"."));
    pop.appendChild(info);
    // this might cause problems with the menu, but as this only happens
    // when something is already wrong I don't think that's too much of a problem
    _body.insertBefore(pop, _body.firstChild);
  }
  if (document.getElementsByTagName('body')[0].hasAttribute("data-autobtns")) {
    if (!/\bauto_buttons\b/.test(pop.className)) {
      pop.className += " auto_buttons";
      var back_btn_sec = document.createElement("div");
      back_btn_sec.className = "nested_only pop_back_sec";
      var back_btn = document.createElement("span");
      back_btn.className = "pop_back";
      back_btn.appendChild(document.createTextNode("<< back"));
      back_btn.addEventListener("click", function(e) {
        help_return();
      }, false);
      back_btn_sec.appendChild(back_btn);
      pop.insertBefore(back_btn_sec, pop.firstChild);
      var close_btn_sec = document.createElement("div");
      close_btn_sec.className = "pop_close_sec";
      var close_btn = document.createElement("span");
      close_btn.className = "pop_close";
      close_btn.appendChild(document.createTextNode("close"));
      close_btn.addEventListener("click", function(e) {
        help_popup();
      }, false);
      close_btn_sec.appendChild(close_btn);
      pop.appendChild(close_btn_sec);
    }
  }
  return pop;
}

/*
 * help_popup
 *
 * Moves around help pop-ups so they appear
 * below an activator.
 */
function help_popup(activator, popup_id) {
  "use strict";
  var pop;
  // set default values
  if (typeof help_popup.popup === "undefined") {
    help_popup.popup = [];
  }
  if (typeof help_popup.activator === "undefined") {
    help_popup.activator = null;
  }
  var last_pop = (help_popup.popup.length > 0 ? help_popup.popup[help_popup.popup.length - 1] : null);
  if (typeof(activator) == "undefined") { // no activator so hide
    if (last_pop != null) {
      last_pop.style.display = 'none';
      help_popup.popup = [];
    }
    return;
  }
  pop = lookup_help_popup(popup_id);
  if (pop == last_pop) {
    if (activator == help_popup.activator) {
      //hide popup (as we've already shown it for the current help button)
      last_pop.style.display = 'none';
      help_popup.popup = [];
      return; // toggling complete!
    }
  } else if (last_pop != null) {
    //activating different popup so hide current one
    last_pop.style.display = 'none';
  }
  help_popup.popup = [pop];
  help_popup.activator = activator;
  toggle_class(pop, "nested", false);
  //must make the popup visible to measure it or it has zero width
  pop.style.display = 'block';
  position_popup(activator, pop);
}

/*
 * help_refine
 * 
 * Intended for links within a help popup. Stores a stack of state so
 * you can go back.
 */
function help_refine(popup_id) {
  if (help_popup.popup == null || help_popup.popup.length == 0 || help_popup.activator == null) {
    throw new Error("Can not refine a help popup when one is not shown!");
  }
  var pop = lookup_help_popup(popup_id);
  var last_pop = help_popup.popup[help_popup.popup.length - 1];
  if (pop == last_pop) return; // slightly odd, but no real cause for alarm
  help_popup.popup.push(pop);
  toggle_class(pop, "nested", true);
  last_pop.style.display = "none";
  //must make the popup visible to measure it or it has zero width
  pop.style.display = "block";
  position_popup(help_popup.activator, pop);
}

/*
 * help_return
 * 
 * Intended for links within a help popup. Stores a stack of state so
 * you can go back.
 */
function help_return() {
  if (help_popup.popup == null || help_popup.popup.length == 0 || help_popup.activator == null) {
    throw new Error("Can not return to a earlier help popup when one is not shown!");
  }
  var last_pop = help_popup.popup.pop();
  last_pop.style.display = "none";
  var pop = (help_popup.popup.length > 0 ? help_popup.popup[help_popup.popup.length - 1] : null);
  if (pop != null) {
    toggle_class(pop, "nested", help_popup.popup.length > 1);
    pop.style.display = "block";
    position_popup(help_popup.activator, pop);
  } else {
    help_popup.activator = null;
  }
}

/*
 * update_scroll_pad
 *
 * Creates padding at the bottom of the page to allow
 * scrolling of anything into view.
 */
function update_scroll_pad() {
  var page, pad;
  page = (document.compatMode === "CSS1Compat") ? document.documentElement : document.body;
  pad = $("scrollpad");
  if (pad === null) {
    pad = document.createElement("div");
    pad.id = 'scrollpad';
    document.getElementsByTagName('body')[0].appendChild(pad);
  }
  pad.style.height = Math.abs(page.clientHeight - 100) + "px";
}

function substitute_classes(node, remove, add) {
  "use strict";
  var list, all, i, cls, classes;
  list = node.className.split(/\s+/);
  all = {};
  for (i = 0; i < list.length; i++) {
    if (list[i].length > 0) all[list[i]] = true;
  }
  for (i = 0; i < remove.length; i++) {
    if (all.hasOwnProperty(remove[i])) {
      delete all[remove[i]];
    }
  }
  for (i = 0; i < add.length; i++) {
    all[add[i]] = true;
  }
  classes = "";
  for (cls in all) {
    classes += cls + " ";
  }
  node.className = classes;
}

/*
 * toggle_class
 *
 * Adds or removes a class from the node. If the parameter 'enabled' is not 
 * passed then the existence of the class will be toggled, otherwise it will be
 * included if enabled is true.
 */
function toggle_class(node, cls, enabled) {
  var classes = node.className;
  var list = classes.replace(/^\s+/, '').replace(/\s+$/, '').split(/\s+/);
  var found = false;
  for (var i = 0; i < list.length; i++) {
    if (list[i] == cls) {
      list.splice(i, 1);
      i--;
      found = true;
    }
  }
  if (typeof enabled == "undefined") {
    if (!found) list.push(cls);
  } else {
    if (enabled) list.push(cls);
  }
  node.className = list.join(" ");
}

/*
 * find_child
 *
 * Searches child nodes in depth first order and returns the first it finds
 * with the className specified.
 * TODO replace with querySelector
 */
function find_child(node, className) {
  var pattern;
  if (node == null || typeof node !== "object") {
    return null;
  }
  if (typeof className === "string") {
    pattern = new RegExp("\\b" + className + "\\b");
  } else {
    pattern = className;
  }
  if (node.nodeType == Node.ELEMENT_NODE && 
      pattern.test(node.className)) {
    return node;
  } else {
    var result = null;
    for (var i = 0; i < node.childNodes.length; i++) {
      result = find_child(node.childNodes[i], pattern);
      if (result != null) break;
    }
    return result;
  }
}

/*
 * find_parent
 *
 * Searches parent nodes outwards from the node and returns the first it finds
 * with the className specified.
 */
function find_parent(node, className) {
  var pattern;
  pattern = new RegExp("\\b" + className + "\\b");
  do {
    if (node.nodeType == Node.ELEMENT_NODE && 
        pattern.test(node.className)) {
      return node;
    }
  } while (node = node.parentNode);
  return null;
}

/*
 * find_parent_tag
 *
 * Searches parent nodes outwards from the node and returns the first it finds
 * with the tag name specified. HTML tags should be specified in upper case.
 */
function find_parent_tag(node, tag_name) {
  do {
    if (node.nodeType == Node.ELEMENT_NODE && node.tagName == tag_name) {
      return node;
    }
  } while (node = node.parentNode);
  return null;
}

/*
 * __toggle_help
 *
 * Uses the 'topic' property of the this object to
 * toggle display of a help topic.
 *
 * This function is not intended to be called directly.
 */
function __toggle_help(e) {
  if (!e) e = window.event;
  if (e.type === "keydown") {
    if (e.keyCode !== 13 && e.keyCode !== 32) {
      return;
    }
    // stop a submit or something like that
    e.preventDefault();
  }

  help_popup(this, this.getAttribute("data-topic"));
}

function setup_help_button(button) {
  "use strict";
  var topic;
  if (button.hasAttribute("data-topic")) {
    topic = button.getAttribute("data-topic");
    if (document.getElementById(topic) != null) {
      button.tabIndex = "0"; // make keyboard selectable
      button.addEventListener("click", function() {
        help_popup(button, topic);
      }, false);
      button.addEventListener("keydown", function(e) {
        // toggle only on Enter or Spacebar, let other keys do their thing
        if (e.keyCode !== 13 && e.keyCode !== 32) return;
        // stop a submit or something like that
        e.preventDefault();
        help_popup(button, topic);
      }, false);
    } else {
      button.style.visibility = "hidden";
    }
  }
  button.className += " active";
}

/*
 * help_button
 *
 * Makes a help button for the passed topic.
 */
function help_button(topic) {
  var btn = document.createElement("div");
  btn.className = "help";
  btn.setAttribute("data-topic", topic);
  setup_help_button(btn);
  return btn;
}

/*
 * prepare_download
 *
 * Sets the attributes of a link to setup a file download using the given content.
 * If no link is provided then create one and click it.
 */
function prepare_download(content, mimetype, filename, link) {
  "use strict";
  // if no link is provided then create one and click it
  var click_link = false;
  if (!link) {
    link = document.createElement("a");
    click_link = true;
  }
  try {
    // Use a BLOB to convert the text into a data URL.
    // We could do this manually with a base 64 conversion.
    // This will only be supported on modern browsers,
    // hence the try block.
    var blob = new Blob([content], {type: mimetype});
    var reader = new FileReader();
    reader.onloadend = function() {
      // If we're lucky the browser will also support the download
      // attribute which will let us suggest a file name to save the link.
      // Otherwise it is likely that the filename will be unintelligible. 
      link.setAttribute("download", filename);
      link.href = reader.result;
      if (click_link) {
        // must add the link to click it
        document.body.appendChild(link);
        link.click();
        document.body.removeChild(link);
      }
    }
    reader.readAsDataURL(blob);
  } catch (error) {
    if (console && console.log) console.log(error);
    // probably an old browser
    link.href = "";
    link.visible = false;
  }
}

/*
 * add_cell
 *
 * Add a cell to the table row.
 */
function add_cell(row, node, cls, click_action) {
  var cell = row.insertCell(row.cells.length);
  if (node) cell.appendChild(node);
  if (cls && cls !== "") cell.className = cls;
  if (click_action) cell.addEventListener("click", click_action, false);
}

/*
 * add_header_cell
 *
 * Add a header cell to the table row.
 */
function add_header_cell(row, node, help_topic, cls, colspan) {
  var th = document.createElement("th");
  if (node) th.appendChild(node);
  if (help_topic && help_topic !== "") th.appendChild(help_button(help_topic));
  if (cls && cls !== "") th.className = cls;
  if (typeof colspan == "number" && colspan > 1) th.colSpan = colspan;
  row.appendChild(th);
}

/*
 * add_text_cell
 *
 * Add a text cell to the table row.
 */
function add_text_cell(row, text, cls, action) {
  var node = null;
  if (typeof(text) != 'undefined') node = document.createTextNode(text);
  add_cell(row, node, cls, action);
}

/*
 * add_text_header_cell
 *
 * Add a text header cell to the table row.
 */
function add_text_header_cell(row, text, help_topic, cls, action, colspan) {
  var node = null;
  if (typeof(text) != 'undefined') {
    var nbsp = (help_topic ? "\u00A0" : "");
    var str = "" + text;
    var parts = str.split(/\n/);
    if (parts.length === 1) {
      if (action) {
        node = document.createElement("span");
        node.appendChild(document.createTextNode(str + nbsp));
      } else {
        node = document.createTextNode(str + nbsp);
      }
    } else {
      node = document.createElement("span");
      for (var i = 0; i < parts.length; i++) {
        if (i !== 0) {
          node.appendChild(document.createElement("br"));
        }
        node.appendChild(document.createTextNode(parts[i]));
      }
    }
    if (action) {
      node.addEventListener("click", action, false);
      node.style.cursor = "pointer";
    }
  }
  add_header_cell(row, node, help_topic, cls, colspan);
}

function setup_help() {
  "use strict";
  var help_buttons, i;
  help_buttons = document.querySelectorAll(".help:not(.active)");
  for (i = 0; i < help_buttons.length; i++) {
    setup_help_button(help_buttons[i]);
  }
}

function setup_scrollpad() {
  "use strict";
  if (document.getElementsByTagName('body')[0].hasAttribute("data-scrollpad") && document.getElementById("scrollpad") == null) {
    window.addEventListener("resize", update_scroll_pad, false);
    update_scroll_pad();
  }
}

// anon function to avoid polluting global scope
(function() {
  "use strict";
  window.addEventListener("load", function load(evt) {
    window.removeEventListener("load", load, false);
    setup_help();
    setup_scrollpad();
  }, false);
})();

/*
 *  make_link
 *
 *  Creates a text node and if a URL is specified it surrounds it with a link.
 *  If the URL doesn't begin with "http://" it automatically adds it, as
 *  relative links don't make much sense in this context.
 */
function make_link(text, url) {
  var textNode = null;
  var link = null;
  if (typeof text !== "undefined" && text !== null) textNode = document.createTextNode(text);
  if (typeof url === "string") {
    if (url.indexOf("//") == -1) {
      url = "http://" + url;
    }
    link = document.createElement('a');
    link.href = url;
    if (textNode) link.appendChild(textNode);
    return link;
  }
  return textNode;
}
</script>
    <script>
function motif_logo_template(inputs) {
  function _input(name) {
    if (typeof inputs[name] === "undefined") {
      throw new Error("Missing template variable: " + name);
    }
    return inputs[name];
  }
  return (
"%!PS-Adobe-3.0 EPSF-3.0\n" +
"%%Title: Sequence Logo : " + _input("TITLE") + "\n" +
"%%Creator: " + _input("CREATOR") + "\n" +
"%%CreationDate: " + _input("CREATIONDATE") + "\n" +
"%%BoundingBox:   0  0  " + _input("BOUNDINGWIDTH") + " " + _input("BOUNDINGHEIGHT") + " \n" +
"%%Pages: 0\n" +
"%%DocumentFonts: \n" +
"%%EndComments\n" +
"\n" +
"% ---- CONSTANTS ----\n" +
"\/cmfactor 72 2.54 div def % defines points -> cm conversion\n" +
"\/cm {cmfactor mul} bind def % defines centimeters\n" +
"\n" +
"% ---- VARIABLES ----\n" +
"\n" +
"% NA = Nucleic Acid, AA = Amino Acid\n" +
"\/logoType (" + _input("LOGOTYPE") + ") def \n" +
"\n" +
"\/logoTitle (" + _input("TITLE") + ") def\n" +
"\n" +
"% Dimensions in cm\n" +
"\/logoWidth " + _input("LOGOWIDTH") + " cm def\n" +
"\/logoHeight " + _input("LOGOLINEHEIGHT") + " cm def\n" +
"\/totalHeight " + _input("LOGOHEIGHT") + " cm def\n" +
"\n" +
"\/yaxis " + _input("YAXIS") + " def\n" +
"\/yaxisLabel (" + _input("YAXISLABEL") + ") def\n" +
"\/yaxisBits  " + _input("BARBITS") + " def % bits\n" +
"\/yaxisTicBits " + _input("TICBITS") + " def\n" +
"\n" +
"\/xaxis " + _input("NUMBERING") + " def\n" +
"\/xaxisLabel (" + _input("XAXISLABEL") + ") def\n" +
"\/showEnds (" + _input("SHOWENDS") + ") def \n" +
"\n" +
"\/showFineprint true def\n" +
"\/fineprint (" + _input("FINEPRINT") + ") def\n" +
"\n" +
"\/charsPerLine " + _input("CHARSPERLINE") + " def\n" +
"\n" +
"\/showingBox " + _input("SHOWINGBOX") + " def    \n" +
"\/shrinking false def   % true falses\n" +
"\/shrink  1.0 def\n" +
"\/outline " + _input("OUTLINE") + " def\n" +
"\n" +
"\/IbeamFraction  " + _input("ERRORBARFRACTION") + " def\n" +
"\/IbeamGray      0.50 def\n" +
"\/IbeamLineWidth 0.5 def\n" +
"\n" +
"\/fontsize       " + _input("FONTSIZE") + " def\n" +
"\/titleFontsize  " + _input("TITLEFONTSIZE") + " def\n" +
"\/smallFontsize  " + _input("SMALLFONTSIZE") + " def\n" +
"\n" +
"\/topMargin      " + _input("TOPMARGIN") + " cm def\n" +
"\/bottomMargin   " + _input("BOTTOMMARGIN") + " cm def\n" +
"\n" +
"\/defaultColor [0 0 0] def \n" +
"\n" +
_input("COLORDICT") + "\n" +
"\n" +
"\/colorDict fullColourDict def\n" +
"\n" +
"% ---- DERIVED PARAMETERS ----\n" +
"\n" +
"\/leftMargin\n" +
"  fontsize 3.5 mul\n" +
"\n" +
"def \n" +
"\n" +
"\/rightMargin \n" +
"  %Add extra room if showing ends\n" +
"  showEnds (false) eq { fontsize}{fontsize 1.5 mul} ifelse\n" +
"def\n" +
"\n" +
"\/yaxisHeight \n" +
"  logoHeight \n" +
"  bottomMargin sub  \n" +
"  topMargin sub\n" +
"def\n" +
"\n" +
"\/ticWidth fontsize 2 div def\n" +
"\n" +
"\/pointsPerBit yaxisHeight yaxisBits div  def\n" +
"\n" +
"\/stackMargin 1 def\n" +
"\n" +
"% Do not add space aroung characters if characters are boxed\n" +
"\/charRightMargin \n" +
"  showingBox { 0.0 } {stackMargin} ifelse\n" +
"def\n" +
"\n" +
"\/charTopMargin \n" +
"  showingBox { 0.0 } {stackMargin} ifelse\n" +
"def\n" +
"\n" +
"\/charWidth\n" +
"  logoWidth\n" +
"  leftMargin sub\n" +
"  rightMargin sub\n" +
"  charsPerLine div\n" +
"  charRightMargin sub\n" +
"def\n" +
"\n" +
"\/charWidth4 charWidth 4 div def\n" +
"\/charWidth2 charWidth 2 div def\n" +
"\n" +
"\/stackWidth \n" +
"  charWidth charRightMargin add\n" +
"def\n" +
" \n" +
"\/numberFontsize \n" +
"  fontsize charWidth lt {fontsize}{charWidth} ifelse\n" +
"def\n" +
"\n" +
"% movements to place 5'\/N and 3'\/C symbols\n" +
"\/leftEndDeltaX  fontsize neg         def\n" +
"\/leftEndDeltaY  fontsize 1.5 mul neg def\n" +
"\/rightEndDeltaX fontsize 0.25 mul     def\n" +
"\/rightEndDeltaY leftEndDeltaY        def\n" +
"\n" +
"% Outline width is proporional to charWidth, \n" +
"% but no less that 1 point\n" +
"\/outlinewidth \n" +
"  charWidth 32 div dup 1 gt  {}{pop 1} ifelse\n" +
"def\n" +
"\n" +
"\n" +
"% ---- PROCEDURES ----\n" +
"\n" +
"\/StartLogo { \n" +
"  % Save state\n" +
"  save \n" +
"  gsave \n" +
"\n" +
"  % Print Logo Title, top center \n" +
"  gsave \n" +
"    SetStringFont\n" +
"\n" +
"    logoWidth 2 div\n" +
"    logoTitle\n" +
"    stringwidth pop 2 div sub\n" +
"    totalHeight\n" +
"    titleFontsize sub\n" +
"    moveto\n" +
"\n" +
"    logoTitle\n" +
"    show\n" +
"  grestore\n" +
"\n" +
"  % Print X-axis label, bottom center\n" +
"  gsave\n" +
"    SetStringFont\n" +
"\n" +
"    logoWidth 2 div\n" +
"    xaxisLabel\n" +
"    stringwidth pop 2 div sub\n" +
"    0\n" +
"    titleFontsize 3 div\n" +
"    add\n" +
"    moveto\n" +
"\n" +
"    xaxisLabel\n" +
"    show\n" +
"  grestore\n" +
"\n" +
"  % Show Fine Print\n" +
"  showFineprint {\n" +
"    gsave\n" +
"      SetSmallFont\n" +
"      logoWidth\n" +
"        fineprint stringwidth pop sub\n" +
"        smallFontsize sub\n" +
"          smallFontsize 3 div\n" +
"      moveto\n" +
"    \n" +
"      fineprint show\n" +
"    grestore\n" +
"  } if\n" +
"\n" +
"  % Move to lower left corner of last line, first stack\n" +
"  leftMargin bottomMargin translate\n" +
"\n" +
"  % Move above first line ready for StartLine \n" +
"  0 totalHeight translate\n" +
"\n" +
"  SetLogoFont\n" +
"} bind def\n" +
"\n" +
"\/EndLogo { \n" +
"  grestore \n" +
"  showpage \n" +
"  restore \n" +
"} bind def\n" +
"\n" +
"\n" +
"\/StartLine { \n" +
"  % move down to the bottom of the line:\n" +
"  0 logoHeight neg translate\n" +
"  \n" +
"  gsave \n" +
"    yaxis { MakeYaxis } if\n" +
"    xaxis { showEnds (true) eq {ShowLeftEnd} if } if\n" +
"} bind def\n" +
"\n" +
"\/EndLine{ \n" +
"    xaxis { showEnds (true) eq {ShowRightEnd} if } if\n" +
"  grestore \n" +
"} bind def\n" +
"\n" +
"\n" +
"\/MakeYaxis {\n" +
"  gsave    \n" +
"    stackMargin neg 0 translate\n" +
"    ShowYaxisBar\n" +
"    ShowYaxisLabel\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"\/ShowYaxisBar { \n" +
"  gsave  \n" +
"    SetStringFont\n" +
"\n" +
"    \/str 10 string def % string to hold number  \n" +
"    \/smallgap stackMargin 2 div def\n" +
"\n" +
"    % Draw first tic and bar\n" +
"    gsave    \n" +
"      ticWidth neg 0 moveto \n" +
"      ticWidth 0 rlineto \n" +
"      0 yaxisHeight rlineto\n" +
"      stroke\n" +
"    grestore\n" +
"\n" +
"   \n" +
"    % Draw the tics\n" +
"    % initial increment limit proc for\n" +
"    0 yaxisTicBits yaxisBits abs %cvi\n" +
"    {\/loopnumber exch def\n" +
"\n" +
"      % convert the number coming from the loop to a string\n" +
"      % and find its width\n" +
"      loopnumber 10 str cvrs\n" +
"      \/stringnumber exch def % string representing the number\n" +
"\n" +
"      stringnumber stringwidth pop\n" +
"      \/numberwidth exch def % width of number to show\n" +
"\n" +
"      \/halfnumberheight\n" +
"         stringnumber CharBoxHeight 2 div\n" +
"      def\n" +
"\n" +
"      numberwidth % move back width of number\n" +
"      neg loopnumber pointsPerBit mul % shift on y axis\n" +
"      halfnumberheight sub % down half the digit\n" +
"\n" +
"      moveto % move back the width of the string\n" +
"\n" +
"      ticWidth neg smallgap sub % Move back a bit more  \n" +
"      0 rmoveto % move back the width of the tic  \n" +
"\n" +
"      stringnumber show\n" +
"      smallgap 0 rmoveto % Make a small gap  \n" +
"\n" +
"      % now show the tic mark\n" +
"      0 halfnumberheight rmoveto % shift up again\n" +
"      ticWidth 0 rlineto\n" +
"      stroke\n" +
"    } for\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\/ShowYaxisLabel {\n" +
"  gsave\n" +
"    SetStringFont\n" +
"\n" +
"    % How far we move left depends on the size of\n" +
"    % the tic labels.\n" +
"    \/str 10 string def % string to hold number  \n" +
"    yaxisBits yaxisTicBits div cvi yaxisTicBits mul \n" +
"    str cvs stringwidth pop\n" +
"    ticWidth 1.5 mul  add neg  \n" +
"\n" +
"\n" +
"    yaxisHeight\n" +
"    yaxisLabel stringwidth pop\n" +
"    sub 2 div\n" +
"\n" +
"    translate\n" +
"    90 rotate\n" +
"    0 0 moveto\n" +
"    yaxisLabel show\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"\/StartStack {  % <stackNumber> startstack\n" +
"  xaxis {MakeNumber}{pop} ifelse\n" +
"  gsave\n" +
"} bind def\n" +
"\n" +
"\/EndStack {\n" +
"  grestore\n" +
"  stackWidth 0 translate\n" +
"} bind def\n" +
"\n" +
"\n" +
"% Draw a character whose height is proportional to symbol bits\n" +
"\/MakeSymbol{ % charbits character MakeSymbol\n" +
"  gsave\n" +
"    \/char exch def\n" +
"    \/bits exch def\n" +
"\n" +
"    \/bitsHeight \n" +
"       bits pointsPerBit mul \n" +
"    def\n" +
"\n" +
"    \/charHeight \n" +
"       bitsHeight charTopMargin sub\n" +
"       dup \n" +
"       0.0 gt {}{pop 0.0} ifelse % if neg replace with zero \n" +
"    def \n" +
" \n" +
"    charHeight 0.0 gt {\n" +
"      char SetColor\n" +
"      charWidth charHeight char ShowChar\n" +
"\n" +
"      showingBox { % Unfilled box\n" +
"        0 0 charWidth charHeight false ShowBox\n" +
"      } if\n" +
"\n" +
"\n" +
"    } if\n" +
"\n" +
"  grestore\n" +
"\n" +
"  0 bitsHeight translate \n" +
"} bind def\n" +
"\n" +
"\n" +
"\/ShowChar { % <width> <height> <char> ShowChar\n" +
"  gsave\n" +
"    \/tc exch def    % The character\n" +
"    \/ysize exch def % the y size of the character\n" +
"    \/xsize exch def % the x size of the character\n" +
"\n" +
"    \/xmulfactor 1 def \n" +
"    \/ymulfactor 1 def\n" +
"    \/limmulfactor 0.01 def\n" +
"    \/drawable true def\n" +
"\n" +
"  \n" +
"    % if ysize is negative, make everything upside down!\n" +
"    ysize 0 lt {\n" +
"      % put ysize normal in this orientation\n" +
"      \/ysize ysize abs def\n" +
"      xsize ysize translate\n" +
"      180 rotate\n" +
"    } if\n" +
"\n" +
"    shrinking {\n" +
"      xsize 1 shrink sub 2 div mul\n" +
"        ysize 1 shrink sub 2 div mul translate \n" +
"\n" +
"      shrink shrink scale\n" +
"    } if\n" +
"\n" +
"    % Calculate the font scaling factors\n" +
"    % Loop twice to catch small correction due to first scaling\n" +
"    2 {\n" +
"      gsave\n" +
"        xmulfactor ymulfactor scale\n" +
"      \n" +
"        ysize % desired size of character in points\n" +
"        tc CharBoxHeight \n" +
"        dup 0.0 ne {\n" +
"          div % factor by which to scale up the character\n" +
"          \/ymulfactor exch def\n" +
"        } % end if\n" +
"        {pop pop}\n" +
"        ifelse\n" +
"\n" +
"        xsize % desired size of character in points\n" +
"        tc CharBoxWidth  \n" +
"        dup 0.0 ne {\n" +
"          div % factor by which to scale up the character\n" +
"          \/xmulfactor exch def\n" +
"        } % end if\n" +
"        {pop pop}\n" +
"        ifelse\n" +
"      grestore\n" +
"      % if the multiplication factors get too small we need to avoid a crash\n" +
"      xmulfactor limmulfactor lt {\n" +
"        \/xmulfactor 1 def\n" +
"        \/drawable false def\n" +
"      } if\n" +
"      ymulfactor limmulfactor lt {\n" +
"        \/ymulfactor 1 def\n" +
"        \/drawable false def\n" +
"      } if\n" +
"    } repeat\n" +
"\n" +
"    % Adjust horizontal position if the symbol is an I\n" +
"    tc (I) eq {\n" +
"      charWidth 2 div % half of requested character width\n" +
"      tc CharBoxWidth 2 div % half of the actual character\n" +
"      sub 0 translate\n" +
"      % Avoid x scaling for I \n" +
"      \/xmulfactor 1 def \n" +
"    } if\n" +
"\n" +
"\n" +
"    % ---- Finally, draw the character\n" +
"    drawable { \n" +
"      newpath\n" +
"      xmulfactor ymulfactor scale\n" +
"\n" +
"      % Move lower left corner of character to start point\n" +
"      tc CharBox pop pop % llx lly : Lower left corner\n" +
"      exch neg exch neg\n" +
"      moveto\n" +
"\n" +
"      outline {  % outline characters:\n" +
"        outlinewidth setlinewidth\n" +
"        tc true charpath\n" +
"        gsave 1 setgray fill grestore\n" +
"        clip stroke\n" +
"      } { % regular characters\n" +
"        tc show\n" +
"      } ifelse\n" +
"    } if\n" +
"\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"\/ShowBox { % x1 y1 x2 y2 filled ShowBox\n" +
"  gsave\n" +
"    \/filled exch def \n" +
"    \/y2 exch def\n" +
"    \/x2 exch def\n" +
"    \/y1 exch def\n" +
"    \/x1 exch def\n" +
"    newpath\n" +
"    x1 y1 moveto\n" +
"    x2 y1 lineto\n" +
"    x2 y2 lineto\n" +
"    x1 y2 lineto\n" +
"    closepath\n" +
"\n" +
"    clip\n" +
"    \n" +
"    filled {\n" +
"      fill\n" +
"    }{ \n" +
"      0 setgray stroke   \n" +
"    } ifelse\n" +
"\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"\/MakeNumber { % number MakeNumber\n" +
"  gsave\n" +
"    SetNumberFont\n" +
"    stackWidth 0 translate\n" +
"    90 rotate % rotate so the number fits\n" +
"    dup stringwidth pop % find the length of the number\n" +
"    neg % prepare for move\n" +
"    stackMargin sub % Move back a bit\n" +
"    charWidth (0) CharBoxHeight % height of numbers\n" +
"    sub 2 div %\n" +
"    moveto % move back to provide space\n" +
"    show\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"\/Ibeam{ % heightInBits Ibeam\n" +
"  gsave\n" +
"    % Make an Ibeam of twice the given height in bits\n" +
"    \/height exch  pointsPerBit mul def \n" +
"    \/heightDRAW height IbeamFraction mul def\n" +
"\n" +
"    IbeamLineWidth setlinewidth\n" +
"    IbeamGray setgray \n" +
"\n" +
"    charWidth2 height neg translate\n" +
"    ShowIbar\n" +
"    newpath\n" +
"      0 0 moveto\n" +
"      0 heightDRAW rlineto\n" +
"    stroke\n" +
"    newpath\n" +
"      0 height moveto\n" +
"      0 height rmoveto\n" +
"      currentpoint translate\n" +
"    ShowIbar\n" +
"    newpath\n" +
"    0 0 moveto\n" +
"    0 heightDRAW neg rlineto\n" +
"    currentpoint translate\n" +
"    stroke\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"\/ShowIbar { % make a horizontal bar\n" +
"  gsave\n" +
"    newpath\n" +
"      charWidth4 neg 0 moveto\n" +
"      charWidth4 0 lineto\n" +
"    stroke\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"\/ShowLeftEnd {\n" +
"  gsave\n" +
"    SetStringFont\n" +
"    leftEndDeltaX leftEndDeltaY moveto\n" +
"    logoType (NA) eq {(5) show ShowPrime} if\n" +
"    logoType (AA) eq {(N) show} if\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"\/ShowRightEnd { \n" +
"  gsave\n" +
"    SetStringFont\n" +
"    rightEndDeltaX rightEndDeltaY moveto\n" +
"    logoType (NA) eq {(3) show ShowPrime} if\n" +
"    logoType (AA) eq {(C) show} if\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"\/ShowPrime {\n" +
"  gsave\n" +
"    SetPrimeFont\n" +
"    (\\242) show \n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
" \n" +
"\/SetColor{ % <char> SetColor\n" +
"  dup colorDict exch known {\n" +
"    colorDict exch get aload pop setrgbcolor\n" +
"  } {\n" +
"    pop\n" +
"    defaultColor aload pop setrgbcolor\n" +
"  } ifelse \n" +
"} bind def\n" +
"\n" +
"% define fonts\n" +
"\/SetTitleFont {\/Times-Bold findfont titleFontsize scalefont setfont} bind def\n" +
"\/SetLogoFont  {\/Helvetica-Bold findfont charWidth  scalefont setfont} bind def\n" +
"\/SetStringFont{\/Helvetica-Bold findfont fontsize scalefont setfont} bind def\n" +
"\/SetPrimeFont {\/Symbol findfont fontsize scalefont setfont} bind def\n" +
"\/SetSmallFont {\/Helvetica findfont smallFontsize scalefont setfont} bind def\n" +
"\n" +
"\/SetNumberFont {\n" +
"    \/Helvetica-Bold findfont \n" +
"    numberFontsize\n" +
"    scalefont\n" +
"    setfont\n" +
"} bind def\n" +
"\n" +
"%Take a single character and return the bounding box\n" +
"\/CharBox { % <char> CharBox <lx> <ly> <ux> <uy>\n" +
"  gsave\n" +
"    newpath\n" +
"    0 0 moveto\n" +
"    % take the character off the stack and use it here:\n" +
"    true charpath \n" +
"    flattenpath \n" +
"    pathbbox % compute bounding box of 1 pt. char => lx ly ux uy\n" +
"    % the path is here, but toss it away ...\n" +
"  grestore\n" +
"} bind def\n" +
"\n" +
"\n" +
"% The height of a characters bounding box\n" +
"\/CharBoxHeight { % <char> CharBoxHeight <num>\n" +
"  CharBox\n" +
"  exch pop sub neg exch pop\n" +
"} bind def\n" +
"\n" +
"\n" +
"% The width of a characters bounding box\n" +
"\/CharBoxWidth { % <char> CharBoxHeight <num>\n" +
"  CharBox\n" +
"  pop exch pop sub neg \n" +
"} bind def\n" +
"\n" +
"% Set the colour scheme to be faded to indicate trimming\n" +
"\/MuteColour {\n" +
"  \/colorDict mutedColourDict def\n" +
"} def\n" +
"\n" +
"% Restore the colour scheme to the normal colours\n" +
"\/RestoreColour {\n" +
"  \/colorDict fullColourDict def\n" +
"} def\n" +
"\n" +
"% Draw the background for a trimmed section\n" +
"% takes the number of columns as a parameter\n" +
"\/DrawTrimBg { % <num> DrawTrimBox\n" +
"  \/col exch def\n" +
"  \n" +
"  \/boxwidth \n" +
"    col stackWidth mul \n" +
"  def\n" +
" \n" +
"  gsave\n" +
"    0.97 setgray\n" +
"\n" +
"    newpath\n" +
"    0 0 moveto\n" +
"    boxwidth 0 rlineto\n" +
"    0 yaxisHeight rlineto\n" +
"    0 yaxisHeight lineto\n" +
"    closepath\n" +
"    \n" +
"    fill\n" +
"  grestore\n" +
"} def\n" +
"\n" +
"\/DrawTrimEdge {\n" +
"  gsave\n" +
"    0.2 setgray\n" +
"    [2] 0 setdash\n" +
"\n" +
"    newpath\n" +
"    0 0 moveto\n" +
"    0 yaxisHeight lineto\n" +
"    \n" +
"    stroke\n" +
"\n" +
"} def\n" +
"\n" +
"\n" +
"% Deprecated names\n" +
"\/startstack {StartStack} bind  def\n" +
"\/endstack {EndStack}     bind def\n" +
"\/makenumber {MakeNumber} bind def\n" +
"\/numchar { MakeSymbol }  bind def\n" +
"\n" +
"%%EndProlog\n" +
"\n" +
"%%Page: 1 1\n" +
"StartLogo\n" +
"\n" +
_input("DATA") + "\n" +
"\n" +
"EndLogo\n" +
"\n" +
"%%EOF\n"
  );
}</script>
    <script>
//======================================================================
// start Alphabet object
//======================================================================
var Alphabet = function(alphabet, background) {
  "use strict";
  var i, j, sym, aliases, complement, comp_e_sym, ambigs, generate_background;
  generate_background = (background == null);
  if (generate_background) {
    background = [];
    for (i = 0; i < alphabet.ncore; i++) background[i] = 1.0 / alphabet.ncore;
  } else if (alphabet.ncore != background.length) {
    throw new Error("The background length does not match the alphabet length.");
  }
  this.name = alphabet.name;
  this.like = (alphabet.like != null ? alphabet.like.toUpperCase() : null);
  this.ncore = alphabet.ncore;
  this.symbols = alphabet.symbols;
  this.background = background;
  this.genbg = generate_background;
  this.encode = {};
  this.encode2core = {};
  this.complement = {};
  // check if all symbols are same case
  var seen_uc = false;
  var seen_lc = false;
  var check_case = function (syms) {
    var s, sym;
    if (typeof syms === "string") {
      for (s = 0; s < syms.length; s++) {
        sym = syms.charAt(s);
        if (sym >= 'a' && sym <= 'z') seen_lc = true;
        else if (sym >= 'A' && sym <= 'Z') seen_uc = true;
      }
    }
  };
  for (i = 0; i < this.symbols.length; i++) {
    check_case(this.symbols[i].symbol);
    check_case(this.symbols[i].aliases);
  }
  // now map symbols to indexes
  var update_array = function(array, syms, index) {
    var s, sym;
    if (typeof syms === "string") {
      for (s = 0; s < syms.length; s++) {
        sym = syms.charAt(s);
        array[sym] = index;
        // when only a single case is used, then encode as case insensitive
        if (seen_uc != seen_lc) {
          if (sym >= 'a' && sym <= 'z') {
            array[sym.toUpperCase()] = index;
          } else if (sym >= 'A' && sym <= 'Z') {
            array[sym.toLowerCase()] = index;
          }
        }
      }
    }
  }
  // map core symbols to index
  for (i = 0; i < this.ncore; i++) {
    update_array(this.encode2core, this.symbols[i].symbol, i);
    update_array(this.encode, this.symbols[i].symbol, i);
    update_array(this.encode2core, this.symbols[i].aliases, i);
    update_array(this.encode, this.symbols[i].aliases, i);
  }
  // map ambigous symbols to index
  ambigs = {};
  for (i = this.ncore; i < this.symbols.length; i++) {
    update_array(this.encode, this.symbols[i].symbol, i);
    update_array(this.encode, this.symbols[i].aliases, i);
    ambigs[this.symbols[i].equals] = i;
  }
  // determine complements
  for (i = 0; i < this.ncore; i++) {
    complement = this.symbols[i].complement;
    if (typeof complement === "string") {
      this.complement[i] = this.encode2core[complement];
    }
  }
  next_symbol:
  for (i = this.ncore; i < this.symbols.length; i++) {
    complement = "";
    for (j = 0; j < this.symbols[i].equals.length; j++) {
      comp_e_sym = this.complement[this.encode2core[this.symbols[i].equals.charAt(j)]];
      if (typeof comp_e_sym !== "number") continue next_symbol;
      complement += this.symbols[comp_e_sym].symbol;
    }
    complement = complement.split("").sort().join("");
    if (typeof ambigs[complement] === "number") {
      this.complement[i] = ambigs[complement];
    }
  }
  // determine case insensitivity
  this.case_insensitive = true;
  if (seen_uc == seen_lc) {
    // when there is a mixture of cases it probably won't
    // be case insensitive but we still need to check
    loop:
    for (i = 0; i < this.symbols.length; i++) {
      sym = this.symbols[i].symbol;
      if (sym >= 'A' && sym <= 'Z') {
        if (this.encode[sym.toLowerCase()] != i) {
          this.case_insensitive = false;
          break loop;
        }
      } else if (sym >= 'a' && sym <= 'z') {
        if (this.encode[sym.toUpperCase()] != i) {
          this.case_insensitive = false;
          break loop;
        }
      }
      aliases = this.symbols[i].aliases;
      if (aliases != null) {
        for (j = 0; j < aliases.length; j++) {
          sym = aliases.charAt(j);
          if (sym >= 'A' && sym <= 'Z') {
            if (this.encode[sym.toLowerCase()] != i) {
              this.case_insensitive = false;
              break loop;
            }
          } else if (sym >= 'a' && sym <= 'z') {
            if (this.encode[sym.toUpperCase()] != i) {
              this.case_insensitive = false;
              break loop;
            }
          }
        }
      }
    }
  }
  // normalise aliases to remove the prime symbol and eliminate
  // the alternate cases when the alphabet is case insensitive
  var seen, out;
  for (i = 0; i < this.symbols.length; i++) {
    sym = this.symbols[i].symbol;
    aliases = this.symbols[i].aliases;
    if (typeof aliases != "string") aliases = "";
    seen = {};
    out = [];
    if (this.case_insensitive) {
      sym = sym.toUpperCase();
      aliases = aliases.toUpperCase();
    }
    seen[sym] = true;
    for (j = 0; j < aliases.length; j++) {
      if (!seen[aliases.charAt(j)]) {
        seen[aliases.charAt(j)] = true;
        out.push(aliases.charAt(j));
      }
    }
    this.symbols[i].aliases = out.sort().join("");
  }
};
// return the name of the alphabet
Alphabet.prototype.get_alphabet_name = function() {
  return this.name;
};
// return if the alphabet can be complemented
Alphabet.prototype.has_complement = function() {
  return (typeof this.symbols[0].complement === "string");
};
// return true if an uppercase letter has the same meaning as the lowercase form
Alphabet.prototype.is_case_insensitive = function() {
  return this.case_insensitive;
};
// return the information content of an alphabet letter
Alphabet.prototype.get_ic = function() {
  return Math.log(this.ncore) / Math.LN2;
};
// return the count of the core alphabet symbols
Alphabet.prototype.get_size_core = function() {
  return this.ncore;
};
// return the count of all alphabet symbols
Alphabet.prototype.get_size_full = function() {
  return this.symbols.length;
};
// return the symbol for the given alphabet index
Alphabet.prototype.get_symbol = function(alph_index) {
  "use strict";
  if (alph_index < 0 || alph_index >= this.symbols.length) {
    throw new Error("Alphabet index out of bounds");
  }
  return this.symbols[alph_index].symbol;
};
// return the aliases for the given alphabet index
Alphabet.prototype.get_aliases = function(alph_index) {
  "use strict";
  if (alph_index < 0 || alph_index >= this.symbols.length) {
    throw new Error("Alphabet index out of bounds");
  }
  var sym_obj = this.symbols[alph_index];
  return (sym_obj.aliases != null ? sym_obj.aliases : "");
};
// return the name for the given alphabet index
Alphabet.prototype.get_name = function(alph_index) {
  "use strict";
  var sym;
  if (alph_index < 0 || alph_index >= this.symbols.length) {
    throw new Error("Alphabet index out of bounds");
  }
  sym = this.symbols[alph_index];
  return (typeof sym.name === "string" ? sym.name : sym.symbol);
};
// return the alphabet it is like or null
Alphabet.prototype.get_like = function() {
  "use strict";
  return this.like;
};
// return the index of the complement for the given alphabet index
Alphabet.prototype.get_complement = function(alph_index) {
  var comp_e_sym = this.complement[alph_index];
  if (typeof comp_e_sym === "number") {
    return comp_e_sym;
  } else {
    return -1;
  }
};
// return a string containing the core symbols
Alphabet.prototype.get_symbols = function() {
  "use strict";
  var i, core_symbols;
  core_symbols = "";
  for (i = 0; i < this.ncore; i++) {
    core_symbols += this.symbols[i].symbol;
  }
  return core_symbols;
};
// return if the background was not a uniform generated background
Alphabet.prototype.has_bg = function() {
  "use strict";
  return !this.genbg;
};
// get the background frequency for the index
Alphabet.prototype.get_bg_freq = function(alph_index) {
  "use strict";
  var freq, i, symbols;
  if (alph_index >= 0) {
    if (alph_index < this.ncore) {
      return this.background[alph_index];
    } else if (alph_index < this.symbols.length) {
      freq = 0;
      symbols = this.symbols[alph_index].equals;
      for (i = 0; i < symbols.length; i++) {
        freq += this.background[this.encode2core[symbols.charAt(i)]];
      }
      return freq;
    } 
  }
  throw new Error("The alphabet index is out of range.");
};
// get the colour of the index
Alphabet.prototype.get_colour = function(alph_index) {
  "use strict";
  if (alph_index < 0 || alph_index >= this.symbols.length) {
    throw new Error("BAD_ALPHABET_INDEX");
  }
  if (typeof this.symbols[alph_index].colour != "string") {
    return "black";
  }
  return "#" + this.symbols[alph_index].colour;
};
// get the rgb componets of the colour at the index
Alphabet.prototype.get_rgb = function(alph_index) {
  "use strict";
  if (alph_index < 0 || alph_index >= this.symbols.length) {
    throw new Error("BAD_ALPHABET_INDEX");
  }
  if (typeof this.symbols[alph_index].colour != "string") {
    return {"red": 0, "green": 0, "blue": 0};
  }
  var colour = this.symbols[alph_index].colour;
  var red = parseInt(colour.substr(0, 2), 16) / 255;
  var green = parseInt(colour.substr(2, 2), 16) / 255;
  var blue = parseInt(colour.substr(4, 2), 16) / 255;
  return {"red": red, "green": green, "blue": blue};
};
// convert a symbol into the index
Alphabet.prototype.get_index = function(letter) {
  "use strict";
  var alph_index;
  alph_index = this.encode[letter];
  if (typeof alph_index === "undefined") {
    return -1;
  }
  return alph_index;
};
// convert a symbol into the list of core indexes that it equals
Alphabet.prototype.get_indexes = function(letter) {
  "use strict";
  var alph_index, comprise_str, i, comprise_list;
  alph_index = this.encode[letter];
  if (typeof alph_index === "undefined") {
    throw new Error("Unknown letter");
  }
  comprise_str = this.symbols[alph_index].equals;
  comprise_list = [];
  if (typeof comprise_str == "string") {
    for (i = 0; i < comprise_str.length; i++) {
      comprise_list.push(this.encode2core[comprise_str.charAt(i)]);
    }
  } else {
    comprise_list.push(alph_index);
  }
  return comprise_list;
};
// check if a symbol is the primary way of representing the symbol in the alphabet
Alphabet.prototype.is_prime_symbol = function(letter) {
  var alph_index;
  alph_index = this.encode[letter];
  if (alph_index == null) return false;
  if (this.is_case_insensitive()) {
    return (this.symbols[alph_index].symbol.toUpperCase() == letter.toUpperCase());
  } else {
    return (this.symbols[alph_index].symbol == letter);
  }
};
// compare 2 alphabets
Alphabet.prototype.equals = function(other) {
  "use strict";
  var i, sym1, sym2;
  // first check that it's actually an alphabet object
  if (!(typeof other === "object" && other != null && other instanceof Alphabet)) {
    return false;
  }
  // second shortcircuit if it's the same object
  if (this === other) return true;
  // compare
  if (this.name !== other.name) return false;
  if (this.ncore !== other.ncore) return false;
  if (this.symbols.length !== other.symbols.length) return false;
  for (i = 0; i < this.symbols.length; i++) {
    sym1 = this.symbols[i];
    sym2 = other.symbols[i];
    if (sym1.symbol !== sym2.symbol) return false;
    if (sym1.aliases !== sym2.aliases) return false;
    if (sym1.name !== sym2.name) return false;
    if (typeof sym1.colour !== typeof sym2.colour || 
        (typeof sym1.colour === "string" && typeof sym2.colour === "string" &&
         parseInt(sym1.colour, 16) != parseInt(sym2.colour, 16))) {
      return false;
    }
    if (sym1.complement !== sym2.complement) return false;
    if (sym1.equals !== sym2.equals) return false;
  }
  return true;
};
Alphabet.prototype.check_core_subset = function(super_alph) {
  var complement_same = true;
  var seen_set = {};
  var sub_i, sub_symbol, super_i, super_symbol;
  for (sub_i = 0; sub_i < this.ncore; sub_i++) {
    sub_symbol = this.symbols[sub_i];
    super_i = super_alph.encode[sub_symbol.symbol]; 
    if (super_i == null) return 0;
    super_symbol = super_alph.symbols[super_i];
    if (seen_set[super_i]) return 0;
    seen_set[super_i] = true;
    // check complement
    if (sub_symbol.complement != null && super_symbol.complement != null) {
      if (super_alph.encode[sub_symbol.complement] != super_alph.encode[super_symbol.complement]) {
        complement_same = false;
      }
    } else if (sub_symbol.complement != null || super_symbol.complement != null) {
      complement_same = false;
    }
  }
  return (complement_same ? 1 : -1);
};
// convert a sequence to its reverse complement
Alphabet.prototype.invcomp_seq = function(seq) {
  "use strict";
  var syms, i, e_sym, comp_e_sym;
  if (!this.has_complement()) throw new Error("Alphabet must be complementable");
  syms = seq.split("");
  for (i = 0; i < syms.length; i++) {
    e_sym = this.encode[syms[i]];
    if (typeof e_sym === "undefined") {
      e_sym = this.ncore; // wildcard
    }
    comp_e_sym = this.complement[e_sym];
    if (typeof comp_e_sym === "undefined") {
      comp_e_sym = e_sym; // not complementable
    }
    syms[i] = this.symbols[comp_e_sym].symbol;
  }
  return syms.reverse().join("");
};
// convert the alphabet to the text version
Alphabet.prototype.as_text = function() {
  "use strict";
  function name_as_text(name) {
    var i, c, out;
    out = "\"";
    for (i = 0; i < name.length; i++) {
      c = name.charAt(i);
      if (c == "\"") {
        out += "\\\"";
      } else if (c == "/") {
        out += "\\/";
      } else if (c == "\\") {
        out += "\\\\";
      } else {
        out += c;
      }
    }
    out += "\"";
    return out;
  }
  function symbol_as_text(sym) {
    var out;
    out = sym.symbol;
    if (typeof sym.name === "string" && sym.name != sym.symbol) {
      out += " " + name_as_text(sym.name);
    }
    if (typeof sym.colour === "string") {
      out += " " + sym.colour;
    }
    return out;
  }
  var out, i, j, c, sym;
  out = "";
  // output core symbols with 2 way complements
  for (i = 0; i < this.ncore; i++) {
    c = this.complement[i];
    if (typeof c === "number" && i < c && this.complement[c] === i) {
      out += symbol_as_text(this.symbols[i]) + " ~ " + symbol_as_text(this.symbols[c]) + "\n";  
    }
  }
  // output core symbols with no complement
  for (i = 0; i < this.ncore; i++) {
    if (typeof this.complement[i] === "undefined") {
      out += symbol_as_text(this.symbols[i]) + "\n";
    }
  }
  // output ambiguous symbols that have comprising characters
  for (i = this.ncore; i < this.symbols.length; i++) {
    if (this.symbols[i].equals.length == 0) break;
    out += symbol_as_text(this.symbols[i]) + " = " + this.symbols[i].equals + "\n";
    if (typeof this.symbols[i].aliases === "string") {
      for (j = 0; j < this.symbols[i].aliases.length; j++) {
        if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue;
        out += this.symbols[i].aliases.charAt(j) + " = " + this.symbols[i].equals + "\n";
      }
    }
  }
  // output aliases of core symbols
  for (i = 0; i < this.ncore; i++) {
    if (typeof this.symbols[i].aliases === "string") {
      for (j = 0; j < this.symbols[i].aliases.length; j++) {
        if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue;
        out += this.symbols[i].aliases.charAt(j) + " = " + this.symbols[i].symbol + "\n";
      }
    }
  }
  // output gap symbols
  i = this.symbols.length - 1;
  if (this.symbols[i].equals.length == 0) {
    out += symbol_as_text(this.symbols[i]) + " =\n";
    if (typeof this.symbols[i].aliases === "string") {
      for (j = 0; j < this.symbols[i].aliases.length; j++) {
        if (this.symbols[i].aliases.charAt(j) == this.symbols[i].symbol) continue;
        out += this.symbols[i].aliases.charAt(j) + " =\n";
      }
    }
  }
  return out;
};
// output the alphabet as it appears in minimal MEME format
Alphabet.prototype.as_meme = function() {
  "use strict";
  function name_as_text(name) {
    var i, c, out;
    out = "\"";
    for (i = 0; i < name.length; i++) {
      c = name.charAt(i);
      if (c == "\"") {
        out += "\\\"";
      } else if (c == "/") {
        out += "\\/";
      } else if (c == "\\") {
        out += "\\\\";
      } else {
        out += c;
      }
    }
    out += "\"";
    return out;
  }
  if (this.equals(AlphStd.DNA)) {
    return "ALPHABET= ACGT\n";
  } else if (this.equals(AlphStd.PROTEIN)) {
    return "ALPHABET= ACDEFGHIKLMNPQRSTVWY\n";
  } else {
    return "ALPHABET" + 
      (this.name != null ? " " + name_as_text(this.name) : "") + 
      (this.like != null ? " " + this.like + "-LIKE" : "") + "\n" +
      this.as_text() + "END ALPHABET\n";
  }
};

// Returns a table showing all the letters in the alphabet
Alphabet.prototype.as_table = function() {
  "use strict";
  var i, j, row, th, td, aliases, equals, sym;
  var table = document.createElement("table");
  // create the core symbol header
  row = table.insertRow(table.rows.length);
  th = document.createElement("th");
  th.appendChild(document.createTextNode("Symbol(s)"));
  row.appendChild(th);
  th = document.createElement("th");
  th.appendChild(document.createTextNode("Name"));
  row.appendChild(th);
  th = document.createElement("th");
  if (this.has_complement()) {
    th.appendChild(document.createTextNode("Complement"));
  }
  row.appendChild(th);
  // list the core symbols
  for (i = 0; i < this.ncore; i++) {
    row = table.insertRow(table.rows.length);
    td = document.createElement("td");
    if (this.symbols[i].colour != null) {
      td.style.color = '#' + this.symbols[i].colour;
    }
    td.appendChild(document.createTextNode(this.symbols[i].symbol));
    aliases = this.get_aliases(i);
    if (aliases.length > 0) {
      td.appendChild(document.createTextNode(' ' + aliases.split('').join(' ')));
    }
    row.appendChild(td);
    td = document.createElement("td");
    if (this.symbols[i].name != null) {
      td.appendChild(document.createTextNode(this.symbols[i].name));
    }
    row.appendChild(td);
    td = document.createElement("td");
    if (this.symbols[i].complement != null) {
      td.style.color = this.get_colour(this.get_index(this.symbols[i].complement));
      td.appendChild(document.createTextNode(this.symbols[i].complement));
    }
    row.appendChild(td);
  }
  // create the ambiguous symbol header
  row = table.insertRow(table.rows.length);
  th = document.createElement("th");
  th.appendChild(document.createTextNode("Symbol(s)"));
  row.appendChild(th);
  th = document.createElement("th");
  th.appendChild(document.createTextNode("Name"));
  row.appendChild(th);
  th = document.createElement("th");
  th.appendChild(document.createTextNode("Matches"));
  row.appendChild(th);
  // list the ambiguous symbols
  for (i = this.ncore; i < this.symbols.length; i++) {
    row = table.insertRow(table.rows.length);
    td = document.createElement("td");
    if (this.symbols[i].colour != null) {
      td.style.color = '#' + this.symbols[i].colour;
    }
    td.appendChild(document.createTextNode(this.symbols[i].symbol));
    aliases = this.get_aliases(i);
    if (aliases.length > 0) {
      td.appendChild(document.createTextNode(' ' + aliases.split('').join(' ')));
    }
    row.appendChild(td);
    td = document.createElement("td");
    if (this.symbols[i].name != null) {
      td.appendChild(document.createTextNode(this.symbols[i].name));
    }
    row.appendChild(td);
    td = document.createElement("td");
    equals = this.symbols[i].equals.split('');
    for (j = 0; j < equals.length; j++) {
      if (j != 0) td.appendChild(document.createTextNode(' '));
      sym = document.createElement("span");
      sym.style.color = this.get_colour(this.get_index(equals[j]));
      sym.appendChild(document.createTextNode(equals[j]));
      td.appendChild(sym);
    }
    row.appendChild(td);
  }
  return table;
};

// returns a dictionary of the colours for EPS
Alphabet.prototype._as_eps_dict = function() {
  "use strict";
  var i, sym, rgb;
  var out = "/fullColourDict <<\n";
  for (i = 0; i < this.ncore; i++) {
    sym = this.get_symbol(i);
    sym = sym.replace(/\\/g, "\\\\");
    sym = sym.replace(/\(/g, "\\(");
    sym = sym.replace(/\)/g, "\\)");
    rgb = this.get_rgb(i);
    out += " (" + sym + ") [" + rgb.red.toFixed(4) + " " + rgb.green.toFixed(4) + " " + rgb.blue.toFixed(4) + "]\n";
  }
  out += ">> def\n";
  out += "/mutedColourDict <<\n";
  for (i = 0; i < this.ncore; i++) {
    sym = this.get_symbol(i);
    sym = sym.replace(/\\/g, "\\\\");
    sym = sym.replace(/\(/g, "\\(");
    sym = sym.replace(/\)/g, "\\)");
    rgb = Alphabet.lighten_colour(this.get_rgb(i));
    out += " (" + sym + ") [" + rgb.red.toFixed(4) + " " + rgb.green.toFixed(4) + " " + rgb.blue.toFixed(4) + "]\n";
  }
  out += ">> def\n";
  return out;
};

// return the alphabet name or a list of primary symbols
Alphabet.prototype.toString = function() {
  "use strict";
  if (this.name != null) {
    return this.name;
  } else {
    return this.get_symbols();
  }
};

//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
// Helper functions
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

// Convert a colour specified in RGB colourspace values into LAB colourspace
Alphabet.rgb2lab = function(rgb) {
  "use strict";
  var xyzHelper, labHelper;
  // XYZ helper
  xyzHelper = function(value) {
    if (value > 0.0445) {
      value = (value + 0.055) / 1.055;
      value = Math.pow(value, 2.4);
    } else {
      value /= 12.92;
    }
    value *= 100;
    return value;
  };
  // lab helper
  labHelper = function(value) {
    if (value > 0.008856) {
      value = Math.pow(value, 1.0 / 3.0);
    } else {
      value = (7.787 * value) + (16.0 / 116.0);
    }
    return value;
  };
  // convert into XYZ colourspace
  var c1, c2, c3;
  if (typeof rgb == "number") {
    c1 = xyzHelper(((rgb >> 16) & 0xFF) / 255.0);
    c2 = xyzHelper(((rgb >> 8) & 0xFF) / 255.0);
    c3 = xyzHelper((rgb & 0xFF) / 255.0);
  } else {
    c1 = xyzHelper(rgb.red);
    c2 = xyzHelper(rgb.green);
    c3 = xyzHelper(rgb.blue);
  }
  var x = (c1 * 0.4124) + (c2 * 0.3576) + (c3 * 0.1805);
  var y = (c1 * 0.2126) + (c2 * 0.7152) + (c3 * 0.0722);
  var z = (c1 * 0.0193) + (c2 * 0.1192) + (c3 * 0.9505);
  // convert into Lab colourspace
  c1 = labHelper(x / 95.047);
  c2 = labHelper(y / 100.0);
  c3 = labHelper(z / 108.883);
  var l = (116.0 * c2) - 16;
  var a = 500.0 * (c1 - c2);
  var b = 200.0 * (c2 - c3);
  return {"l": l, "a": a, "b": b};
};

// Convert a colour specified in HSV colourspace into RGB colourspace
Alphabet.hsv2rgb = function(hue, sat, value, output_object) {
  // achromatic (grey)
  var r = value;
  var g = value;
  var b = value;
  if (sat != 0) {
    var h = hue / 60.0;
    var i = Math.floor(h);
    var f = h - i;
    var p = value * (1.0 - sat);
    var q = value * (1.0 - (sat * f));
    var t = value * (1.0 - (sat * (1.0 - f)));
    if (i == 0) {
      r = value;
      g = t;
      b = p;
    } else if (i == 1) {
      r = q;
      g = value;
      b = p;
    } else if (i == 2) {
      r = p;
      g = value;
      b = t;
    } else if (i == 3) {
      r = p;
      g = q;
      b = value;
    } else if (i == 4) {
      r = t;
      g = p;
      b = value;
    } else {
      r = value;
      g = p;
      b = q;
    }
  }
  if (output_object) {
    return {"red": r, "green": g, "blue": b};
  } else {
    return (Math.floor(r * 255) << 15) | (Math.floor(g * 255) << 8) | (Math.floor(b * 255));
  }
};

// Calculate a distance score between two colours in LAB colourspace
Alphabet.lab_dist = function(lab1, lab2) {
  var c1 = Math.sqrt((lab1.l * lab1.l) + (lab1.a * lab1.a));
  var c2 = Math.sqrt((lab2.l * lab2.l) + (lab2.a * lab2.a));
  var dc = c1 - c2;
  var dl = lab1.l - lab2.l;
  var da = lab1.a - lab2.a;
  var db = lab1.b - lab2.b;
  // we don't want NaN due to rounding errors so fudge things a bit...
  var dh = 0;
  var dh_squared = (da * da) + (db * db) - (dc * dc);
  if (dh_squared > 0) {
    dh = Math.sqrt(dh_squared);
  }
  var first = dl;
  var second = dc / (1.0 + (0.045 * c1));
  var third = dh / (1.0 + (0.015 * c1));
  return Math.sqrt((first * first) + (second * second) + (third * third));
};

// convert an RGB value into a HSL value
Alphabet.rgb2hsl = function(rgb) {
  "use strict";
  var min, max, delta, h, s, l, r, g, b;
  if (typeof rgb == "number") {
    r = ((rgb >> 16) & 0xFF) / 255.0;
    g = ((rgb >> 8) & 0xFF) / 255.0;
    b = (rgb & 0xFF) / 255.0;
  } else {
    r = rgb.red;
    g = rgb.green;
    b = rgb.blue;
  }
  min = Math.min(r, g, b);
  max = Math.max(r, g, b);
  delta = max - min;
  l = min + (delta / 2);
  if (max == min) {
    h = 0; // achromatic (grayscale)
    s = 0;
  } else {
    if (l > 0.5) {
      s = delta / (2 - max - min);
    } else {
      s = delta / (max + min);
    }
    if (max == r) {
      h = (g - b) / delta;
      if (g < b) h += 6;
    } else if (max == g) {
      h = ((b - r) / delta) + 2;
    } else {
      h = ((r - g) / delta) + 4;
    }
    h /= 6;
  }
  return {"h": h, "s": s, "l": l};
};

// convert a HSL value into an RGB value
Alphabet.hsl2rgb = function(hsl, output_object) {
  "use strict";
  function _hue(p, q, t) {
    "use strict";
    if (t < 0) t += 1;
    else if (t > 1) t -= 1;
    if (t < (1.0 / 6.0)) {
      return p + ((q - p) * 6.0 * t);
    } else if (t < 0.5) {
      return q;
    } else if (t < (2.0 / 3.0)) {
      return p + ((q - p) * ((2.0 / 3.0) - t) * 6.0);
    } else {
      return p;
    }
  }
  var r, g, b, p, q;
  if (hsl.s == 0) {
    // achromatic (grayscale)
    r = hsl.l;
    g = hsl.l;
    b = hsl.l;
  } else {
    if (hsl.l < 0.5) {
      q = hsl.l * (1 + hsl.s);
    } else {
      q = hsl.l + hsl.s - (hsl.l * hsl.s);
    }
    p = (2 * hsl.l) - q;
    r = _hue(p, q, hsl.h + (1.0 / 3.0));
    g = _hue(p, q, hsl.h);
    b = _hue(p, q, hsl.h - (1.0 / 3.0));
  }
  if (output_object) {
    return {"red": r, "green": g, "blue": b};
  } else {
    return (Math.floor(r * 255) << 15) | (Math.floor(g * 255) << 8) | (Math.floor(b * 255));
  }
};

Alphabet.lighten_colour = function(rgb) {
  "use strict";
  var hsl = Alphabet.rgb2hsl(rgb);
  hsl.l += (1.0 - hsl.l) * 2 / 3;
  return Alphabet.hsl2rgb(hsl, typeof rgb != "number");
};

//======================================================================
// end Alphabet object
//======================================================================

//======================================================================
// start StandardAlphabet object
//======================================================================

// an extension of the alphabet object to support some additional fields 
// only present in standard alphabets.
var StandardAlphabet = function(enum_code, enum_name, alphabet_data) {
  Alphabet.apply(this, [alphabet_data]);
  this.enum_code = enum_code;
  this.enum_name = enum_name;
};
StandardAlphabet.prototype = Alphabet.prototype;
StandardAlphabet.prototype.constructor = StandardAlphabet;

// A unique code for this standard alphabet.
// This code will be a power of 2 to enable creation of bitsets for
// a selection of standard alphabets.
StandardAlphabet.prototype.get_code = function() {
  return this.enum_code;
};

// A unique name for this standard alphabet.
// this name will be all upper case and the same as the property that
// refers to this alphabet in the AlphStd collection.
StandardAlphabet.prototype.get_enum = function() {
  return this.enum_name;
};

//======================================================================
// end StandardAlphabet object
//======================================================================

// A collection of standard alphabets.
var AlphStd = {
  RNA: new StandardAlphabet(1, "RNA", {
    "name": "RNA",
    "like": "RNA",
    "ncore": 4,
    "symbols": [
      {"symbol": "A", "name": "Adenine", "colour": "CC0000"},
      {"symbol": "C", "name": "Cytosine", "colour": "0000CC"},
      {"symbol": "G", "name": "Guanine", "colour": "FFB300"},
      {"symbol": "U", "name": "Uracil", "colour": "008000",
        "aliases": "T"},
      {"symbol": "N", "name": "Any base", "equals": "ACGU", "aliases": "X."},
      {"symbol": "V", "name": "Not U", "equals": "ACG"},
      {"symbol": "H", "name": "Not G", "equals": "ACU"},
      {"symbol": "D", "name": "Not C", "equals": "AGU"},
      {"symbol": "B", "name": "Not A", "equals": "CGU"},
      {"symbol": "M", "name": "Amino", "equals": "AC"},
      {"symbol": "R", "name": "Purine", "equals": "AG"},
      {"symbol": "W", "name": "Weak", "equals": "AU"}, 
      {"symbol": "S", "name": "Strong", "equals": "CG"},
      {"symbol": "Y", "name": "Pyrimidine", "equals": "CU"},
      {"symbol": "K", "name": "Keto", "equals": "GU"}
    ]
  }), 
  DNA: new StandardAlphabet(2, "DNA", {
    "name": "DNA",
    "like": "DNA",
    "ncore": 4,
    "symbols": [
      {"symbol": "A", "name": "Adenine", "colour": "CC0000", "complement": "T"},
      {"symbol": "C", "name": "Cytosine", "colour": "0000CC", "complement": "G"},
      {"symbol": "G", "name": "Guanine", "colour": "FFB300", "complement": "C"},
      {"symbol": "T", "name": "Thymine", "colour": "008000", "complement": "A",
        "aliases": "U"},
      {"symbol": "N", "name": "Any base", "equals": "ACGT", "aliases": "X."},
      {"symbol": "V", "name": "Not T", "equals": "ACG"},
      {"symbol": "H", "name": "Not G", "equals": "ACT"},
      {"symbol": "D", "name": "Not C", "equals": "AGT"},
      {"symbol": "B", "name": "Not A", "equals": "CGT"},
      {"symbol": "M", "name": "Amino", "equals": "AC"},
      {"symbol": "R", "name": "Purine", "equals": "AG"},
      {"symbol": "W", "name": "Weak", "equals": "AT"}, 
      {"symbol": "S", "name": "Strong", "equals": "CG"},
      {"symbol": "Y", "name": "Pyrimidine", "equals": "CT"},
      {"symbol": "K", "name": "Keto", "equals": "GT"}
    ]
  }), 
  PROTEIN: new StandardAlphabet(4, "PROTEIN", {
    "name": "Protein",
    "like": "PROTEIN",
    "ncore": 20,
    "symbols": [
      {"symbol": "A", "name": "Alanine", "colour": "0000CC"},
      {"symbol": "C", "name": "Cysteine", "colour": "0000CC"},
      {"symbol": "D", "name": "Aspartic acid", "colour": "FF00FF"},
      {"symbol": "E", "name": "Glutamic acid", "colour": "FF00FF"},
      {"symbol": "F", "name": "Phenylalanine", "colour": "0000CC"},
      {"symbol": "G", "name": "Glycine", "colour": "FFB300"},
      {"symbol": "H", "name": "Histidine", "colour": "FFCCCC"},
      {"symbol": "I", "name": "Isoleucine", "colour": "0000CC"},
      {"symbol": "K", "name": "Lysine", "colour": "CC0000"},
      {"symbol": "L", "name": "Leucine", "colour": "0000CC"},
      {"symbol": "M", "name": "Methionine", "colour": "0000CC"},
      {"symbol": "N", "name": "Asparagine", "colour": "008000"},
      {"symbol": "P", "name": "Proline", "colour": "FFFF00"},
      {"symbol": "Q", "name": "Glutamine", "colour": "008000"},
      {"symbol": "R", "name": "Arginine", "colour": "CC0000"},
      {"symbol": "S", "name": "Serine", "colour": "008000"},
      {"symbol": "T", "name": "Threonine", "colour": "008000"},
      {"symbol": "V", "name": "Valine", "colour": "0000CC"},
      {"symbol": "W", "name": "Tryptophan", "colour": "0000CC"},
      {"symbol": "Y", "name": "Tyrosine", "colour": "33E6CC"},
      {"symbol": "X", "name": "Any amino acid", "equals": "ACDEFGHIKLMNPQRSTVWY", "aliases": "*."},
      {"symbol": "B", "name": "Asparagine or Aspartic acid", "equals": "DN"}, 
      {"symbol": "Z", "name": "Glutamine or Glutamic acid", "equals": "EQ"}, 
      {"symbol": "J", "name": "Leucine or Isoleucine", "equals": "IL"}
    ]
  })
};

//======================================================================
// start Symbol object
//======================================================================
var Symbol = function(alph_index, scale, alphabet) {
  "use strict";
  //variable prototype
  this.symbol = alphabet.get_symbol(alph_index);
  this.scale = scale;
  this.colour = alphabet.get_colour(alph_index);
};

Symbol.prototype.get_symbol = function() {
  "use strict";
  return this.symbol;
};

Symbol.prototype.get_scale = function() {
  "use strict";
  return this.scale;
};

Symbol.prototype.get_colour = function() {
  "use strict";
  return this.colour;
};

Symbol.prototype.toString = function() {
  "use strict";
  return this.symbol + " " + (Math.round(this.scale*1000)/10) + "%";
};

function compare_symbol(sym1, sym2) {
  "use strict";
  if (sym1.get_scale() < sym2.get_scale()) {
    return -1;
  } else if (sym1.get_scale() > sym2.get_scale()) {
    return 1;
  } else {
    return 0;
  }
}
//======================================================================
// end Symbol object
//======================================================================

//======================================================================
// start Pspm object
//======================================================================
var Pspm = function(matrix, name, ltrim, rtrim, nsites, evalue, pssm, alt) {
  "use strict";
  var row, col, data, row_sum, delta, evalue_re;
  if (typeof name !== "string") {
    name = "";
  }
  this.name = name;
  //construct
  if (matrix instanceof Pspm) {
    // copy constructor
    this.alph_length = matrix.alph_length;
    this.motif_length = matrix.motif_length;
    this.name = matrix.name;
    this.alt = matrix.alt;
    this.nsites = matrix.nsites;
    this.evalue = matrix.evalue;
    this.ltrim = matrix.ltrim;
    this.rtrim = matrix.rtrim;
    this.pspm = [];
    for (row = 0; row < matrix.motif_length; row++) {
      this.pspm[row] = [];
      for (col = 0; col < matrix.alph_length; col++) {
        this.pspm[row][col] = matrix.pspm[row][col];
      }
    }
    if (matrix.pssm != null) {
      this.pssm = [];
      for (row = 0; row < matrix.motif_length; row++) {
        this.pspm[row] = [];
        for (col = 0; col < matrix.alph_length; col++) {
          this.pssm[row][col] = matrix.pssm[row][col];
        }
      }
    }
  } else {
    // check parameters
    if (ltrim == null) {
      ltrim = 0;
    } else if (typeof ltrim !== "number" || ltrim % 1 !== 0 || ltrim < 0) {
      throw new Error("ltrim must be a non-negative integer, got: " + ltrim);
    }
    if (rtrim == null) {
      rtrim = 0;
    } else if (typeof rtrim !== "number" || rtrim % 1 !== 0 || rtrim < 0) {
      throw new Error("rtrim must be a non-negative integer, got: " + rtrim);
    }
    if (nsites != null) {
      if (typeof nsites !== "number" || nsites < 0) {
        throw new Error("nsites must be a positive number, got: " + nsites);
      } else if (nsites == 0) {
        nsites = null;
      }
    }
    if (evalue != null) {
      if (typeof evalue === "number") {
        if (evalue < 0) {
          throw new Error("evalue must be a non-negative number, got: " + evalue);
        }
      } else if (typeof evalue === "string") {
        evalue_re = /^((?:[+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)|inf)$/;
        if (!evalue_re.test(evalue)) {
          throw new Error("evalue must be a non-negative number, got: " + evalue);
        }
      } else {
        throw new Error("evalue must be a non-negative number, got: " + evalue);
      }
    }
    // set properties
    this.name = name;
    this.alt = alt;
    this.nsites = nsites;
    this.evalue = evalue;
    this.ltrim = ltrim;
    this.rtrim = rtrim;
    if (typeof matrix === "string") {
      // string constructor
      data = parse_pspm_string(matrix);
      this.alph_length = data["alph_length"];
      this.motif_length = data["motif_length"];
      this.pspm = data["pspm"];
      if (this.evalue == null) {
        if (data["evalue"] != null) {
          this.evalue = data["evalue"];
        } else {
          this.evalue = 0;
        }
      }
      if (this.nsites == null) {
        if (typeof data["nsites"] === "number") {
          this.nsites = data["nsites"];
        } else {
          this.nsites = 20;
        }
      }
    } else {
      // assume pspm is a nested array
      this.motif_length = matrix.length;
      this.alph_length = (matrix.length > 0 ? matrix[0].length : 0);
      if (this.nsites == null) {
        this.nsites = 20;
      }
      if (this.evalue == null) {
        this.evalue = 0;
      }
      this.pspm = [];
      // copy pspm and check
      for (row = 0; row < this.motif_length; row++) {
        if (this.alph_length != matrix[row].length) {
          throw new Error("COLUMN_MISMATCH");
        }
        this.pspm[row] = [];
        row_sum = 0;
        for (col = 0; col < this.alph_length; col++) {
          this.pspm[row][col] = matrix[row][col];
          row_sum += this.pspm[row][col];
        }
        delta = 0.1;
        if (isNaN(row_sum) || (row_sum > 1 && (row_sum - 1) > delta) || 
            (row_sum < 1 && (1 - row_sum) > delta)) {
          throw new Error("INVALID_SUM");
        }
      }
      // copy pssm
      if (pssm != null) {
        this.pssm = [];
        for (row = 0; row < this.motif_length; row++) {
          this.pssm[row] = [];
          for (col = 0; col < this.alph_length; col++) {
            this.pssm[row][col] = pssm[row][col];
          }
        }
      }
    }
  }
};

Pspm.prototype.copy = function() {
  "use strict";
  return new Pspm(this);
};

Pspm.prototype.reverse = function() {
  "use strict";
  var x, y, temp, temp_trim;
  //reverse
  x = 0;
  y = this.motif_length-1;
  while (x < y) {
    temp = this.pspm[x];
    this.pspm[x] = this.pspm[y];
    this.pspm[y] = temp;
    x++;
    y--;
  }
  // reverse pssm (if defined)
  if (typeof this.pssm !== "undefined") {
    //reverse
    x = 0;
    y = this.motif_length-1;
    while (x < y) {
      temp = this.pssm[x];
      this.pspm[x] = this.pssm[y];
      this.pssm[y] = temp;
      x++;
      y--;
    }
  }
  //swap triming
  temp_trim = this.ltrim;
  this.ltrim = this.rtrim;
  this.rtrim = temp_trim;
  return this; //allow function chaining...
};

Pspm.prototype.reverse_complement = function(alphabet) {
  "use strict";
  var x, y, temp, i, row, c, temp_trim;
  if (this.alph_length != alphabet.get_size_core()) {
    throw new Error("The alphabet size does not match the size of the pspm.");
  }
  if (!alphabet.has_complement()) {
    throw new Error("The specified alphabet can not be complemented.");
  }
  // reverse motif
  this.reverse();
  //complement
  for (x = 0; x < this.motif_length; x++) {
    row = this.pspm[x];
    for (i = 0; i < row.length; i++) {
      c = alphabet.get_complement(i);
      if (c < i) continue;
      temp = row[i];
      row[i] = row[c];
      row[c] = temp;
    }
  }
  // complement pssm (if defined)
  if (typeof this.pssm !== "undefined") {
    //complement
    for (x = 0; x < this.motif_length; x++) {
      row = this.pssm[x];
      for (i = 0; i < row.length; i++) {
        c = alphabet.get_complement(i);
        if (c < i) continue;
        temp = row[i];
        row[i] = row[c];
        row[c] = temp;
      }
    }
  }
  return this; //allow function chaining...
};

Pspm.prototype.get_stack = function(position, alphabet, ssc) {
  "use strict";
  var row, stack_ic, alphabet_ic, stack, i, sym;
  if (this.alph_length != alphabet.get_size_core()) {
    throw new Error("The alphabet size does not match the size of the pspm.");
  }
  row = this.pspm[position];
  stack_ic = this.get_stack_ic(position, alphabet);
  if (ssc) stack_ic -= this.get_error(alphabet);
  alphabet_ic = alphabet.get_ic();
  stack = [];
  for (i = 0; i < this.alph_length; i++) {
    sym = new Symbol(i, row[i]*stack_ic/alphabet_ic, alphabet);
    if (sym.get_scale() <= 0) {
      continue;
    }
    stack.push(sym);
  }
  stack.sort(compare_symbol);
  return stack;
};

Pspm.prototype.get_stack_ic = function(position, alphabet) {
  "use strict";
  var row, H, i;
  if (this.alph_length != alphabet.get_size_core()) {
    throw new Error("The alphabet size does not match the size fo the pspm.");
  }
  row = this.pspm[position];
  H = 0;
  for (i = 0; i < this.alph_length; i++) {
    if (row[i] === 0) {
      continue;
    }
    H -= (row[i] * (Math.log(row[i]) / Math.LN2));
  }
  return alphabet.get_ic() - H;
};

Pspm.prototype.get_error = function(alphabet) {
  "use strict";
  if (this.nsites === 0) {
    return 0;
  }
  return (alphabet.get_size_core()-1) / (2 * Math.LN2 * this.nsites);
};

Pspm.prototype.get_motif_length = function() {
  "use strict";
  return this.motif_length;
};

Pspm.prototype.get_alph_length = function() {
  "use strict";
  return this.alph_length;
};

Pspm.prototype.get_left_trim = function() {
  "use strict";
  return this.ltrim;
};

Pspm.prototype.get_right_trim = function() {
  "use strict";
  return this.rtrim;
};

Pspm.prototype.as_best_match = function(alphabet) {
  "use strict";
  var match, odds, best_odds, best_index;
  var i, j;
  match = "";
  for (i = 0; i < this.motif_length; i++) {
    best_index = 0;
    best_odds = this.pspm[i][0] / alphabet.get_bg_freq(0);
    for (j = 1; j < this.alph_length; j++) {
      odds = this.pspm[i][j] / alphabet.get_bg_freq(j);
      if (odds > best_odds) {
        best_odds = odds;
        best_index = j;
      }
    }
    match += alphabet.get_symbol(best_index);
  }
  return match;
};

Pspm.prototype.as_count_matrix = function() {
  "use strict";
  var count, count_text, text;
  var i, j;
  text = "";
  for (i = 0; i < this.motif_length; i++) {
    if (i !== 0) {
      text += "\n";
    }
    for (j = 0; j < this.alph_length; j++) {
      if (j !== 0) {
        text += " ";
      }
      count = Math.round(this.nsites * this.pspm[i][j]);
      count_text = "" + count;
      // pad up to length of 4
      if (count_text.length < 4) {
        text += (new Array(5 - count_text.length)).join(" ") + count_text;
      } else {
        text += count_text;
      }
    }
  }
  return text; 
};

Pspm.prototype.as_probability_matrix = function() {
  "use strict";
  var text;
  var i, j;
  text = "";
  for (i = 0; i < this.motif_length; i++) {
    if (i !== 0) {
      text += "\n";
    }
    for (j = 0; j < this.alph_length; j++) {
      if (j !== 0) {
        text += " ";
      }
      text += this.pspm[i][j].toFixed(6);
    }
  }
  return text; 
};

Pspm.prototype.as_score_matrix = function(alphabet, pseudo) {
  "use strict";
  var me, score, out, row, col, score_text;
  me = this;
  if (typeof this.pssm === "undefined") {
    if (!(typeof alphabet === "object" && alphabet != null && alphabet instanceof Alphabet)) {
      throw new Error("The alphabet is required to generate the pssm.");
    }
    if (typeof pseudo === "undefined") {
      pseudo = 0.01;
    } else if (typeof pseudo !== "number" || pseudo < 0) {
      throw new Error("Expected positive number for pseudocount");
    }
    score = function(row, col) {
      "use strict";
      var p, bg, p2;
      p = me.pspm[row][col];
      bg = alphabet.get_bg_freq(col);
      p2 = (p * me.nsites + bg * pseudo) / (me.nsites + pseudo);
      return (p2 > 0 ? Math.round((Math.log(p2 / bg) / Math.LN2) * 100) : -10000);
    };
  } else {
    score = function(row, col) {
      "use strict";
      return me.pssm[row][col];
    };
  }
  out = "";
  for (row = 0; row < this.motif_length; row++) {
    for (col = 0; col < this.alph_length; col++) {
      if (col !== 0) {
        out += " ";
      }
      score_text = "" + score(row, col);
      // pad out to 6 characters
      if (score_text.length < 6) {
        out += (new Array(7 - score_text.length)).join(" ") + score_text;
      } else {
        out += score_text;
      }
    }
    out += "\n";
  }
  return out;
}

Pspm.prototype.as_pspm = function() {
  "use strict";
  return "letter-probability matrix: alength= " + this.alph_length + 
      " w= " + this.motif_length + " nsites= " + this.nsites + 
      " E= " + (typeof this.evalue === "number" ? 
          this.evalue.toExponential() : this.evalue) + "\n" +
      this.as_probability_matrix();
};

Pspm.prototype.as_pssm = function(alphabet, pseudo) {
  "use strict";
  return "log-odds matrix: alength= " + this.alph_length + 
      " w= " + this.motif_length + 
      " E= " + (typeof this.evalue == "number" ?
          this.evalue.toExponential() : this.evalue) + "\n" +
      this.as_score_matrix(alphabet, pseudo);
};

Pspm.prototype.as_meme = function(options) {
  var with_header, with_pspm, with_pssm, version, alphabet, bg_source, pseudocount, strands;
  var out, alen, i;
  // get the options
  if (typeof options !== "object" || options === null) {
    options = {};
  }
  with_header = (typeof options["with_header"] === "boolean" ? options["with_header"] : false);
  with_pspm = (typeof options["with_pspm"] === "boolean" ? options["with_pspm"] : false);
  with_pssm = (typeof options["with_pssm"] === "boolean" ? options["with_pssm"] : false);
  if (!with_pspm && !with_pssm) with_pspm = true;
  if (with_header) {
    if (typeof options["version"] === "string" && /^\d+(?:\.\d+){0,2}$/.test(options["version"])) {
      version = options["version"];
    } else if (typeof options["version"] === "number") {
      version = options["version"].toFixed(0);
    } else {
      version = "4";
    }
    if (typeof options["strands"] === "number" && options["strands"] === 1) {
      strands = 1;
    } else {
      strands = 2;
    }
    if (typeof options["bg_source"] === "string") {
      bg_source = options["bg_source"];
    } else {
      bg_source = "unknown source";
    }
    if (typeof options["alphabet"] === "object" && options["alphabet"] != null
        && options["alphabet"] instanceof Alphabet) {
      alphabet = options["alphabet"];
    } else {
      throw new Error("The alphabet is required to generate the header.");
    }
  }
  // now create the output
  out = "";
  if (with_header) {
    out = "MEME version " + version + "\n\n";
    out += alphabet.as_meme() + "\n";
    if (alphabet.has_complement()) { // assume DNA has both strands unless otherwise specified
      out += "strands: " + (strands === 1 ? "+" : "+ -") + "\n\n";
    }
    out += "Background letter frequencies (from " + bg_source + "):\n";
    alen = alphabet.get_size_core();
    for (i = 0; i < alen; i++) {
      if (i !== 0) {
        if (i % 9 === 0) { // maximum of nine entries per line
          out += "\n";
        } else {
          out += " ";
        }
      }
      out += alphabet.get_symbol(i) + " " + alphabet.get_bg_freq(i).toFixed(3);
    }
  }
  out += "\n\n";
  out += "MOTIF " + this.name + (this.alt == null ? "" : " " + this.alt);
  if (with_pssm) {
    out += "\n\n";
    out += this.as_pssm(options["alphabet"], options["pseudocount"]);
  }
  if (with_pspm) {
    out += "\n\n";
    out += this.as_pspm();
  }
  return out;
}

Pspm.prototype.toString = function() {
  "use strict";
  var str, i, row;
  str = "";
  for (i = 0; i < this.pspm.length; i++) {
    row = this.pspm[i];
    str += row.join("\t") + "\n";
  }
  return str;
};

function parse_pspm_properties(str) {
  "use strict";
  var parts, i, eqpos, before, after, properties, prop, num, num_re;
  num_re = /^((?:[+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)|inf)$/;
  parts = trim(str).split(/\s+/);
  // split up words containing =
  for (i = 0; i < parts.length;) {
    eqpos = parts[i].indexOf("=");
    if (eqpos != -1) {
      before = parts[i].substr(0, eqpos);
      after = parts[i].substr(eqpos+1);
      if (before.length > 0 && after.length > 0) {
        parts.splice(i, 1, before, "=", after);
        i += 3;
      } else if (before.length > 0) {
        parts.splice(i, 1, before, "=");
        i += 2;
      } else if (after.length > 0) {
        parts.splice(i, 1, "=", after);
        i += 2;
      } else {
        parts.splice(i, 1, "=");
        i++;
      }
    } else {
      i++;
    }
  }
  properties = {};
  for (i = 0; i < parts.length; i += 3) {
    if (parts.length - i < 3) {
      throw new Error("Expected PSPM property was incomplete. "+
          "Remaing parts are: " + parts.slice(i).join(" "));
    }
    if (parts[i+1] !== "=") {
      throw new Error("Expected '=' in PSPM property between key and " +
          "value but got " + parts[i+1]); 
    }
    prop = parts[i].toLowerCase();
    num = parts[i+2];
    if (!num_re.test(num)) {
      throw new Error("Expected numeric value for PSPM property '" + 
          prop + "' but got '" + num + "'");
    }
    properties[prop] = num;
  }
  return properties;
}

function parse_pspm_string(pspm_string) {
  "use strict";
  var header_re, lines, first_line, line_num, col_num, alph_length, 
      motif_length, nsites, evalue, pspm, i, line, match, props, parts,
      j, prob;
  header_re = /^letter-probability\s+matrix:(.*)$/i;
  lines = pspm_string.split(/\n/);
  first_line = true;
  line_num = 0;
  col_num = 0;
  alph_length;
  motif_length;
  nsites;
  evalue;
  pspm = [];
  for (i = 0; i < lines.length; i++) {
    line = trim(lines[i]);
    if (line.length === 0) { 
      continue;
    }
    // check the first line for a header though allow matrices without it
    if (first_line) {
      first_line = false;
      match = header_re.exec(line);
      if (match !== null) {
        props = parse_pspm_properties(match[1]);
        if (props.hasOwnProperty("alength")) {
          alph_length = parseFloat(props["alength"]);
          if (alph_length != 4 && alph_length != 20) {
            throw new Error("PSPM property alength should be 4 or 20" +
                " but got " + alph_length);
          }
        }
        if (props.hasOwnProperty("w")) {
          motif_length = parseFloat(props["w"]);
          if (motif_length % 1 !== 0 || motif_length < 1) {
            throw new Error("PSPM property w should be an integer larger " +
                "than zero but got " + motif_length);
          }
        }
        if (props.hasOwnProperty("nsites")) {
          nsites = parseFloat(props["nsites"]);
          if (nsites <= 0) {
            throw new Error("PSPM property nsites should be larger than " +
                "zero but got " + nsites);
          }
        }
        if (props.hasOwnProperty("e")) {
          evalue = props["e"];
          if (evalue < 0) {
            throw new Error("PSPM property evalue should be " +
                "non-negative but got " + evalue);
          }
        }
        continue;
      }
    }
    pspm[line_num] = [];
    col_num = 0;
    parts = line.split(/\s+/);
    for (j = 0; j < parts.length; j++) {
      prob = parseFloat(parts[j]);
      if (prob != parts[j] || prob < 0 || prob > 1) {
        throw new Error("Expected probability but got '" + parts[j] + "'"); 
      }
      pspm[line_num][col_num] = prob;
      col_num++;
    }
    line_num++;
  }
  if (typeof motif_length === "number") {
    if (pspm.length != motif_length) {
      throw new Error("Expected PSPM to have a motif length of " + 
          motif_length + " but it was actually " + pspm.length);
    }
  } else {
    motif_length = pspm.length;
  }
  if (typeof alph_length !== "number") {
    alph_length = pspm[0].length;
    if (alph_length != 4 && alph_length != 20) {
      throw new Error("Expected length of first row in the PSPM to be " +
          "either 4 or 20 but got " + alph_length);
    }
  }
  for (i = 0; i < pspm.length; i++) {
    if (pspm[i].length != alph_length) {
      throw new Error("Expected PSPM row " + i + " to have a length of " + 
          alph_length + " but the length was " + pspm[i].length);
    }
  }
  return {"pspm": pspm, "motif_length": motif_length, 
    "alph_length": alph_length, "nsites": nsites, "evalue": evalue};
}
//======================================================================
// end Pspm object
//======================================================================

//======================================================================
// start Logo object
//======================================================================

var Logo = function(alphabet, options) {
  "use strict";
  this.alphabet = alphabet;
  this.fine_text = "";
  this.x_axis = 1;
  this.y_axis = true;
  this.xlate_nsyms = 1;
  this.xlate_start = null;
  this.xlate_end = null;
  this.pspm_list = [];
  this.pspm_column = [];
  this.rows = 0;
  this.columns = 0;
  if (typeof options === "string") {
    // the old method signature had fine_text here so we support that
    this.fine_text = options;
  } else if (typeof options === "object" && options != null) {
    this.fine_text = (typeof options.fine_text === "string" ? options.fine_text : "");
    this.x_axis = (typeof options.x_axis === "boolean" ? (options.x_axis ? 1 : 0) : 1);
    if (options.x_axis_hidden != null && options.x_axis_hidden) this.x_axis = -1;
    this.y_axis = (typeof options.y_axis === "boolean" ? options.y_axis : true);
    this.xlate_nsyms = (typeof options.xlate_nsyms === "number" ? options.xlate_nsyms : this.xlate_nsyms);
    this.xlate_start = (typeof options.xlate_start === "number" ? options.xlate_start : this.xlate_start);
    this.xlate_end = (typeof options.xlate_end === "number" ? options.xlate_end : this.xlate_end);
  }
};

Logo.prototype.add_pspm = function(pspm, column) {
  "use strict";
  var col;
  if (typeof column === "undefined") {
    column = 0;
  } else if (column < 0) {
    throw new Error("Column index out of bounds.");
  }
  this.pspm_list[this.rows] = pspm;
  this.pspm_column[this.rows] = column;
  this.rows++;
  col = column + pspm.get_motif_length();
  if (col > this.columns) {
    this.columns = col;
  }
};

Logo.prototype.get_columns = function() {
  "use strict";
  return this.columns;
};

Logo.prototype.get_xlate_nsyms = function() {
  "use strict";
  return this.xlate_nsyms;
};

Logo.prototype.get_xlate_start = function() {
  "use strict";
  return (this.xlate_start != null ? this.xlate_start : 0);
};

Logo.prototype.get_xlate_end = function() {
  "use strict";
  return (this.xlate_end != null ? this.xlate_end : this.columns * this.xlate_nsyms);
};

Logo.prototype.get_xlate_columns = function() {
  "use strict";
  return this.get_xlate_end() - this.get_xlate_start();
};

Logo.prototype.get_rows = function() {
  "use strict";
  return this.rows;
};

Logo.prototype.get_pspm = function(row_index) {
  "use strict";
  if (row_index < 0 || row_index >= this.rows) {
    throw new Error("INDEX_OUT_OF_BOUNDS");
  }
  return this.pspm_list[row_index];
};

Logo.prototype.get_offset = function(row_index) {
  "use strict";
  if (row_index < 0 || row_index >= this.rows) {
    throw new Error("INDEX_OUT_OF_BOUNDS");
  }
  return this.pspm_column[row_index];
};

Logo.prototype._as_eps_data = function(ssc, errbars) {
  var i, j, pos, stack_pos, pspm, stack, sym, out;
  out = "";
  for (i = 0; i < this.rows; i++) {
    out += "\nStartLine\n";
    // Indent
    for (j = 0; j < this.pspm_column[i]; j++) {
      out += "() startstack\nendstack\n\n";
    }
    pspm = this.pspm_list[i];
    if (pspm.get_left_trim() > 0) {
      out += "MuteColour\nDrawTrimEdge\n" + pspm.get_left_trim() + " DrawTrimBg\n";
    }
    for (pos = 0; pos < pspm.get_motif_length(); pos++) {
      if (pos != 0 && pos == pspm.get_left_trim()) { // enable full colour
        out += "DrawTrimEdge\nRestoreColour\n";
      } else if (pos == (pspm.get_motif_length() - pspm.get_right_trim())) {
        out += "MuteColour\n" + pspm.get_right_trim() + " DrawTrimBg\n";
      }
      out += "(" + (pos + 1) + ") startstack\n";
      stack = pspm.get_stack(pos, this.alphabet, ssc);
      for (stack_pos = 0; stack_pos < stack.length; stack_pos++) {
        sym = stack[stack_pos];
        out += " " + (sym.get_scale() * this.alphabet.get_ic()) + " (" + sym.get_symbol() + ") numchar\n";
      }
      if (errbars) {
        out += " " + pspm.get_error(this.alphabet) + " Ibeam\n";
      }
      out += "endstack\n\n";
    }
    if (pspm.get_right_trim() > 0 || pspm.get_left_trim() == pspm.get_motif_length()) {
      out += "RestoreColour\n";
    }
    out += "EndLine\n";
  }
  return out;
};

Logo.prototype.as_eps = function(options) {
  "use strict";
  if (this.xlate_nsyms != 1) throw new Error("Unsupported setting xlate_nsyms for EPS");
  if (this.xlate_start != null) throw new Error("Unsupported setting xlate_start for EPS");
  if (this.xlate_end != null) throw new Error("Unsupported setting xlate_end for EPS");

  var LOGOHEIGHT = 7.5; // default height of line in cm
  var cm2pts, height, width, now, ssc, errbars;
  if (typeof options === "undefined") {
    options = {};
  }
  cm2pts = 72 / 2.54;
  if (typeof options.logo_height == "number") {
    height = options.logo_height;
  } else {
    height = LOGOHEIGHT * this.rows;
  }
  if (typeof options.logo_width == "number") {
    width = options.logo_width;
  } else {
    width = this.columns + 2;
  }
  now = new Date();
  ssc = (typeof options.ssc == "boolean" ? options.ssc : false);
  errbars = (typeof options.show_error_bar == "boolean" ? options.show_error_bar : ssc);
  var values = {
    "LOGOHEIGHT": height,
    "LOGOWIDTH": width,
    "BOUNDINGHEIGHT": Math.round(height * cm2pts),
    "BOUNDINGWIDTH": Math.round(width * cm2pts),
    "LOGOLINEHEIGHT": (height / this.rows),
    "CHARSPERLINE": this.columns,
    "BARBITS": this.alphabet.get_ic(),
    "LOGOTYPE": (this.alphabet.has_complement() ? "NA" : "AA"),
    "CREATIONDATE": now.getDate() + "." + (now.getMonth() + 1) + "." + now.getFullYear() + " " + now.getHours() + ":" + now.getMinutes() + ":" + now.getSeconds(),
    "ERRORBARFRACTION": (typeof options.error_bar_fraction == "number" ? options.error_bar_fraction : 1.0),
    "TICBITS": (typeof options.ticbits == "number" ? options.ticbits : 1.0),
    "TITLE": (typeof options.title == "string" ? options.title : ""),
    "FINEPRINT": (typeof options.fineprint == "string" ? options.fineprint : this.fine_text),
    "XAXISLABEL": (typeof options.xaxislabel == "string" ? options.xaxislabel : ""),
    "YAXISLABEL": (typeof options.yaxislabel == "string" ? options.yaxislabel : "bits"),
    "SSC": ssc,
    "YAXIS": (typeof options.show_y_axis == "boolean" ? options.show_y_axis : this.y_axis),
    "SHOWENDS": (typeof options.show_ends == "boolean" ? options.show_ends : false),
    "ERRBAR": errbars,
    "OUTLINE": (typeof options.show_outline == "boolean" ? options.show_outline : false),
    "NUMBERING": (typeof options.show_numbering == "boolean" ? options.show_numbering : this.x_axis != 0),
    "SHOWINGBOX": (typeof options.show_box == "boolean" ? options.show_box : false),
    "CREATOR": (typeof options.creator == "string" ? options.creator : "motif_logo.js"),
    "FONTSIZE": (typeof options.label_font_size == "number" ? options.label_font_size : 12),
    "TITLEFONTSIZE": (typeof options.title_font_size == "number" ? options.title_font_size : 12),
    "SMALLFONTSIZE": (typeof options.small_font_size == "number" ? options.small_font_size : 6),
    "TOPMARGIN" : (typeof options.top_margin == "number" ? options.top_margin : 0.9),
    "BOTTOMMARGIN": (typeof options.bottom_margin == "number" ? options.bottom_margin : 0.9),
    "COLORDICT": this.alphabet._as_eps_dict(),
    "DATA": this._as_eps_data(ssc, errbars)
  };
  // now this requires that the script containing the template has been imported!
  return motif_logo_template(values);
};

//======================================================================
// end Logo object
//======================================================================

// calculate the exact size (in pixels) of an object drawn on the
// canvas assuming that the background of the canvas is transparent.
function canvas_bounds(ctx, cwidth, cheight) {
  "use strict";
  var data, r, c, top_line, bottom_line, left_line, right_line, 
      txt_width, txt_height;

  // extract the image data
  data = ctx.getImageData(0, 0, cwidth, cheight).data;

  // set initial values
  top_line = -1; bottom_line = -1; left_line = -1; right_line = -1;
  txt_width = 0; txt_height = 0;

  // Find the top-most line with a non-transparent pixel
  for (r = 0; r < cheight; r++) {
    for (c = 0; c < cwidth; c++) {
      if (data[r * cwidth * 4 + c * 4 + 3]) {
        top_line = r;
        break;
      }
    }
    if (top_line != -1) {
      break;
    }
  }
  
  // Only bother looking if we found at least one set pixel... 
  if (top_line != -1) {

    //find the last line with a non-transparent pixel
    for (r = cheight-1; r >= top_line; r--) {
      for(c = 0; c < cwidth; c++) {
        if(data[r * cwidth * 4 + c * 4 + 3]) {
          bottom_line = r;
          break;
        }
      }
      if (bottom_line != -1) {
        break;
      }
    }
    // calculate height
    txt_height = bottom_line - top_line + 1;

    // Find the left-most line with a non-transparent pixel
    for (c = 0; c < cwidth; c++) {
      for (r = top_line; r <= bottom_line; r++) {
        if (data[r * cwidth * 4 + c * 4 + 3]) {
          left_line = c;
          break;
        }
      }
      if (left_line != -1) {
        break;
      }
    }

    //find the right most line with a non-transparent pixel
    for (c = cwidth-1; c >= left_line; c--) {
      for(r = top_line; r <= bottom_line; r++) {
        if(data[r * cwidth * 4 + c * 4 + 3]) {
          right_line = c;
          break;
        }
      }
      if (right_line != -1) {
        break;
      }
    }
    txt_width = right_line - left_line + 1;
  }

  //return the bounds
  return {bound_top: top_line, bound_bottom: bottom_line, 
    bound_left: left_line, bound_right: right_line, width: txt_width, 
    height: txt_height};
}

//======================================================================
// start RasterizedAlphabet
//======================================================================

// Rasterize Alphabet
// 1) Measure width of text at default font for all symbols in alphabet
// 2) sort in width ascending
// 3) Drop the top and bottom 10% (designed to ignore outliers like 'W' and 'I')
// 4) Calculate the average as the maximum scaling factor (designed to stop I becoming a rectangular blob).
// 5) Assume scale of zero would result in width of zero, interpolate scale required to make perfect width font
// 6) Draw text onto temp canvas at calculated scale
// 7) Find bounds of drawn text
// 8) Paint on to another canvas at the desired height (but only scaling width to fit if larger).
var RasterizedAlphabet = function(alphabet, logo_scale, font, width) {
  "use strict";
  var default_size, safety_pad, canvas, ctx, middle, baseline, widths, sizes,
      i, sym, size, tenpercent, avg_width, scale, 
      target_width, target_height;
  //variable prototypes
  this.alphabet = alphabet;
  this.scale = logo_scale;
  this.sym_cache = {};
  this.stack_num_cache = [];
  this.scale_num_cache = [];
  // size of canvas
  default_size = 60; // size of measuring canvas
  safety_pad = 20; // pixels to pad around so we don't miss the edges
  // create a canvas to do our measuring
  canvas = document.createElement("canvas");
  if (!canvas.getContext) throw new Error("No canvas support");
  canvas.width = default_size + 2 * safety_pad;
  canvas.height = default_size + 2 * safety_pad;
  middle = Math.round(canvas.width / 2);
  baseline = Math.round(canvas.height - safety_pad);
  ctx = canvas.getContext('2d');
  if (!supports_text(ctx)) throw new Error("Canvas does not support text");
  ctx.font = font;
  ctx.textAlign = "center";
  ctx.translate(middle, baseline);
  // list of widths
  widths = [];
  sizes = [];
  //now measure each letter in the alphabet
  for (i = 0; i < alphabet.get_size_core(); ++i) {
    // reset the canvas
    ctx.clearRect(0, 0, canvas.width, canvas.height);
    ctx.fillStyle = alphabet.get_colour(i);
    // draw the test text
    ctx.fillText(alphabet.get_symbol(i), 0, 0);
    //measure
    size = canvas_bounds(ctx, canvas.width, canvas.height);
    if (size.width === 0) throw new Error("Invisible symbol!");
    widths.push(size.width);
    sizes[i] = size;
  }
  //sort the widths
  widths.sort(function(a,b) {return a - b;});
  //drop 10% of the items off each end
  tenpercent = Math.floor(widths.length / 10);
  for (i = 0; i < tenpercent; ++i) {
    widths.pop();
    widths.shift();
  }
  //calculate average width
  avg_width = 0;
  for (i = 0; i < widths.length; ++i) {
    avg_width += widths[i];
  }
  avg_width /= widths.length;
  // calculate the target width
  target_width = width * this.scale * 2;
  // calculate scales
  for (i = 0; i < alphabet.get_size_core(); ++i) {
    sym = alphabet.get_symbol(i);
    size = sizes[i];
    // calculate scale
    scale = target_width / Math.max(avg_width, size.width);
    // estimate scaled height
    target_height = size.height * scale;
    // create an appropriately sized canvas
    canvas = document.createElement("canvas");
    canvas.width = target_width;
    canvas.height = target_height + safety_pad * 2;
    // calculate the middle
    middle = Math.round(canvas.width / 2);
    // calculate the baseline
    baseline = Math.round(canvas.height - safety_pad);
    // get the context and prepare to draw the rasterized text
    ctx = canvas.getContext('2d');
    ctx.font = font;
    ctx.fillStyle = alphabet.get_colour(i);
    ctx.textAlign = "center";
    ctx.translate(middle, baseline);
    ctx.save();
    ctx.scale(scale, scale);
    // draw the text
    ctx.fillText(sym, 0, 0);
    ctx.restore();
    this.sym_cache[sym] = {"image": canvas, "size": canvas_bounds(ctx, canvas.width, canvas.height)};
  }
};

RasterizedAlphabet.prototype.get_alphabet = function() {
  return this.alphabet;
};

RasterizedAlphabet.prototype.get_scale = function() {
  return this.scale;
};

RasterizedAlphabet.prototype.draw_stack_sym = function(ctx, letter, dx, dy, dWidth, dHeight) {
  "use strict";
  var entry, image, size;
  entry = this.sym_cache[letter];
  image = entry.image;
  size = entry.size;
  ctx.drawImage(image, 0, size.bound_top -1, image.width, size.height+1, dx, dy, dWidth, dHeight);
};

RasterizedAlphabet.prototype.draw_stack_num = function(ctx, font, stack_width, index) {
  var image, image_ctx, text_length;
  if (index >= this.stack_num_cache.length) {
    image = document.createElement("canvas");
    // measure the text
    image_ctx = image.getContext('2d');
    image_ctx.save();
    image_ctx.font = font;
    text_length = image_ctx.measureText("" + (index + 1)).width;
    image_ctx.restore();
    // resize the canvas to fit
    image.width = Math.ceil(stack_width);
    image.height = Math.ceil(text_length);
    // draw the text
    image_ctx = image.getContext('2d');
    image_ctx.translate(Math.round(stack_width / 2), 0);
    image_ctx.font = font;
    image_ctx.textBaseline = "middle";
    image_ctx.textAlign = "right";
    image_ctx.rotate(-(Math.PI / 2));
    image_ctx.fillText("" + (index + 1), 0, 0);
    this.stack_num_cache[index] = image;
  } else {
    image = this.stack_num_cache[index];
  }
  ctx.drawImage(image, 0, 0);
}

RasterizedAlphabet.prototype.draw_scale_num = function(ctx, font, num) {
  var image, image_ctx, text_size, m_length;
  if (num >= this.scale_num_cache.length) {
    image = document.createElement("canvas");
    // measure the text
    image_ctx = image.getContext('2d');
    image_ctx.font = font;
    text_size = image_ctx.measureText("" + num);
    if (text_size.actualBoundingBoxAscent && text_size.actualBoundingBoxDesent) {
      // resize the canvas to fit
      image.width = Math.ceil(text_size.width);
      image.height = Math.ceil(text_size.actualBoundingBoxAscent + text_size.actualBoundingBoxDesent);
      // draw the text
      image_ctx = image.getContext('2d');
      image_ctx.font = font;
      image_ctx.textAlign = "right";
      image_ctx.fillText("" + num, image.width, text_size.actualBoundingBoxAscent);
    } else {
      // measure width of 'm' to approximate height, we double it later anyway
      m_length = image_ctx.measureText("m").width;
      // resize the canvas to fit
      image.width = Math.ceil(text_size.width);
      image.height = Math.ceil(2 * m_length);
      // draw the text
      image_ctx = image.getContext('2d');
      image_ctx.font = font;
      image_ctx.textAlign = "right";
      image_ctx.textBaseline = "middle";
      image_ctx.fillText("" + num, image.width, m_length);
    }
    this.scale_num_cache[num] = image;
  } else {
    image = this.scale_num_cache[num];
  }
  ctx.drawImage(image, -image.width, -Math.round(image.height / 2))
}

//======================================================================
// end RasterizedAlphabet
//======================================================================

//======================================================================
// start LogoMetrics object
//======================================================================

var LogoMetrics = function(ctx, logo_columns, logo_rows, has_names, has_finetext, x_axis, y_axis) {
  "use strict";
  var i, row_height;
  //variable prototypes
  this.pad_top = (has_names ? 5 : 0);
  this.pad_left = (y_axis ? 10 : 0);
  this.pad_right = (has_finetext ? 15 : 0);
  this.pad_bottom = 0;
  this.pad_middle = 20;
  this.name_height = 14;
  this.name_font = "bold " + this.name_height + "px Times, sans-serif";
  this.name_spacer = 0;
  this.y_axis = y_axis;
  this.y_label = "bits";
  this.y_label_height = 12;
  this.y_label_font = "bold " + this.y_label_height + "px Helvetica, sans-serif";
  this.y_label_spacer = 3;
  this.y_num_height = 12;
  this.y_num_width = 0;
  this.y_num_font = "bold " + this.y_num_height + "px Helvetica, sans-serif";
  this.y_tic_width = 5;
  this.stack_pad_left = 0;
  this.stack_font = "bold 25px Helvetica, sans-serif";
  this.stack_height = 90;
  this.stack_width = 26;
  this.stacks_pad_right = 5;
  this.x_axis = x_axis;
  this.x_num_above = 2;
  this.x_num_height = 12;
  this.x_num_width = 0;
  this.x_num_font = "bold " + this.x_num_height + "px Helvetica, sans-serif";
  this.fine_txt_height = 6;
  this.fine_txt_above = 2;
  this.fine_txt_font = "normal " + this.fine_txt_height + "px Helvetica, sans-serif";
  this.letter_metrics = new Array();
  this.summed_width = 0;
  this.summed_height = 0;
  //calculate the width of the y axis numbers
  ctx.font = this.y_num_font;
  for (i = 0; i <= 2; i++) {
    this.y_num_width = Math.max(this.y_num_width, ctx.measureText("" + i).width);
  }
  //calculate the width of the x axis numbers (but they are rotated so it becomes height)
  if (x_axis == 1) {
    ctx.font = this.x_num_font;
    for (i = 1; i <= logo_columns; i++) {
      this.x_num_width = Math.max(this.x_num_width, ctx.measureText("" + i).width);
    }
  } else if (x_axis == 0) {
    this.x_num_height = 4;
    this.x_num_width = 4;
  } else {
    this.x_num_height = 0;
    this.x_num_width = 0;
  }
  
  //calculate how much vertical space we want to draw this
  //first we add the padding at the top and bottom since that's always there
  this.summed_height += this.pad_top + this.pad_bottom;
  //all except the last row have the same amount of space allocated to them
  if (logo_rows > 1) {
    row_height = this.stack_height + this.pad_middle;
    if (has_names) {
      row_height += this.name_height;
      //the label is allowed to overlap into the spacer
      row_height += Math.max(this.y_num_height/2, this.name_spacer); 
      //the label is allowed to overlap the space used by the other label
      row_height += Math.max(this.y_num_height/2, this.x_num_height + this.x_num_above); 
    } else {
      row_height += this.y_num_height/2; 
      //the label is allowed to overlap the space used by the other label
      row_height += Math.max(this.y_num_height/2, this.x_num_height + this.x_num_above); 
    }
    this.summed_height += row_height * (logo_rows - 1);
  }
  //the last row has the name and fine text below it but no padding
  this.summed_height += this.stack_height + (this.y_axis ? this.y_num_height/2 : 0);

  var fine_txt_total = (has_finetext ? this.fine_txt_height + this.fine_txt_above : 0);
  if (has_names) {
    this.summed_height += fine_txt_total + this.name_height;
    this.summed_height += Math.max((this.y_axis ? this.y_num_height/2 : 0), 
        this.x_num_height + this.x_num_above + this.name_spacer);
  } else {
    this.summed_height += Math.max((this.y_axis ? this.y_num_height/2 : 0), 
        this.x_num_height + this.x_num_above + fine_txt_total);
  }

  //calculate how much horizontal space we want to draw this
  //first add the padding at the left and right since that's always there
  this.summed_width += this.pad_left + this.pad_right;
  if (this.y_axis) {
    //add on the space for the y-axis label
    this.summed_width += this.y_label_height + this.y_label_spacer;
    //add on the space for the y-axis
    this.summed_width += this.y_num_width + this.y_tic_width;
  }
  //add on the space for the stacks
  this.summed_width += (this.stack_pad_left + this.stack_width) * logo_columns;
  //add on the padding after the stacks (an offset from the fine text)
  this.summed_width += this.stacks_pad_right;

};

//======================================================================
// end LogoMetrics object
//======================================================================

//found this trick at http://talideon.com/weblog/2005/02/detecting-broken-images-js.cfm
function image_ok(img) {
  "use strict";
  // During the onload event, IE correctly identifies any images that
  // weren't downloaded as not complete. Others should too. Gecko-based
  // browsers act like NS4 in that they report this incorrectly.
  if (!img.complete) {
    return false;
  }
  // However, they do have two very useful properties: naturalWidth and
  // naturalHeight. These give the true size of the image. If it failed
  // to load, either of these should be zero.
  if (typeof img.naturalWidth !== "undefined" && img.naturalWidth === 0) {
    return false;
  }
  // No other way of checking: assume it's ok.
  return true;
}
  
function supports_text(ctx) {
  "use strict";
  if (!ctx.fillText) {
    return false;
  }
  if (!ctx.measureText) {
    return false;
  }
  return true;
}

//draws the scale, returns the width
function draw_scale(ctx, metrics, alphabet_ic, raster) {
  "use strict";
  var tic_height, i;
  tic_height = metrics.stack_height / alphabet_ic;
  ctx.save();
  ctx.translate(metrics.y_label_height, metrics.y_num_height/2);
  //draw the axis label
  ctx.save();
  ctx.font = metrics.y_label_font;
  ctx.translate(0, metrics.stack_height/2);
  ctx.rotate(-(Math.PI / 2));
  ctx.textAlign = "center";
  ctx.fillText("bits", 0, 0);
  ctx.restore();

  ctx.translate(metrics.y_label_spacer + metrics.y_num_width, 0);

  //draw the axis tics
  ctx.save();
  ctx.translate(0, metrics.stack_height);
  for (i = 0; i <= alphabet_ic; i++) {
    //draw the number
    ctx.save();
    ctx.translate(-1, 0);
    raster.draw_scale_num(ctx, metrics.y_num_font, i);
    ctx.restore();
    //draw the tic
    ctx.fillRect(0, -1, metrics.y_tic_width, 2);
    //prepare for next tic
    ctx.translate(0, -tic_height);
  }
  ctx.restore();

  ctx.fillRect(metrics.y_tic_width - 2, 0, 2, metrics.stack_height)

  ctx.restore();
}

function draw_stack_num(ctx, metrics, row_index, raster) {
  "use strict";
  ctx.save();
  ctx.translate(0, Math.round(metrics.stack_height + metrics.x_num_above));
  if (metrics.x_axis == 1) {
    raster.draw_stack_num(ctx, metrics.x_num_font, metrics.stack_width, row_index);
  } else if (metrics.x_axis == 0) {
    // draw dots instead of the numbers (good for small logos)
    ctx.beginPath();
    var radius = Math.round(metrics.x_num_height / 2);
    ctx.arc(Math.round(metrics.stack_width / 2), radius, radius, 0, 2 * Math.PI, false);
    ctx.fill();
  }
  ctx.restore();
}

function draw_stack(ctx, metrics, symbols, raster) {
  "use strict";
  var preferred_pad, sym_min, i, sym, sym_height, pad;
  preferred_pad = 0;
  sym_min = 5;

  ctx.save();//1
  ctx.translate(0, metrics.stack_height);
  for (i = 0; i < symbols.length; i++) {
    sym = symbols[i];
    sym_height = metrics.stack_height * sym.get_scale();
    
    pad = preferred_pad;
    if (sym_height - pad < sym_min) {
      pad = Math.min(pad, Math.max(0, sym_height - sym_min));
    }
    sym_height -= pad;

    //translate to the correct position
    ctx.translate(0, -(pad/2 + sym_height));

    //draw
    raster.draw_stack_sym(ctx, sym.get_symbol(), 0, 0, metrics.stack_width, sym_height);
    //translate past the padding
    ctx.translate(0, -(pad/2));
  }
  ctx.restore();//1
}

function draw_dashed_line(ctx, pattern, start, x1, y1, x2, y2) {
  "use strict";
  var x, y, len, i, dx, dy, tlen, theta, mulx, muly, lx, ly;
  dx = x2 - x1;
  dy = y2 - y1;
  tlen = Math.pow(dx*dx + dy*dy, 0.5);
  theta = Math.atan2(dy,dx);
  mulx = Math.cos(theta);
  muly = Math.sin(theta);
  lx = [];
  ly = [];
  for (i = 0; i < pattern; ++i) {
    lx.push(pattern[i] * mulx);
    ly.push(pattern[i] * muly);
  }
  i = start;
  x = x1;
  y = y1;
  len = 0;
  ctx.beginPath();
  while (len + pattern[i] < tlen) {
    ctx.moveTo(x, y);
    x += lx[i];
    y += ly[i];
    ctx.lineTo(x, y);
    len += pattern[i];
    i = (i + 1) % pattern.length;
    x += lx[i];
    y += ly[i];
    len += pattern[i];
    i = (i + 1) % pattern.length;
  }
  if (len < tlen) {
    ctx.moveTo(x, y);
    x += mulx * (tlen - len);
    y += muly * (tlen - len);
    ctx.lineTo(x, y);
  }
  ctx.stroke();
}

function draw_trim_background(ctx, metrics, left_start, left_end, left_divider, right_start, right_end, right_divider) {
  "use strict";
  var left_size = left_end - left_start;
  var right_size = right_end - right_start;
  var line_x;

  ctx.save();//s8
  ctx.fillStyle = "rgb(240, 240, 240)";
  if (left_size > 0) {
    ctx.fillRect(left_start * metrics.stack_width, 0, left_size * metrics.stack_width, metrics.stack_height);
  }
  if (right_size > 0) {
    ctx.fillRect(right_start * metrics.stack_width, 0, right_size * metrics.stack_width, metrics.stack_height);
  }
  ctx.fillStyle = "rgb(51, 51, 51)";
  if (left_size > 0 && left_divider) {
    line_x = (left_end * metrics.stack_width) - 0.5;
    draw_dashed_line(ctx, [3], 0, line_x, 0, line_x, metrics.stack_height);
  }
  if (right_size > 0 && right_divider) {
    line_x = (right_start * metrics.stack_width) + 0.5;
    draw_dashed_line(ctx, [3], 0, line_x, 0, line_x, metrics.stack_height);
  }
  ctx.restore();//s8
}

function size_logo_on_canvas(logo, canvas, show_names, scale) {
  "use strict";
  var draw_name, draw_finetext, metrics;
  draw_name = (typeof show_names === "boolean" ? show_names : (logo.get_rows() > 1));
  draw_finetext = (logo.fine_text.length > 0);
  if (canvas.width !== 0 && canvas.height !== 0) {
    return;
  }
  metrics = new LogoMetrics(canvas.getContext('2d'), 
      logo.get_xlate_columns(), logo.get_rows(), draw_name, draw_finetext, logo.x_axis, logo.y_axis);
  if (typeof scale == "number") {
    //resize the canvas to fit the scaled logo
    canvas.width = metrics.summed_width * scale;
    canvas.height = metrics.summed_height * scale;
  } else {
    if (canvas.width === 0 && canvas.height === 0) {
      canvas.width = metrics.summed_width;
      canvas.height = metrics.summed_height;
    } else if (canvas.width === 0) {
      canvas.width = metrics.summed_width * (canvas.height / metrics.summed_height);
    } else if (canvas.height === 0) {
      canvas.height = metrics.summed_height * (canvas.width / metrics.summed_width);
    }
  }
}

function draw_logo_on_canvas(logo, canvas, show_names, scale) {
  "use strict";
  var i, draw_name, draw_finetext, ctx, metrics, raster, pspm_i, pspm, 
      offset, col_index, motif_position, ssc;
  ssc = false;
  draw_name = (typeof show_names === "boolean" ? show_names : (logo.get_rows() > 1));
  draw_finetext = (logo.fine_text.length > 0);
  ctx = canvas.getContext('2d');
  //assume that the user wants the canvas scaled equally so calculate what the best width for this image should be
  metrics = new LogoMetrics(ctx, logo.get_xlate_columns(), logo.get_rows(), draw_name, draw_finetext, logo.x_axis, logo.y_axis);
  if (typeof scale == "number") {
    //resize the canvas to fit the scaled logo
    canvas.width = metrics.summed_width * scale;
    canvas.height = metrics.summed_height * scale;
  } else {
    if (canvas.width === 0 && canvas.height === 0) {
      scale = 1;
      canvas.width = metrics.summed_width;
      canvas.height = metrics.summed_height;
    } else if (canvas.width === 0) {
      scale = canvas.height / metrics.summed_height;
      canvas.width = metrics.summed_width * scale;
    } else if (canvas.height === 0) {
      scale = canvas.width / metrics.summed_width;
      canvas.height = metrics.summed_height * scale;
    } else {
      scale = Math.min(canvas.width / metrics.summed_width, canvas.height / metrics.summed_height);
    }
  }
  // cache the raster based on the assumption that we will be drawing a lot
  // of logos the same size and alphabet
  if (typeof draw_logo_on_canvas.raster_cache === "undefined") {
    draw_logo_on_canvas.raster_cache = [];
  }
  for (i = 0; i < draw_logo_on_canvas.raster_cache.length; i++) {
    raster = draw_logo_on_canvas.raster_cache[i];
    if (raster.get_alphabet().equals(logo.alphabet) &&
        Math.abs(raster.get_scale() - scale) < 0.1) break;
    raster = null;
  }
  if (raster == null) {
    raster = new RasterizedAlphabet(logo.alphabet, scale, metrics.stack_font, metrics.stack_width);
    draw_logo_on_canvas.raster_cache.push(raster);
  }
  ctx = canvas.getContext('2d');
  ctx.save();//s1
  ctx.scale(scale, scale);
  ctx.save();//s2
  ctx.save();//s7
  //create margin
  ctx.translate(Math.round(metrics.pad_left), Math.round(metrics.pad_top));
  for (pspm_i = 0; pspm_i < logo.get_rows(); ++pspm_i) {
    pspm = logo.get_pspm(pspm_i);
    offset = logo.get_offset(pspm_i);
    //optionally draw name if this isn't the last row or is the only row 
    if (draw_name && (logo.get_rows() == 1 || pspm_i != (logo.get_rows()-1))) {
      ctx.save();//s4
      ctx.translate(Math.round(metrics.summed_width/2), Math.round(metrics.name_height));
      ctx.font = metrics.name_font;
      ctx.textAlign = "center";
      ctx.fillText(pspm.name, 0, 0);
      ctx.restore();//s4
      ctx.translate(0, Math.round(metrics.name_height + 
          Math.min(0, metrics.name_spacer - metrics.y_num_height/2)));
    }
    //draw scale
    if (logo.y_axis) draw_scale(ctx, metrics, logo.alphabet.get_ic(), raster);
    ctx.save();//s5
    //translate across past the scale
    if (logo.y_axis) {
      ctx.translate(Math.round(metrics.y_label_height + metrics.y_label_spacer + 
        metrics.y_num_width + metrics.y_tic_width), Math.round(metrics.y_num_height / 2));
    }
    //draw the trimming background
    if (pspm.get_left_trim() > 0 || pspm.get_right_trim() > 0) {
      var left_start = offset * logo.get_xlate_nsyms();
      var left_end = (offset + pspm.get_left_trim()) * logo.get_xlate_nsyms();
      var left_divider = true;
      if (left_end < logo.get_xlate_start() || left_start > logo.get_xlate_end()) {
        // no overlap
        left_start = 0;
        left_end = 0;
        left_divider = false;
      } else {
        if (left_start < logo.get_xlate_start()) {
          left_start = logo.get_xlate_start();
        }
        if (left_end > logo.get_xlate_end()) {
          left_end = logo.get_xlate_end();
          left_divider = false;
        }
        left_start -= logo.get_xlate_start();
        left_end -= logo.get_xlate_start();
        if (left_end < left_start) {
          left_start = 0;
          left_end = 0;
          left_divider = false;
        }
      }
      var right_end = (offset + pspm.get_motif_length()) * logo.get_xlate_nsyms();
      //var right_start = right_end - (pspm.get_left_trim() * logo.get_xlate_nsyms());
      var right_start = right_end - (pspm.get_right_trim() * logo.get_xlate_nsyms());
      var right_divider = true;
      if (right_end < logo.get_xlate_start() || right_start > logo.get_xlate_end()) {
        // no overlap
        right_start = 0;
        right_end = 0;
        right_divider = false;
      } else {
        if (right_start < logo.get_xlate_start()) {
          right_start = logo.get_xlate_start();
          right_divider = false;
        }
        if (right_end > logo.get_xlate_end()) {
          right_end = logo.get_xlate_end();
        }
        right_start -= logo.get_xlate_start();
        right_end -= logo.get_xlate_start();
        if (right_end < right_start) {
          right_start = 0;
          right_end = 0;
          right_divider = false;
        }
      }
      draw_trim_background(ctx, metrics, left_start, left_end, left_divider, right_start, right_end, right_divider);
    }
    //draw letters
    var xlate_col;
    for (xlate_col = logo.get_xlate_start(); xlate_col < logo.get_xlate_end(); xlate_col++) {
      ctx.translate(metrics.stack_pad_left,0);
      col_index = Math.floor(xlate_col / logo.get_xlate_nsyms());
      if (xlate_col % logo.get_xlate_nsyms() == 0) {
        if (col_index >= offset && col_index < (offset + pspm.get_motif_length())) {
          motif_position = col_index - offset;
          draw_stack_num(ctx, metrics, motif_position, raster);
          draw_stack(ctx, metrics, pspm.get_stack(motif_position, logo.alphabet, ssc), raster);
        }
      } else {
        if (col_index >= offset && col_index < (offset + pspm.get_motif_length())) {
          ctx.save();// s5.1
          ctx.translate(0, Math.round(metrics.stack_height));
          // TODO draw a dot or dash or something to indicate continuity of the motif
          ctx.restore(); //s5.1
        }
      }
      ctx.translate(Math.round(metrics.stack_width), 0);
    }
    ctx.restore();//s5
    ////optionally draw name if this is the last row but isn't the only row 
    if (draw_name && (logo.get_rows() != 1 && pspm_i == (logo.get_rows()-1))) {
      //translate vertically past the stack and axis's        
      ctx.translate(0, metrics.y_num_height/2 + metrics.stack_height + 
          Math.max(metrics.y_num_height/2, metrics.x_num_above + metrics.x_num_width + metrics.name_spacer));

      ctx.save();//s6
      ctx.translate(metrics.summed_width/2, metrics.name_height);
      ctx.font = metrics.name_font;
      ctx.textAlign = "center";
      ctx.fillText(pspm.name, 0, 0);
      ctx.restore();//s6
      ctx.translate(0, metrics.name_height);
    } else {
      //translate vertically past the stack and axis's        
      ctx.translate(0, metrics.y_num_height/2 + metrics.stack_height + 
          Math.max(metrics.y_num_height/2, metrics.x_num_above + metrics.x_num_width));
    }
    //if not the last row then add middle padding
    if (pspm_i != (logo.get_rows() -1)) {
      ctx.translate(0, metrics.pad_middle);
    }
  }
  ctx.restore();//s7
  if (logo.fine_text.length > 0) {
    ctx.translate(metrics.summed_width - metrics.pad_right, metrics.summed_height - metrics.pad_bottom);
    ctx.font = metrics.fine_txt_font;
    ctx.textAlign = "right";
    ctx.fillText(logo.fine_text, 0,0);
  }
  ctx.restore();//s2
  ctx.restore();//s1
}

function create_canvas(c_width, c_height, c_id, c_title, c_display) {
  "use strict";
  var canvas = document.createElement("canvas");
  //check for canvas support before attempting anything
  if (!canvas.getContext) {
    return null;
  }
  var ctx = canvas.getContext('2d');
  //check for html5 text drawing support
  if (!supports_text(ctx)) {
    return null;
  }
  //size the canvas
  canvas.width = c_width;
  canvas.height = c_height;
  canvas.id = c_id;
  canvas.title = c_title;
  canvas.style.display = c_display;
  return canvas;
}

function logo_1(alphabet, fine_text, pspm) {
  "use strict";
  var logo = new Logo(alphabet, fine_text);
  logo.add_pspm(pspm);
  return logo;
}

function logo_2(alphabet, fine_text, target, query, query_offset) {
  "use strict";
  var logo = new Logo(alphabet, fine_text);
  if (query_offset < 0) {
    logo.add_pspm(target, -query_offset);
    logo.add_pspm(query);
  } else {
    logo.add_pspm(target);
    logo.add_pspm(query, query_offset);
  }      
  return logo;
}

/*
 * Specifies an alternate source for an image.
 * If the image with the image_id specified has
 * not loaded then a generated logo will be used 
 * to replace it.
 *
 * Note that the image must either have dimensions
 * or a scale must be set.
 */
function alternate_logo(logo, image_id, scale) {
  "use strict";
  var image = document.getElementById(image_id);
  if (!image) {
    alert("Can't find specified image id (" +  image_id + ")");
    return;
  }
  //if the image has loaded then there is no reason to use the canvas
  if (image_ok(image)) {
    return;
  }
  //the image has failed to load so replace it with a canvas if we can.
  var canvas = create_canvas(image.width, image.height, image_id, image.title, image.style.display);
  if (canvas === null) {
    return;
  }
  //draw the logo on the canvas
  draw_logo_on_canvas(logo, canvas, null, scale);
  //replace the image with the canvas
  image.parentNode.replaceChild(canvas, image);
}

/*
 * Specifes that the element with the specified id
 * should be replaced with a generated logo.
 */
function replace_logo(logo, replace_id, scale, title_txt, display_style) {
  "use strict";
  var element = document.getElementById(replace_id);
  if (!replace_id) {
    alert("Can't find specified id (" + replace_id + ")");
    return;
  }
  //found the element!
  var canvas = create_canvas(50, 120, replace_id, title_txt, display_style);
  if (canvas === null) {
    return;
  }
  //draw the logo on the canvas
  draw_logo_on_canvas(logo, canvas, null, scale);
  //replace the element with the canvas
  element.parentNode.replaceChild(canvas, element);
}

/*
 * Fast string trimming implementation found at
 * http://blog.stevenlevithan.com/archives/faster-trim-javascript
 *
 * Note that regex is good at removing leading space but
 * bad at removing trailing space as it has to first go through
 * the whole string.
 */
function trim (str) {
  "use strict";
  var ws, i;
  str = str.replace(/^\s\s*/, '');
  ws = /\s/; i = str.length;
  while (ws.test(str.charAt(--i)));
  return str.slice(0, i + 1);
}
</script>
    <script>
var current_motif = 0;
var dreme_alphabet = new Alphabet(data.alphabet, data.control_db.freqs);

/*
 * Create a pspm for the given motif data
 */
function motif_pspm(m) {
  return new Pspm(m.pwm, m.id, 0, 0, m.nsites, m.evalue);
}

/*
 * Create a count matrix from the given motif data
 */
function motif_count_matrix(motif) {
  return motif_pspm(motif).as_count_matrix();
}

/*
 * Create a probablity matrix from the given motif data
 */
function motif_prob_matrix(motif) {
  return motif_pspm(motif).as_probability_matrix();
}

/*
 * Create a minimal meme format motif from the given motif data
 */
function motif_minimal_meme(motif) {
  return motif_pspm(motif).as_meme({
    "with_header": true, 
    "with_pspm": true,
    "with_pssm": false,
    "version": data["version"],
    "alphabet": dreme_alphabet,
    "strands": (data.options.revcomp ? 2 : 1)
  });
}

/*
 * Fill in a template variable
 */
function set_tvar(template, tvar, value) {
  var node;
  node = find_child(template, tvar);
  if (node === null) {
    throw new Error("Template does not contain variable " + tvar);
  }
  node.innerHTML = "";
  if (typeof value !== "object") {
    node.appendChild(document.createTextNode(value));
  } else {
    node.appendChild(value);
  }
}

/*
 * Make a canvas with the motif logo drawn on it. 
 */
function make_logo(motif, height, rc) {
  var pspm = new Pspm(motif["pwm"]);
  if (rc) pspm = pspm.copy().reverse_complement(dreme_alphabet);
  var logo = new Logo(dreme_alphabet);
  logo.add_pspm(pspm, 0);
  var canvas = document.createElement('canvas');
  canvas.height = height;
  canvas.width = 0;
  draw_logo_on_canvas(logo, canvas, false);
  return canvas;
}

/*
 * Create a button designed to contain a single symbol
 */
function make_sym_btn(symbol, title, action) {
  var box, sbox;
  box = document.createElement("div");
  box.tabIndex = 0;
  box.className = "sym_btn";
  sbox = document.createElement("span");
  if (typeof symbol == "string") {
    sbox.appendChild(document.createTextNode(symbol));
  } else {
    sbox.appendChild(symbol);
  }
  box.appendChild(sbox);
  box.title = title;
  box.addEventListener('click', action, false);
  box.addEventListener('keydown', action, false);
  return box;
}

/*
 * Create a pair of text spans with different classes.
 * This is useful when using CSS to only display one of them.
 */
function text_pair(txt1, cls1, txt2, cls2) {
  var container, part1, part2;
  container = document.createElement("span");
  part1 = document.createElement("span");
  part1.appendChild(document.createTextNode(txt1));
  part1.className = cls1;
  container.appendChild(part1);
  part2 = document.createElement("span");
  part2.appendChild(document.createTextNode(txt2));
  part2.className = cls2;
  container.appendChild(part2);
  return container;
}

/*
 * Make a colourised sequence.
 */
function make_seq(seq) {
  var i, j, letter, lbox, sbox;
  sbox = document.createElement("span");
  for (i = 0; i < seq.length; i = j) {
    letter = seq.charAt(i);
    for (j = i+1; j < seq.length; j++) {
      if (seq.charAt(j) !== letter) {
        break;
      }
    }
    lbox = document.createElement("span");
    lbox.style.color = dreme_alphabet.get_colour(dreme_alphabet.get_index(letter));
    lbox.appendChild(document.createTextNode(seq.substring(i, j)));
    sbox.appendChild(lbox);
  }
  return sbox;
}

/*
 * Create a description element taking into account the newlines in the source text.
 */
function make_description(text) {
  var i, j, lines, p;
  var container = document.createElement("div");
  var paragraphs = text.split(/\n\n+/);
  for (i = 0; i < paragraphs.length; i++) {
    lines = paragraphs[i].split(/\n/);
    p = document.createElement("p");
    p.appendChild(document.createTextNode(lines[0]));
    for (j = 1; j < lines.length; j++) {
      p.appendChild(document.createElement("br"));
      p.appendChild(document.createTextNode(lines[j]));
    }
    container.appendChild(p);
  }
  return container;
}

/*
 * Make the table header for the discovered motifs.
 */
function make_motif_header() {
  var row = document.createElement("tr");
  add_text_header_cell(row, "", "", "motif_ordinal");
  add_text_header_cell(row, "Motif", "pop_motifs_word", "motif_word");
  add_text_header_cell(row, "Logo", "pop_motifs_logo", "motif_logo");
  if (data.options.revcomp) {
    add_text_header_cell(row, "RC Logo", "pop_motifs_rc_logo", "motif_logo");
  }
  add_text_header_cell(row, "E-value", "pop_motifs_evalue", "motif_evalue");
  add_text_header_cell(row, "Unerased E-value", "pop_motifs_uevalue", "motif_evalue");
  add_text_header_cell(row, "More", "pop_more", "motif_more");
  add_text_header_cell(row, "Submit/Download", "pop_submit_dl", "motif_submit");
  row.className = "more";
  return row;
}

/*
 * Make a compact motif summary row for the discovered motifs.
 */
function make_motif_row(tbody, ordinal, motif) {
  var row = document.createElement("tr");
  add_text_cell(row, "" + ordinal + ".", "motif_ordinal");
  add_text_cell(row, motif["id"], "motif_word");
  add_cell(row, make_logo(motif, 50, false), "motif_logo");
  if (data.options.revcomp) {
    add_cell(row, make_logo(motif, 50, true), "motif_logo");
  }
  add_text_cell(row, motif["evalue"], "motif_evalue");
  add_text_cell(row, motif["unerased_evalue"], "motif_evalue");
  add_cell(row, make_sym_btn(text_pair("\u21A7", "less", "\u21A5", "more"), "Show more information.", function(e) { toggle_class(tbody, "collapsed"); }, "\u21A5", ""), "motif_more");
  add_cell(row, make_sym_btn("\u21E2", "Submit the motif to another MEME Suite program or download it.", function(e) { action_show_outpop(e, ordinal); }), "motif_submit");
  return row;
}

/*
 * Make a sortable table of enriched matching rows.
 */
function make_motif_words(motif) {
  var row, i, match;
  var table = document.createElement("table");
  var thead = document.createElement("thead");
  row = document.createElement("tr");
  add_text_header_cell(row, "Word", "pop_match_word", "match_word", function(e) {sort_table(this, compare_words);});
  add_text_header_cell(row, "Positives", "pop_match_pos", "match_count", function(e) {sort_table(this, compare_counts);});
  add_text_header_cell(row, "Negatives", "pop_match_neg", "match_count", function(e) {sort_table(this, compare_counts);});
  add_text_header_cell(row, "P-value", "pop_match_pval", "match_evalue", function(e) {sort_table(this, compare_evalues);});
  add_text_header_cell(row, "E-value", "pop_match_eval", "match_evalue", function(e) {sort_table(this, compare_evalues);});
  thead.appendChild(row);
  table.appendChild(thead);
  var tbody = document.createElement("tbody");
  for (i = 0; i < motif.matches.length; i++) {
    match = motif.matches[i];
    row = document.createElement("tr");
    add_cell(row, make_seq(match.seq), "match_word");
    add_text_cell(row, match.p + " / " + data.sequence_db.count, "match_count");
    add_text_cell(row, match.n + " / " + data.control_db.count, "match_count");
    add_text_cell(row, match.pvalue, "match_evalue");
    add_text_cell(row, match.evalue, "match_evalue");
    tbody.appendChild(row);
  }
  table.appendChild(tbody);
  return table;
}

/*
 * Make an expanded view of a discovered motif.
 */
function make_motif_exp(tbody, ordinal, motif) {
  "use strict";
  var box, pspm, logo_box;
  box = $("tmpl_motif_expanded").cloneNode(true);
  toggle_class(box, "template", false);
  box.id = "";
  find_child(box, "tvar_logo").appendChild(make_logo(motif, 150, false));
  if (data.options.revcomp) {
    find_child(box, "tvar_rclogo").appendChild(make_logo(motif, 150, true));
  }
  set_tvar(box, "tvar_p", motif["p"]);
  set_tvar(box, "tvar_p_total", data.sequence_db.count);
  set_tvar(box, "tvar_n", motif["n"]);
  set_tvar(box, "tvar_n_total", data.control_db.count);
  set_tvar(box, "tvar_pvalue", motif["pvalue"]);
  set_tvar(box, "tvar_evalue", motif["evalue"]);
  set_tvar(box, "tvar_uevalue", motif["unerased_evalue"]);
  set_tvar(box, "tvar_words", make_motif_words(motif));
  var cell = document.createElement("td");
  cell.colSpan = 8;
  cell.appendChild(box);
  var row = document.createElement("tr");
  row.className = "more";
  row.appendChild(cell);
  return row;
}

/*
 * Convert a string containing a scientific number into the log of that number
 * without having an intermediate representation of the number.
 * This is intended to avoid underflow problems with the tiny evalues that
 * MEME and DREME can create.
 */
function sci2log(scinum) {
  "use strict";
  var ev_re, match, sig, exp;
  ev_re = /^(.*)e(.*)$/;
  if (match = ev_re.exec(scinum)) {
    sig = parseFloat(match[1]);
    exp = parseInt(match[2]);
    return Math.log(sig) + (exp * Math.log(10));
  }
  return 0;
}

/*
 * Create a table of discovered motifs. A fresh table body is used for each
 * motif to make hiding/showing rows with css easier.
 */
function make_motifs() {
  "use strict";
  var i, row, tbody, motif, ordinal;
  // make the motifs table
  var container = $("motifs");
  container.innerHTML = ""; // clear content
  var table = document.createElement("table");
  // add a header that is always shown
  var thead = document.createElement("thead");
  thead.appendChild(make_motif_header());
  table.appendChild(thead);
  for (i = 0; i < data.motifs.length; i++) {
    ordinal = i + 1;
    motif = data.motifs[i];
    tbody = document.createElement("tbody");
    tbody.className = "collapsed";
    tbody.appendChild(make_motif_row(tbody, ordinal, motif));
    tbody.appendChild(make_motif_exp(tbody, ordinal, motif));
    // create a following header for every row except the last one
    if ((i + 1) < data.motifs.length) tbody.appendChild(make_motif_header());
    table.appendChild(tbody);
  }
  container.appendChild(table);
}

/*
 * Create a table showing all the alphabet symbols, their names and frequencies.
 */
function make_alpha_bg(alph, freqs) {
  function colour_symbol(index) {
    var span = document.createElement("span");
    span.appendChild(document.createTextNode(alph.get_symbol(index)));
    span.style.color = alph.get_colour(index);
    span.className = "alpha_symbol";
    return span;
  }
  var table, thead, tbody, row, th, span, i;
  // create table
  table = document.createElement("table");
  table.className = "inputs";
  // create header
  thead = document.createElement("thead");
  table.appendChild(thead);
  row = thead.insertRow(thead.rows.length);
  if (alph.has_complement()) {
    add_text_header_cell(row, "Name", "pop_alph_name");
    add_text_header_cell(row, "Bg.", "pop_alph_control");
    add_text_header_cell(row, "");
    add_text_header_cell(row, "");
    add_text_header_cell(row, "");
    add_text_header_cell(row, "Bg.", "pop_alph_control");
    add_text_header_cell(row, "Name", "pop_alph_name");
  } else {
    add_text_header_cell(row, "");
    add_text_header_cell(row, "Name", "pop_alph_name");
    add_text_header_cell(row, "Bg.", "pop_alph_control");
  }
  // add alphabet entries
  tbody = document.createElement("tbody");
  table.appendChild(tbody);
  if (alph.has_complement()) {
    for (i = 0; i < alph.get_size_core(); i++) {
      var c = alph.get_complement(i);
      if (i > c) continue;
      row = tbody.insertRow(tbody.rows.length);
      add_text_cell(row, alph.get_name(i));
      add_text_cell(row, "" + freqs[i].toFixed(3));
      add_cell(row, colour_symbol(i)); 
      add_text_cell(row, "~");
      add_cell(row, colour_symbol(c)); 
      add_text_cell(row, "" + freqs[c].toFixed(3));
      add_text_cell(row, alph.get_name(c));
    }
  } else {
    for (i = 0; i < alph.get_size_core(); i++) {
      row = tbody.insertRow(tbody.rows.length);
      add_cell(row, colour_symbol(i)); 
      add_text_cell(row, alph.get_name(i));
      add_text_cell(row, "" + freqs[i].toFixed(3));
    }
  }
  return table;
}

/*
 * Updates the format download text in the popup.
 * This is called when either the format or current motif changes.
 */
function update_outpop_format(index) {
  var motif = data.motifs[index];
  var fn = [motif_count_matrix, motif_prob_matrix, motif_minimal_meme];
  var suffix = ["_counts.txt", "_freqs.txt", ".meme"];
  var format = parseInt($("text_format").value);
  var text = fn[format](motif);
  prepare_download(text, "text/plain", motif.id + suffix[format], $("outpop_text_dl"));
  $("outpop_text").value = text;
}

/*
 * Updates the motif logos and format download text in the popup.
 * This is called whenever the current motif changes.
 */
function update_outpop_motif(index) {
  "use strict";
  var motifs, motif, pspm, logo, canvas, num;
  motifs = data["motifs"];
  if (index < 0 || index >= motifs.length) {return;}
  current_motif = index;
  motif = motifs[index];
  pspm = new Pspm(motif["pwm"]);
  logo = new Logo(dreme_alphabet, "");
  logo.add_pspm(pspm, 0);
  canvas = $("outpop_logo");
  canvas.width = canvas.width; // clear canvas
  draw_logo_on_canvas(logo, canvas, false);
  canvas = $("outpop_logo_rc");
  canvas.width = canvas.width; // clear rc canvas
  if (data.options.revcomp) {
    pspm.reverse_complement(dreme_alphabet);
    logo = new Logo(dreme_alphabet, "");
    logo.add_pspm(pspm, 0);
    draw_logo_on_canvas(logo, canvas, false);
  }
  num = $("outpop_num");
  num.innerHTML = "";
  num.appendChild(document.createTextNode("" + (index + 1)));
  update_outpop_format(index);
}


/*
 * Initialise and display the download popup.
 */
function action_show_outpop(e, ordinal) {
  "use strict";
  function init() {
    "use strict";
    var close_btn, next_btn, prev_btn, cancel_btn, do_btn;
    var tab1, tab2, tab3;
    var pnl1, pnl2, pnl3;
    var format_list;
    var tbl_submit, inputs, i, default_prog;
    close_btn = $("outpop_close");
    close_btn.addEventListener("click", action_hide_outpop, false);
    close_btn.addEventListener("keydown", action_hide_outpop, false);
    next_btn = $("outpop_next");
    next_btn.addEventListener("click", action_outpop_next, false);
    next_btn.addEventListener("keydown", action_outpop_next, false);
    prev_btn = $("outpop_prev");
    prev_btn.addEventListener("click", action_outpop_prev, false);
    prev_btn.addEventListener("keydown", action_outpop_prev, false);
    cancel_btn = $("outpop_cancel");
    cancel_btn.addEventListener("click", action_hide_outpop, false);
    do_btn = $("outpop_do");
    do_btn.addEventListener("click", action_outpop_submit, false);
    tab1 = $("outpop_tab_1");
    tab1.tabIndex = 0;
    tab1.addEventListener("click", action_outpop_tab, false);
    tab1.addEventListener("keydown", action_outpop_tab, false);
    tab2 = $("outpop_tab_2");
    tab2.tabIndex = 0;
    tab2.addEventListener("click", action_outpop_tab, false);
    tab2.addEventListener("keydown", action_outpop_tab, false);
    tab3 = $("outpop_tab_3");
    tab3.tabIndex = 0;
    tab3.addEventListener("click", action_outpop_tab, false);
    tab3.addEventListener("keydown", action_outpop_tab, false);
    pnl1 = $("outpop_pnl_1");
    pnl2 = $("outpop_pnl_2");
    pnl3 = $("outpop_pnl_3");
    toggle_class(tab1, "activeTab", true);
    toggle_class(tab2, "activeTab", false);
    toggle_class(tab3, "activeTab", false);
    pnl1.style.display = "block";
    pnl2.style.display = "none";
    pnl3.style.display = "none";
    format_list = $("text_format");
    format_list.addEventListener("change", action_outpop_format, false);
    // setup program selection
    tbl_submit = $("programs");
    // when not dna, hide the inputs for programs that require dna motifs
    toggle_class(tbl_submit, "alphabet_dna", dreme_alphabet.has_complement());//TODO FIXME alphabet_dna is a bad name for a field when allowing custom alphabets
    // add a click listener for the radio buttons
    inputs = tbl_submit.querySelectorAll("input[type='radio']");
    for (i = 0; i < inputs.length; i++) {
      inputs[i].addEventListener("click", action_outpop_program, false);
    }
    // ensure that a default program option is selected for DNA and Protein
    default_prog = document.getElementById(dreme_alphabet.has_complement() ? "submit_tomtom" : "submit_fimo");
    default_prog.checked = true;
    action_outpop_program.call(default_prog);
    // disable reverse-complement when not DNA
    $("logo_rc_option").disabled = !dreme_alphabet.has_complement(); 
    // set errorbars on when ssc is on
    $("logo_ssc").addEventListener("change", action_outpop_ssc, false);
  }
  // store the focused element
  action_hide_outpop.last_active = document.activeElement;
  if (!e) e = window.event;
  if (e.type === "keydown") {
    if (e.keyCode !== 13 && e.keyCode !== 32) {
      return;
    }
    // stop a submit or something like that
    e.preventDefault();
  }
  // hide the help popup
  help_popup();
  // on first load initilize the popup
  if (!action_show_outpop.ready) {
    init();
    action_show_outpop.ready = true;
  }
  update_outpop_motif(ordinal - 1);
  // display the download popup
  $("grey_out_page").style.display = "block";
  $("download").style.display = "block";
  $("outpop_close").focus();
}

/*
 * Hide the download popup.
 */
function action_hide_outpop(e) {
  if (!e) e = window.event;
  if (e.type === "keydown") {
    if (e.keyCode !== 13 && e.keyCode !== 32) {
      return;
    }
    // stop a submit or something like that
    e.preventDefault();
  }
  $("download").style.display = "none";
  $("grey_out_page").style.display = "none";
  if (typeof action_hide_outpop.last_active !== "undefined") {
    action_hide_outpop.last_active.focus();
  }
}

/*
 * Show the next motif in the download popup.
 */
function action_outpop_next(e) {
  if (!e) e = window.event;
  if (e.type === "keydown") {
    if (e.keyCode !== 13 && e.keyCode !== 32) {
      return;
    }
    // stop a submit or something like that
    e.preventDefault();
  }
  update_outpop_motif(current_motif + 1);
}

/*
 * Show the previous motif in the download popup.
 */
function action_outpop_prev(e) {
  if (!e) e = window.event;
  if (e.type === "keydown") {
    if (e.keyCode !== 13 && e.keyCode !== 32) {
      return;
    }
    // stop a submit or something like that
    e.preventDefault();
  }
  update_outpop_motif(current_motif - 1);
}

/*
 * Highlight the selected row in the program list.
 */
function action_outpop_program() {
  "use strict";
  var table, tr, rows, i;
  tr = find_parent_tag(this, "TR");
  table = find_parent_tag(tr, "TABLE");
  rows = table.querySelectorAll("tr");
  for (i = 0; i < rows.length; i++) {
    toggle_class(rows[i], "selected", rows[i] === tr);
  }
}

/*
 * Enable error bars when small sample correction is enabled.
 */
function action_outpop_ssc() {
  "use strict";
  $("logo_err").value = $("logo_ssc").value;
}

/*
 * Submit the motif to the selected program.
 */
function action_outpop_submit(e) {
  "use strict";
  var form, input, program, motifs;
  // find out which program is selected
  var radios, i;
  radios = document.getElementsByName("program");
  program = "fimo"; // default to fimo, since it works with all alphabet types
  for (i = 0; i < radios.length; i++) {
    if (radios[i].checked) program = radios[i].value;
  }

  motifs = motif_minimal_meme(data.motifs[current_motif]);
  form = document.createElement("form");
  form.setAttribute("method", "post");
  form.setAttribute("action", site_url + "/tools/" + program);
  
  input = document.createElement("input");
  input.setAttribute("type", "hidden");
  input.setAttribute("name", "motifs_embed");
  input.setAttribute("value", motifs);
  form.appendChild(input);

  document.body.appendChild(form);
  form.submit();
  document.body.removeChild(form);
}

/*
 * Download the format text.
 * Wire the link containing the data URI text to a download button so it looks
 * the same as the server submit stuff.
 */
function action_outpop_download_motif(e) {
  $("outpop_text_dl").click();
}

/*
 * Download the motif logo.
 * The EPS format can be calculated locally in Javascript
 */
function action_outpop_download_logo(e) {
  "use strict";
  var pspm, logo, eps;
  var logo_rc, logo_ssc, logo_width, logo_height;
  var motif = data.motifs[current_motif];
  if ($("logo_format").value == "0") { // EPS
    logo_rc = ($("logo_rc").value == "1");
    logo_ssc = ($("logo_ssc").value == "1");
    logo_width = parseFloat($("logo_width").value);
    if (isNaN(logo_width) || !isFinite(logo_width) || logo_width <= 0) logo_width = null;
    logo_height = parseFloat($("logo_height").value);
    if (isNaN(logo_height) || !isFinite(logo_height) || logo_height <= 0) logo_height = null;
    // create a PSPM from the motif
    pspm = motif_pspm(motif);
    if (logo_rc) pspm.reverse_complement(dreme_alphabet);
    logo = new Logo(dreme_alphabet);
    logo.add_pspm(pspm, 0);
    eps = logo.as_eps({"ssc": logo_ssc, "logo_width": logo_width, "logo_height": logo_height});
    prepare_download(eps, "application/postscript", motif.id + ".eps");
  } else {
    $("logo_motifs").value = motif_minimal_meme(motif);
    $("logo_form").submit();
  }
}

/*
 * Change the selected tab in the download popup.
 */
function action_outpop_tab(e) {
  "use strict";
  var tab1, tab2, tab3, pnl1, pnl2, pnl3, do_btn;
  if (!e) e = window.event;
  if (e.type === "keydown") {
    if (e.keyCode !== 13 && e.keyCode !== 32) {
      return;
    }
    // stop a submit or something like that
    e.preventDefault();
  }
  tab1 = $("outpop_tab_1");
  tab2 = $("outpop_tab_2");
  tab3 = $("outpop_tab_3");
  pnl1 = $("outpop_pnl_1");
  pnl2 = $("outpop_pnl_2");
  pnl3 = $("outpop_pnl_3");
  do_btn = $("outpop_do");

  toggle_class(tab1, "activeTab", (this === tab1));
  toggle_class(tab2, "activeTab", (this === tab2));
  toggle_class(tab3, "activeTab", (this === tab3));
  pnl1.style.display = ((this === tab1) ? "block" : "none");
  pnl2.style.display = ((this === tab2) ? "block" : "none");
  pnl3.style.display = ((this === tab3) ? "block" : "none");
  do_btn.value = ((this === tab1) ? "Submit" : "Download");
  do_btn.removeEventListener("click", action_outpop_submit, false);
  do_btn.removeEventListener("click", action_outpop_download_logo, false);
  do_btn.removeEventListener("click", action_outpop_download_motif, false);
  if (this === tab1) {
    do_btn.addEventListener("click", action_outpop_submit, false);
  } else if (this === tab2) {
    do_btn.addEventListener("click", action_outpop_download_motif, false);
  } else {
    do_btn.addEventListener("click", action_outpop_download_logo, false);
  }
}

/*
 * Update the text in the download format popup.
 */
function action_outpop_format() {
  update_outpop_format(current_motif);
}

/*
 * Find all text nodes in the given container.
 */
function text_nodes(container) {
  var textNodes = [];
  var stack = [container];
  // depth first search to maintain ordering when flattened 
  while (stack.length > 0) {
    var node = stack.pop();
    if (node.nodeType == Node.TEXT_NODE) {
      textNodes.push(node);
    } else {
      for (var i = node.childNodes.length-1; i >= 0; i--) {
        stack.push(node.childNodes[i]);
      }
    }
  }
  return textNodes;
}

/*
 * Get the text out of a specific text node.
 */
function node_text(node) {
  if (node === undefined) {
    return '';
  } else if (node.textContent) {
    return node.textContent;
  } else if (node.innerText) {
    return node.innerText;
  } else {
    return '';
  }
}

/*
 * Get the text contained within the element.
 */
function elem_text(elem, separator) {
  if (separator === undefined) separator = '';
  return text_nodes(elem).map(node_text).join(separator);
}

/*
 * Sort all rows in the first table body based on the column of the given element and the comparison function.
 * The sort is not very fast and is intended for small tables only.
 */
function sort_table(colEle, compare_function) {
  //find the parent of colEle that is either a td or th
  var i, j;
  var cell = colEle;
  while (true) {
    if (cell == null) return;
    if (cell.nodeType == Node.ELEMENT_NODE && 
        (cell.tagName.toLowerCase() == "td" || cell.tagName.toLowerCase() == "th")) {
      break;
    }
    cell = cell.parentNode;
  }
  //find the parent of cell that is a tr
  var row = cell;
  while (true) {
    if (row == null) return;
    if (row.nodeType == Node.ELEMENT_NODE && row.tagName.toLowerCase() == "tr") {
      break;
    }
    row = row.parentNode;
  }
  //find the parent of row that is a table
  var table = row;
  while (true) {
    if (table == null) return;
    if (table.nodeType == Node.ELEMENT_NODE && table.tagName.toLowerCase() == "table") {
      break;
    }
    table = table.parentNode;
  }
  var column_index = cell.cellIndex;
  // do a bubble sort, because the tables are so small it doesn't matter
  var change;
  var trs = table.tBodies[0].getElementsByTagName('tr');
  var already_sorted = true;
  var reverse = false;
  while (true) {
    do {
      change = false;
      for (i = 0; i < trs.length -1; i++) {
        var v1 = elem_text(trs[i].cells[column_index]);
        var v2 = elem_text(trs[i+1].cells[column_index]);
        if (reverse) {
          var tmp = v1;
          v1 = v2;
          v2 = tmp;
        }
        if (compare_function(v1, v2) > 0) {
          exchange(trs[i], trs[i+1], table);
          change = true;
          already_sorted = false;
          trs = table.tBodies[0].getElementsByTagName('tr');
        }
      }
    } while (change);
    if (reverse) break;// we've sorted twice so exit
    if (!already_sorted) break;// sort did something so exit
    // when it's sorted one way already then sort the opposite way
    reverse = true;
  }
  // put arrows on the headers
  var headers = table.tHead.getElementsByTagName('tr');
  for (i = 0; i < headers.length; i++) {
    for (j = 0; j < headers[i].cells.length; j++) {
      var cell = headers[i].cells[j];
      var arrows = cell.getElementsByClassName("sort_arrow");
      var arrow;
      if (arrows.length == 0) {
        arrow = document.createElement("span");
        arrow.className = "sort_arrow";
        cell.insertBefore(arrow, cell.firstChild);
      } else {
        arrow = arrows[0];
      }
      arrow.innerHTML = "";
      if (j == column_index) {
        arrow.appendChild(document.createTextNode(reverse ? "\u25B2" : "\u25BC"));
      }
    }
  }
}

/*
 * Swap two rows in a table.
 */
function exchange(oRowI, oRowJ, oTable) {
  var i = oRowI.rowIndex;
  var j = oRowJ.rowIndex;
   if (i == j+1) {
    oTable.tBodies[0].insertBefore(oRowI, oRowJ);
  } if (j == i+1) {
    oTable.tBodies[0].insertBefore(oRowJ, oRowI);
  } else {
    var tmpNode = oTable.tBodies[0].replaceChild(oRowI, oRowJ);
    if(typeof(oRowI) != "undefined") {
      oTable.tBodies[0].insertBefore(tmpNode, oRowI);
    } else {
      oTable.appendChild(tmpNode);
    }
  }
}

/*
 * Compare two E-values which may be very small.
 */
function compare_evalues(v1, v2) {
  var e1 = sci2log(v1);
  var e2 = sci2log(v2);
  if (e1 < e2) return -1;
  else if (e1 > e2) return 1;
  return 0;
}

/*
 * Compare two counts.
 */
function compare_counts(v1, v2) {
  var re = /(\d+)\s*\/\s*\d+/;
  var m1 = re.exec(v1);
  var m2 = re.exec(v2);
  if (m1 == null && m2 == null) return 0;
  if (m1 == null) return -1;
  if (m2 == null) return 1;
  return parseInt(m2[1]) - parseInt(m1[1]);
}

/*
 * Compare two sequence words.
 */
function compare_words(v1, v2) {
  return v1.localeCompare(v2);
}


</script>
    <style>
/* The following is the content of meme.css */
body { background-color:white; font-size: 12px; font-family: Verdana, Arial, Helvetica, sans-serif;}

div.help {
  display: inline-block;
  margin: 0px;
  padding: 0px;
  width: 12px;
  height: 13px;
  cursor: pointer;
  background-image: url(data:image/gif;base64,R0lGODlhDAANAIABANR0AP///yH5BAEAAAEALAAAAAAMAA0AAAIdhI8Xy22MIFgv1DttrrJ7mlGNNo4c+aFg6SQuUAAAOw==);
}

div.help:hover {
  background-image: url(data:image/gif;base64,R0lGODlhDAANAKEAANR0AP///9R0ANR0ACH+EUNyZWF0ZWQgd2l0aCBHSU1QACH5BAEAAAIALAAAAAAMAA0AAAIdDGynCe3PgoxONntvwqz2/z2K2ImjR0KhmSIZUgAAOw==);
}

p.spaced { line-height: 1.8em;}

span.citation { font-family: "Book Antiqua", "Palatino Linotype", serif; color: #004a4d;}

p.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;}

td.jump { font-size: 13px; color: #ffffff; background-color: #00666a;
  font-family: Georgia, "Times New Roman", Times, serif;}

a.jump { margin: 15px 0 0; font-style: normal; font-variant: small-caps;
  font-weight: bolder; font-family: Georgia, "Times New Roman", Times, serif;}

h2.mainh {font-size: 1.5em; font-style: normal; margin: 15px 0 0;
  font-variant: small-caps; font-family: Georgia, "Times New Roman", Times, serif;}

h2.line {border-bottom: 1px solid #CCCCCC; font-size: 1.5em; font-style: normal;
  margin: 15px 0 0; padding-bottom: 3px; font-variant: small-caps;
  font-family: Georgia, "Times New Roman", Times, serif;}

h4 {border-bottom: 1px solid #CCCCCC; font-size: 1.2em; font-style: normal;
  margin: 10px 0 0; padding-bottom: 3px; font-family: Georgia, "Times New Roman", Times, serif;}

h5 {margin: 0px}

a.help { font-size: 9px; font-style: normal; text-transform: uppercase;
  font-family: Georgia, "Times New Roman", Times, serif;}

div.pad { padding-left: 30px; padding-top: 5px; padding-bottom: 10px;}

div.pad1 { margin: 10px 5px;}

div.pad2 { margin: 25px 5px 5px;}
h2.pad2 { padding: 25px 5px 5px;}

div.pad3 { padding: 5px 0px 10px 30px;}

div.box { border: 2px solid #CCCCCC; padding:10px; overflow: hidden;}

div.bar { border-left: 7px solid #00666a; padding:5px; margin-top:25px; }

div.subsection {margin:25px 0px;}

img {border:0px none;}

th.majorth {text-align:left;}
th.minorth {font-weight:normal; text-align:left; width:8em; padding: 3px 0px;}
th.actionth {font-weight:normal; text-align:left;}

.explain h5 {font-size:1em; margin-left: 1em;}

div.doc {margin-left: 2em; margin-bottom: 3em;}

th.trainingset {
  border-bottom: thin dashed black; 
  font-weight:normal; 
  padding:0px 10px;
}
div.pop_content {
  position:absolute;
  z-index:50;
  width:300px;
  padding: 5px;
  background: #E4ECEC;
  font-size: 12px;
  font-family: Arial;
  border-style: double;
  border-width: 3px;
  border-color: #AA2244;
  display:none;
}

div.pop_content > *:first-child {
  margin-top: 0px;
}

div.pop_content h1, div.pop_content h2, div.pop_content h3, div.pop_content h4, 
div.pop_content h5, div.pop_content h6, div.pop_content p {
  margin: 0px;
}

div.pop_content p + h1, div.pop_content p + h2, div.pop_content p + h3, 
div.pop_content p + h4, div.pop_content p + h5, div.pop_content p + h6 {
  margin-top: 5px;
}

div.pop_content p + p {
  margin-top: 5px;
}

div.pop_content > *:last-child {
  margin-bottom: 0px;
}

div.pop_content div.pop_close {
  /* old definition */
  float:right;
  bottom: 0;
}

div.pop_content span.pop_close, div.pop_content span.pop_back {
  display: inline-block;
  border: 2px outset #661429;
  background-color: #CCC;
  padding-left: 1px;
  padding-right: 1px;
  padding-top: 0px;
  padding-bottom: 0px;
  cursor: pointer;
  color: #AA2244; /*#661429;*/
  font-weight: bold;
}

div.pop_content span.pop_close:active, div.pop_content span.pop_back:active {
  border-style: inset;
}

div.pop_content span.pop_close {
  float:right;
  /*border: 2px outset #AA002B;*/
  /*color: #AA2244;*/
}

div.pop_content:not(.nested) .nested_only {
  display: none;
}

div.pop_back_sec {
  margin-bottom: 5px;
}

div.pop_close_sec {
  margin-top: 5px;
}

table.hide_advanced tr.advanced {
  display: none;
}
span.show_more {
  display: none;
}
table.hide_advanced span.show_more {
  display: inline;
}
table.hide_advanced span.show_less {
  display: none;
}


/*****************************************************************************
 * Program logo styling
 ****************************************************************************/
div.prog_logo {
  border-bottom: 0.25em solid #0f5f60;
  height: 4.5em;
  width: 24em;
  display:inline-block;
}
div.prog_logo img {
  float:left;
  width: 4em;
  border-style: none;
  margin-right: 0.2em;
}
div.prog_logo h1, div.prog_logo h1:hover, div.prog_logo h1:active, div.prog_logo h1:visited {
  margin:0;
  padding:0;
  font-family: Arial, Helvetica,  sans-serif;
  font-size: 3.2em;
  line-height: 1em;
  vertical-align: top;
  display: block;
  color: #026666;
  letter-spacing: -0.06em;
  text-shadow: 0.04em 0.06em 0.05em #666;
}
div.prog_logo h2, div.prog_logo h2:hover, div.prog_logo h2:active, div.prog_logo h2:visited {
  display: block;
  margin:0;
  padding:0;
  font-family: Helvetica, sans-serif;
  font-size: 0.9em;
  line-height: 1em;
  letter-spacing: -0.06em;
  color: black;
}

div.big.prog_logo {
  font-size: 18px;
}

</style>
    <style>
/* dreme output specific css */
div.header {
  position: relative;
  overflow: hidden;
  margin-top: 15px;
  margin-bottom: 5px;
  margin-right: 3px;
  margin-left: 3px;
}
div.header > h2 {
  font-size: 1.5em;
  font-style: normal;
  margin: 0;
  font-variant: small-caps; 
  font-family: Georgia, "Times New Roman", Times, serif;
}
div.header > span {
  position: absolute;
  right: 0;
  bottom: 0;
}

div.template {
  position: absolute;
  z-index: 1;
  left: 0;
  top: 0;
  visibility: hidden;
}

div.sym_btn {
  display:inline-block;
  text-decoration: underline;
  cursor: pointer;
  font-size: 20px;
  line-height:20px; 
  text-align: center;
  width: 20px;
  height: 20px;
  color: blue;
}
div.sym_btn:hover {
  color: white;
  background-color: blue;
}

div.sym_btn.positioned {
  position: absolute;
  top: 0px;
}

div.box + div.box {
  margin-top: 5px;
}

th.motif_ordinal {

}
td.motif_ordinal {
  text-align: right;
  padding-right: 10px;
  font-weight: bold;
  font-size: large;
}
th.motif_word {
  padding-right: 10px;
}
td.motif_word {
  font-size:15px; 
  font-family: 'Courier New', Courier, monospace;
  padding-right: 10px;
}
th.motif_logo {
  padding-right: 10px;
}
td.motif_logo {
  padding-right: 10px;
}
th.motif_evalue {
  text-align:right;
  padding-right: 10px;
}
td.motif_evalue {
  text-align: right;
  white-space: nowrap;
  padding-right: 20px;
}
th.motif_more {
  padding: 0 5px;
}
td.motif_more {
  text-align: center;
  padding: 0 5px;
}
th.motif_submit {
  padding: 0 5px;
}
td.motif_submit {
  text-align: center;
  padding: 0 5px;
}
th.match_word {
  padding-right: 10px;
}
td.match_word {
  padding-right: 10px;
  font-weight: bold;
  font-size: large; 
  font-family: 'Courier New', Courier, monospace;
}
th.match_evalue, th.match_count {
  text-align: right;
  padding-right: 10px;
}
td.match_evalue, td.match_count {
  text-align: right;
  white-space: nowrap;
  padding-right: 20px;
}

div.tabArea {
  font-size: 80%;
  font-weight: bold;
}

.norc div.tabArea {
  display: none;
}

span.tab, span.tab:visited {
  cursor: pointer;
  color: #888;
  background-color: #ddd;
  border: 2px solid #ccc;
  padding: 2px 1em;
  text-decoration: none;
}
span.tab.middle {
  border-left-width: 0px;
}
div.tabArea.base span.tab {
  border-top-width: 0px;
}
div.tabArea.top span.tab {
  border-bottom-width: 0px;
}

span.tab:hover {
  background-color: #bbb;
  border-color: #bbb;
  color: #666;
}
span.tab.activeTab, span.tab.activeTab:hover, span.tab.activeTab:visited {
  background-color: white;
  color: black;
  cursor: default;
}
div.tabMain {
  border: 2px solid #ccc;
  background-color: white;
  padding: 10px;
}
div.tabMain.base {
  margin-top: 5px;
  display: inline-block;
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div.navarrow > span.active {
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div.navarrow:hover > span.active {
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div.navarrow:hover > span.inactive {
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table.programs {
  width: 100%;
}

table.programs tr {
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}

table.programs tr.selected {
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  color: #FFF;
}

table.programs tr.dna_only {
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}

table.programs.alphabet_dna tr.dna_only {
  display: table-row;
}

table.inputs {
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}
table.inputs * td, table.inputs * th {
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  padding-right: 15px;
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/* program settings */
span.strand_none, span.strand_given, span.strand_both {
  display: none;
}
td.none span.strand_none, td.given span.strand_given, td.both span.strand_both {
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/* show the expanded motif only when the collapsed one is hidden */
tbody *.less, tbody.collapsed *.more {
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}

tbody.collapsed *.less {
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</style>
  </head>
  <body data-scrollpad="true">
    <!--  -->
    <div id="grey_out_page" class="grey_background" style="display:none;">
    </div>

    <!-- Help popups -->
    <div class="pop_content" id="pop_">
      <p>Help poup.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_motifs_word">
      <p>
        The name of the motif uses the IUPAC codes for nucleotides which has 
        a different letter to represent each of the 15 possible combinations.
      </p>
      <p>
        The name is itself a representation of the motif though the position
        weight matrix is not directly equalivant as it is generated from the
        sites found that matched the letters given in the name.
      </p>
      <p>
        <a id="doc_alphabets_url" href="#">
        Read more about the MEME suite's use of the IUPAC alphabets.
        </a>
        <script>$("doc_alphabets_url").href = site_url + "/doc/alphabets.html";</script>
      </p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_motifs_logo">
      <p>The logo of the motif.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_motifs_rc_logo">
      <p>The logo of the reverse complement motif.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_motifs_evalue">
      <p>The E-value is the enrichment p-value times the number of candidate 
        motifs tested.</p>
      <p>The enrichment p-value is calculated using Fisher's Exact Test for 
        enrichment of the motif in the positive sequences.</p>
      <p>Note that the counts used in Fisher's Exact Test are made after 
        erasing sites that match previously found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_motifs_uevalue">
      <p>The E-value of the motif calculated without erasing the sites of 
        previously found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_more">
      <p>Show more information on the motif.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_submit_dl">
      <p>Submit your motif to another MEME Suite program or download your motif.</p>
      <h5>Supported Programs</h5>
      <dl>
        <dt>Tomtom</dt>
        <dd>Tomtom is a tool for searching for similar known motifs. 
          </dd>
        <dt>MAST</dt>
        <dd>MAST is a tool for searching biological sequence databases for 
          sequences that contain one or more of a group of known motifs.
          </dd>
        <dt>FIMO</dt>
        <dd>FIMO is a tool for searching biological sequence databases for 
          sequences that contain one or more known motifs.
          </dd>
        <dt>GOMO</dt>
        <dd>GOMO is a tool for identifying possible roles (Gene Ontology 
          terms) for DNA binding motifs.
          </dd>
        <dt>SpaMo</dt>
        <dd>SpaMo is a tool for inferring possible transcription factor
          complexes by finding motifs with enriched spacings.
          </dd>
      </dl>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_motif_positives">
      <p># positive sequences matching the motif / # positive sequences.</p>
      <p>Note these counts are made after erasing sites that match previously
        found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_motif_negatives">
      <p># negative sequences matching the motif / # negative sequences.</p>
      <p>Note these counts are made after erasing sites that match previously
        found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_motif_pvalue">
      <p>The p-value of Fisher's Exact Test for enrichment of the motif in 
        the positive sequences.</p>
      <p>Note that the counts used in Fisher's Exact Test are made after 
        erasing sites that match previously found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_motif_evalue">
      <p>The E-value is the motif p-value times the number of candidate motifs 
        tested.</p>
      <p>Note that the p-value was calculated with counts made after 
        erasing sites that match previously found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_motif_uevalue">
      <p>The E-value of the motif calculated without erasing the sites of 
        previously found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_match_word">
      <p>All words matching the motif whose uncorrected p-value is less than
      <span id="help_add_pv_thresh"></span>.</p>
      <script>$("help_add_pv_thresh").innerHTML = data.options.add_pv_thresh;</script>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_match_pos">
      <p># positive sequences with matches to the word / # positive sequences.</p>
      <p>Note these counts are made after erasing sites that match previously
        found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_match_neg">
      <p># negative sequences with matches to the word / # negative sequences.</p>
      <p>Note these counts are made after erasing sites that match previously
        found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_match_pval">
      <p>The p-value of Fisher's Exact Test for enrichment of the word in 
        the positive sequences.</p>
      <p>Note that the counts used in Fisher's Exact Test are made after 
        erasing sites that match previously found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_match_eval">
      <p>The word p-value times the number of candidates tested.</p>
      <p>Note that the p-value was calculated with counts made after 
        erasing sites that match previously found motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_seq_source">
      <p>The sequence file used by DREME to find the motifs.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_seq_alph">
      <p>The alphabet of the sequences.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>
    <div class="pop_content" id="pop_seq_count">
      <p>The count of the sequences.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_alph_name">
      <p>The name of the alphabet symbol.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <div class="pop_content" id="pop_alph_control">
      <p>The frequency of the alphabet symbol in the control dataset.</p>
      <div class="pop_close">[<a href="javascript:help_popup()">close</a> ]</div>
    </div>

    <!-- templates -->

    <div class="template box expanded_motif" id="tmpl_motif_expanded">
      <div>
        <span class="tvar_logo"></span>
        <span class="tvar_rclogo"></span>
      </div>
      <h4>Details</h4>
      <table class="details">
        <thead>
          <tr>
            <th class="match_count">Positives <div class="help" data-topic="pop_motif_positives"></div></th>
            <th class="match_count">Negatives <div class="help" data-topic="pop_motif_negatives"></div></th>
            <th class="match_evalue">P-value <div class="help" data-topic="pop_motif_pvalue"></div></th>
            <th class="match_evalue">E-value <div class="help" data-topic="pop_motif_evalue"></div></th>
            <th class="match_evalue">Unerased E-value <div class="help" data-topic="pop_motif_uevalue"></div></th>
          </tr>
        </thead>
        <tbody>
          <tr>
            <td class="match_count">
              <span class="tvar_p"></span> / <span class="tvar_p_total"></span>
            </td>
            <td class="match_count">
              <span class="tvar_n"></span> / <span class="tvar_n_total"></span>
            </td>
            <td class="tvar_pvalue match_evalue"></td>
            <td class="tvar_evalue match_evalue"></td>
            <td class="tvar_uevalue match_evalue"></td>
          </tr>
        </tbody>
      </table>
      <h4>Enriched Matching Words</h4>
      <div class="tvar_words"></div>
    </div>


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                <h4 class="compact">Submit to program</h4>
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                  <tr class="dna_only">
                    <td><input type="radio" name="program" value="tomtom" id="submit_tomtom"></td>
                    <td><label for="submit_tomtom">Tomtom</label></td>
                    <td><label for="submit_tomtom">Find similar motifs in
                        published libraries or a library you supply.</label></td>
                  </tr>
                  <tr>
                    <td><input type="radio" name="program" value="fimo" id="submit_fimo"></td>
                    <td><label for="submit_fimo">FIMO</label></td>
                    <td><label for="submit_fimo">Find motif occurrences in
                        sequence data.</label></td>
                  </tr>
                  <tr>
                    <td><input type="radio" name="program" value="mast" id="submit_mast"></td>
                    <td><label for="submit_mast">MAST</label></td>
                    <td><label for="submit_mast">Rank sequences by affinity to
                        groups of motifs.</label></td>
                  </tr>
                  <tr class="dna_only">
                    <td><input type="radio" name="program" value="gomo" id="submit_gomo"></td>
                    <td><label for="submit_gomo">GOMo</label></td>
                    <td><label for="submit_gomo">Identify possible roles (Gene
                        Ontology terms) for motifs.</label></td>
                  </tr>
                  <tr class="dna_only">
                    <td><input type="radio" name="program" value="spamo" id="submit_spamo"></td>
                    <td><label for="submit_spamo">SpaMo</label></td>
                    <td><label for="submit_spamo">Find other motifs that are
                        enriched at specific close spacings which might imply the existance of a complex.</label></td>
                  </tr>
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                  <input type="hidden" id="logo_motifs" name="motifs" value=""/>
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                      <td><label for="logo_format">Format:</label></td>
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                        </select>
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                    <tr>
                      <td><label for="logo_rc">Orientation:</label></td>
                      <td>
                        <select id="logo_rc" name="rc1">
                          <option value="0">Normal</option>
                          <option value="1" id="logo_rc_option">Reverse Complement</option>
                        </select>
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                      <td><label for="logo_width">Width:</label></td>
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                        <input type="text" id="logo_width" size="4" placeholder="default" name="width"/>&nbsp;cm
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                      <td>
                        <input type="text" id="logo_height" size="4" placeholder="default" name="height"/>&nbsp;cm
                      </td>
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                </form>
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" alt="DREME Logo"/>
        <h1>DREME</h1>
        <h2>Discriminative Regular Expression Motif Elicitation</h2>
      </div>
      <p class="spaced">
        For further information on how to interpret these results or to get a 
        copy of the MEME software please access 
        <a href="http://meme.nbcr.net/">http://meme.nbcr.net</a>. 
      </p>
      <p>
        If you use DREME in your research please cite the following paper:<br />
        <span class="citation">
          Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.
          <a href="http://bioinformatics.oxfordjournals.org/content/27/12/1653">[full text]</a>
        </span>
      </p>
    </div>
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    <div class="pad2">
      <a class="jump" href="#motifs_sec">Discovered Motifs</a>
      &nbsp;&nbsp;|&nbsp;&nbsp;
      <a class="jump" href="#inputs_sec">Inputs &amp; Settings</a>
      &nbsp;&nbsp;|&nbsp;&nbsp;
      <a class="jump" href="#info_sec">Program information</a>
    </div>
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    <script>
      if (!window.HTMLCanvasElement) $("html5_warning").style.display = "block";
    </script>
    <!-- description -->
    <div id="description_section" style="display:none">
      <div id="description" class="header">
        <h2>Description</h2>
      </div>
      <div id="description_text" class="box">
      </div>
    </div>
    <script>
      if (data.description) {
        $("description_text").innerHTML = "";
        $("description_text").appendChild(make_description(data.description));
        $("description_section").style.display = "block";
      }
    </script>
    <!-- motifs -->
    <div id="motifs_sec" class="header">
      <h2>Discovered Motifs</h2>
      <span><a href="#inputs_sec">Next</a>&nbsp;<a href="#">Top</a></span>
    </div>
    <div id="motifs" class="box">
      <p>No motifs were discovered!</p>
    </div>
    <script>make_motifs();</script>
    <!-- inputs and settings -->
    <div id="inputs_sec" class="header">
      <h2>Inputs &amp; Settings</h2>
      <span><a href="#motifs_sec">Previous</a>&nbsp;<a href="#info_sec">Next</a>&nbsp;<a href="#">Top</a></span>
    </div>
    <div class="box">
      <h4>Sequences</h4>
      <table id="seq_info" class="inputs">
        <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>
          <th>Alphabet <div class="help" data-topic="pop_seq_alph"></div></th>
          <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>
        </tr>
        <tr>
          <td id="ins_seq_source"></td>
          <td id="ins_seq_alphabet"></td>
          <td id="ins_seq_count"></td>
        </tr>
      </table>
      <script>
      {
        var db = data.sequence_db;
        $("ins_seq_source").innerHTML = db.file;
        $("ins_seq_alphabet").innerHTML = dreme_alphabet.get_alphabet_name();
        $("ins_seq_count").innerHTML = db.count;
      }
      </script>
      <h4>Control Sequences</h4>
      <table id="seq_info" class="inputs">
        <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th>
          <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th>
        </tr>
        <tr>
          <td id="ins_cseq_source"></td>
          <td id="ins_cseq_count"></td>
        </tr>
      </table>
      <script>
      {
        var db = data.control_db;
        if (db.from == "shuffled") {
          $("ins_cseq_source").innerHTML = "Shuffled Sequences";
        } else {
          $("ins_cseq_source").innerHTML = db.file;
        }
        $("ins_cseq_count").innerHTML = db.count;
      }
      </script>
      <h4>Background</h4>
      <span id="alpha_bg"></span>
      <script>
      {
        $("alpha_bg").appendChild(make_alpha_bg(dreme_alphabet, data.control_db.freqs));
      }
      </script>
      <h4>Other Settings</h4>
      <table id="tbl_settings" class="inputs hide_advanced">
        <tr>
          <th>Strand Handling</th>
          <td id="opt_strand">
            <span class="strand_none">This alphabet only has one strand</span>
            <span class="strand_given">Only the given strand is processed</span>
            <span class="strand_both">Both the given and reverse complement strands are processed</span>
          </td>
        </tr>
        <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr>
        <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr>
        <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr>
        <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr>
        <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr>
      </table>
      <script>
      {
        $("opt_strand").className = (dreme_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none");
        $("opt_ngen").innerHTML = data.options.ngen;
        $("opt_seed").innerHTML = data.options.seed;
        $("opt_stop_evalue").innerHTML = data.options.stop.evalue;
        $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count.");
        $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time.");
      }
      </script>
    </div>
    <!-- list information on this program -->
    <div id="info_sec" class="bar" style="position:relative">
      <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div>
      <div class="subsection">
        <h5 id="version">DREME version</h5>
        <span id="ins_version"></span> 
        (Release date: <span id="ins_release"></span>)<br>
      </div>
      <script>
        $("ins_version").innerHTML = data["version"];
        $("ins_release").innerHTML = data["release"];
      </script>
      <div class="subsection">
        <h5 id="reference">Reference</h5>
        <span class="citation">
          Timothy L. Bailey, "DREME: Motif discovery in transcription factor ChIP-seq data", <i>Bioinformatics</i>, <b>27</b>(12):1653-1659, 2011.
          <a href="http://bioinformatics.oxfordjournals.org/content/27/12/1653">[full text]</a>
        </span>
      </div>
      <div class="subsection">
        <h5 id="command">Command line</h5>
        <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly">
        </textarea>
        <script>$("cmd").value = data["cmd"].join(" ");</script>
      </div>
    </div>
    
  </body>
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2:3e5c80594237

    <title>DREME</title>
    <script>
      // @JSON_VAR data
      var data = {
        "program": "dreme",
        "version": "5.0.5",
        "cmd": [
          "dreme", "-o", "./dreme_out", "-p",
          "-norc", "-rna", "-s", "1"
        ],
        "options": {
          "revcomp": false,
          "ngen": 100,
          "add_pv_thresh": 0.01,
          "seed": 1,
          "stop": {
            "evalue": "0.05"
        "alphabet": {
          "name": "RNA",
          "like": "rna",
          "ncore": 4,
          "symbols": [
        "background": {
          "freqs": [0.221, 0.245, 0.221, 0.312]
        "control_db": {
          "name": "shuffled positive sequences",
          "from": "shuffled",
          "count": 1000,
          "freqs": [0.221, 0.245, 0.221, 0.312]
        "motifs": [
            "db": 0,
            "id": "UUYUCY",
            "alt": "DREME-1",
            "len": 6,
            "nsites": 459,

              [0.000000, 0.000000, 0.000000, 1.000000], 
              [0.000000, 0.294118, 0.000000, 0.705882], 
              [0.000000, 0.000000, 0.000000, 1.000000], 
              [0.000000, 1.000000, 0.000000, 0.000000], 
              [0.000000, 0.474946, 0.000000, 0.525054]
            "matches": [
                "seq": "UUUUCC",
                "p": 147,
                "n": 75,
                "pvalue": "1.8e-007",
                "evalue": "8.1e-003"

                "seq": "UUUUCU",
                "p": 155,
                "n": 94,
                "pvalue": "2.2e-005",
                "evalue": "1.0e+000"
                "seq": "UUCUCU",
                "p": 94,
                "n": 51,
                "pvalue": "1.3e-004",
                "evalue": "6.1e+000"
                "seq": "UUCUCC",
                "p": 75,
                "n": 42,
                "pvalue": "1.1e-003",
                "evalue": "5.0e+001"
    <script>
var site_url = "http://meme-suite.org";
</script>
/* dreme output specific css */
/* program settings */
</style>
  </head>
  <body data-scrollpad="true">
        The name of the motif uses the IUPAC codes for nucleotides which has 
        a different letter to represent each of the 15 possible combinations.
        The name is itself a representation of the motif though the position
        weight matrix is not directly equivalent as it is generated from the
        sites found that matched the letters given in the name.
      <p>The E-value is the enrichment p-value times the number of candidate 
        motifs tested.</p>
      <p>The enrichment p-value is calculated using Fisher's Exact Test for 
        enrichment of the motif in the positive sequences.</p>
      <p>Note that the counts used in Fisher's Exact Test are made after 
        erasing sites that match previously found motifs.</p>
      <p>The E-value of the motif calculated without erasing the sites of 
        previously found motifs.</p>
      <p>Show more information on the motif.</p>
      <p>Submit your motif to another MEME Suite program or download your motif.</p>
      <h5>Supported Programs</h5>
        <dt>Tomtom</dt>
        <dd>Tomtom is a tool for searching for similar known motifs. 
        <dt>MAST</dt>
        <dd>MAST is a tool for searching biological sequence databases for 
          sequences that contain one or more of a group of known motifs.
        <dt>FIMO</dt>
        <dd>FIMO is a tool for searching biological sequence databases for 
          sequences that contain one or more known motifs.
        <dt>GOMo</dt>
        <dd>GOMo is a tool for identifying possible roles (Gene Ontology 
          terms) for DNA binding motifs.
        <dt>SpaMo</dt>
        <dd>SpaMo is a tool for inferring possible transcription factor
          complexes by finding motifs with enriched spacings.
  </body>
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