bio-svgenes 0.2.3 → 0.3.0

data/doc/js/navigation.js

@@ -0,0 +1,142 @@
+/*
+ * Navigation allows movement using the arrow keys through the search results.
+ *
+ * When using this library you will need to set scrollIntoView to the
+ * appropriate function for your layout.  Use scrollInWindow if the container
+ * is not scrollable and scrollInElement if the container is a separate
+ * scrolling region.
+ */
+Navigation = new function() {
+  this.initNavigation = function() {
+    var _this = this;
+
+    $(document).keydown(function(e) {
+      _this.onkeydown(e);
+    }).keyup(function(e) {
+      _this.onkeyup(e);
+    });
+
+    this.navigationActive = true;
+  }
+
+  this.setNavigationActive = function(state) {
+    this.navigationActive = state;
+    this.clearMoveTimeout();
+  }
+
+  this.onkeyup = function(e) {
+    if (!this.navigationActive) return;
+
+    switch(e.keyCode) {
+      case 37: //Event.KEY_LEFT:
+      case 38: //Event.KEY_UP:
+      case 39: //Event.KEY_RIGHT:
+      case 40: //Event.KEY_DOWN:
+        this.clearMoveTimeout();
+        break;
+    }
+  }
+
+  this.onkeydown = function(e) {
+    if (!this.navigationActive) return;
+    switch(e.keyCode) {
+      case 37: //Event.KEY_LEFT:
+        if (this.moveLeft()) e.preventDefault();
+        break;
+      case 38: //Event.KEY_UP:
+        if (e.keyCode == 38 || e.ctrlKey) {
+          if (this.moveUp()) e.preventDefault();
+          this.startMoveTimeout(false);
+        }
+        break;
+      case 39: //Event.KEY_RIGHT:
+        if (this.moveRight()) e.preventDefault();
+        break;
+      case 40: //Event.KEY_DOWN:
+        if (e.keyCode == 40 || e.ctrlKey) {
+          if (this.moveDown()) e.preventDefault();
+          this.startMoveTimeout(true);
+        }
+        break;
+      case 13: //Event.KEY_RETURN:
+        if (this.$current)
+          e.preventDefault();
+          this.select(this.$current);
+        break;
+    }
+    if (e.ctrlKey && e.shiftKey) this.select(this.$current);
+  }
+
+  this.clearMoveTimeout = function() {
+    clearTimeout(this.moveTimeout);
+    this.moveTimeout = null;
+  }
+
+  this.startMoveTimeout = function(isDown) {
+    if (!$.browser.mozilla && !$.browser.opera) return;
+    if (this.moveTimeout) this.clearMoveTimeout();
+    var _this = this;
+
+    var go = function() {
+      if (!_this.moveTimeout) return;
+      _this[isDown ? 'moveDown' : 'moveUp']();
+      _this.moveTimout = setTimeout(go, 100);
+    }
+    this.moveTimeout = setTimeout(go, 200);
+  }
+
+  this.moveRight = function() {
+  }
+
+  this.moveLeft = function() {
+  }
+
+  this.move = function(isDown) {
+  }
+
+  this.moveUp = function() {
+    return this.move(false);
+  }
+
+  this.moveDown = function() {
+    return this.move(true);
+  }
+
+  /*
+   * Scrolls to the given element in the scrollable element view.
+   */
+  this.scrollInElement = function(element, view) {
+    var offset, viewHeight, viewScroll, height;
+    offset = element.offsetTop;
+    height = element.offsetHeight;
+    viewHeight = view.offsetHeight;
+    viewScroll = view.scrollTop;
+
+    if (offset - viewScroll + height > viewHeight) {
+      view.scrollTop = offset - viewHeight + height;
+    }
+    if (offset < viewScroll) {
+      view.scrollTop = offset;
+    }
+  }
+
+  /*
+   * Scrolls to the given element in the window.  The second argument is
+   * ignored
+   */
+  this.scrollInWindow = function(element, ignored) {
+    var offset, viewHeight, viewScroll, height;
+    offset = element.offsetTop;
+    height = element.offsetHeight;
+    viewHeight = window.innerHeight;
+    viewScroll = window.scrollY;
+
+    if (offset - viewScroll + height > viewHeight) {
+      window.scrollTo(window.scrollX, offset - viewHeight + height);
+    }
+    if (offset < viewScroll) {
+      window.scrollTo(window.scrollX, offset);
+    }
+  }
+}
+

data/doc/js/search.js

@@ -0,0 +1,94 @@
+Search = function(data, input, result) {
+  this.data = data;
+  this.$input = $(input);
+  this.$result = $(result);
+
+  this.$current = null;
+  this.$view = this.$result.parent();
+  this.searcher = new Searcher(data.index);
+  this.init();
+}
+
+Search.prototype = $.extend({}, Navigation, new function() {
+  var suid = 1;
+
+  this.init = function() {
+    var _this = this;
+    var observer = function() {
+      _this.search(_this.$input[0].value);
+    };
+    this.$input.keyup(observer);
+    this.$input.click(observer); // mac's clear field
+
+    this.searcher.ready(function(results, isLast) {
+      _this.addResults(results, isLast);
+    })
+
+    this.initNavigation();
+    this.setNavigationActive(false);
+  }
+
+  this.search = function(value, selectFirstMatch) {
+    value = jQuery.trim(value).toLowerCase();
+    if (value) {
+      this.setNavigationActive(true);
+    } else {
+      this.setNavigationActive(false);
+    }
+
+    if (value == '') {
+      this.lastQuery = value;
+      this.$result.empty();
+      this.setNavigationActive(false);
+    } else if (value != this.lastQuery) {
+      this.lastQuery = value;
+      this.firstRun = true;
+      this.searcher.find(value);
+    }
+  }
+
+  this.addResults = function(results, isLast) {
+    var target = this.$result.get(0);
+    if (this.firstRun && (results.length > 0 || isLast)) {
+      this.$current = null;
+      this.$result.empty();
+    }
+
+    for (var i=0, l = results.length; i < l; i++) {
+      target.appendChild(this.renderItem.call(this, results[i]));
+    };
+
+    if (this.firstRun && results.length > 0) {
+      this.firstRun = false;
+      this.$current = $(target.firstChild);
+      this.$current.addClass('current');
+    }
+    if (jQuery.browser.msie) this.$element[0].className += '';
+  }
+
+  this.move = function(isDown) {
+    if (!this.$current) return;
+    var $next = this.$current[isDown ? 'next' : 'prev']();
+    if ($next.length) {
+      this.$current.removeClass('current');
+      $next.addClass('current');
+      this.scrollIntoView($next[0], this.$view[0]);
+      this.$current = $next;
+    }
+    return true;
+  }
+
+  this.hlt = function(html) {
+    return this.escapeHTML(html).
+      replace(/\u0001/g, '<em>').
+      replace(/\u0002/g, '</em>');
+  }
+
+  this.escapeHTML = function(html) {
+    return html.replace(/[&<>]/g, function(c) {
+      return '&#' + c.charCodeAt(0) + ';';
+    });
+  }
+
+});
+

data/doc/js/search_index.js

@@ -0,0 +1 @@
+var search_data = {"index":{"info":[["Bio","","Bio.html","",""],["Bio::Graphics","","Bio/Graphics.html","",""],["Bio::Graphics::Glyph","","Bio/Graphics/Glyph.html","","<p>A Glyph is an array of Primitive objects, holding information about the\ntype of Glyph being created. …\n"],["Bio::Graphics::MiniFeature","","Bio/Graphics/MiniFeature.html","","<p>The MiniFeature class represents any feature (e.g. a gene, transcript,\nexon, start codon, etc) on a track. …\n"],["Bio::Graphics::Page","","Bio/Graphics/Page.html","","<p>The Page class represents the top level container on which svg objects are\nwritten. It will contain a …\n"],["Bio::Graphics::Primitive","","Bio/Graphics/Primitive.html","","<p>The Primitive class is used to hold information about Glyphs. They contain\na Glyph type and then a Hash …\n"],["Bio::Graphics::SVGEE","","Bio/Graphics/SVGEE.html","","<p>The SVGEE class is used to create the text that will go into the final SVG\nfile. It takes information …\n"],["Bio::Graphics::Track","","Bio/Graphics/Track.html","","<p>The Track class holds and organises the features, ordering them into\ndifferent rows if they overlap\n"],["add","Bio::Graphics::Track","Bio/Graphics/Track.html#method-i-add","(feature)","<p>Adds a new MiniFeature to the the @features array\n"],["add_primitive","Bio::Graphics::SVGEE","Bio/Graphics/SVGEE.html#method-i-add_primitive","(primitive_object)","<p>Adds a Primitive object to the SVGEE object and makes the svg text for that\nPrimitive\n"],["add_track","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-add_track","(args)","<p>Calculates the colour or gradient for the supplied Bio::Graphics::Track\nobjects and adds them to the …\n"],["circle","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-circle","(args)","<p>Creates a circular Glyph\n<p><code>args</code>\n<p>radius = the radius of the circle  (10)\n"],["close_tag","Bio::Graphics::SVGEE","Bio/Graphics/SVGEE.html#method-i-close_tag","()","<p>Produces the closing text for an svg file\n"],["directed","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-directed","(args)","<p>Creates a polygon Glyph to indicate the direction in which the Glyph is\npointing <code>args</code>\n<p>width = the width …\n"],["down_triangle","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-down_triangle","(args)","<p>Creates a polygon Glyph for a downward-pointing triangle <code>args</code>\n<p>height = the height of the Glyph (10)\n<p>fill_color …\n"],["draw","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw","()","<p>Prints out the svg text\n"],["draw","Bio::Graphics::SVGEE","Bio/Graphics/SVGEE.html#method-i-draw","()","<p>Produces the svg text to display all the features on a Page\n"],["draw_circle","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_circle","(args)","<p>Adds the Bio::Graphics::Primitive objects to the SVGEE object\n<p><code>args</code> - an Array of Bio::Graphics::Primitive …\n\n"],["draw_directed","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_directed","(args)","<p>Adds the Bio::Graphics::Primitive objects to the SVGEE object\n<p><code>args</code> - an Array of Bio::Graphics::Primitive …\n\n"],["draw_down_triangle","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_down_triangle","(args)","<p>Adds the Bio::Graphics::Primitive objects to the SVGEE object\n<p><code>args</code> - an Array of Bio::Graphics::Primitive …\n\n"],["draw_features","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_features","(track)","<p>Takes a Bio::Graphics::Track object and sorts out the input information\ninto a user friendly format. …\n"],["draw_generic","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_generic","(args)","<p>Adds the Bio::Graphics::Primitive objects to the SVGEE object\n<p><code>args</code> - an Array of Bio::Graphics::Primitive …\n\n"],["draw_histogram","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_histogram","(args)","<p>Adds the Bio::Graphics::Primitive objects to the SVGEE object\n<p><code>args</code> - an Array of Bio::Graphics::Primitive …\n\n"],["draw_label","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_label","(args)","<p>Adds the Bio::Graphics::Primitive objects to the SVGEE object\n<p><code>args</code> - an Array of Bio::Graphics::Primitive …\n\n"],["draw_scale","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_scale","()","<p>Adds the  Bio::Graphics::Primitive objects to the SVGEE object\n"],["draw_span","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_span","(args)","<p>Adds the Bio::Graphics::Primitive objects to the SVGEE object\n<p><code>args</code> - an Array of Bio::Graphics::Primitive …\n\n"],["draw_transcript","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_transcript","(args)","<p>Adds the Bio::Graphics::Primitive objects to the SVGEE object\n<p><code>args</code> - an Array of Bio::Graphics::Primitive …\n\n"],["draw_up_triangle","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-draw_up_triangle","(args)","<p>Adds the Bio::Graphics::Primitive objects to the SVGEE object\n<p><code>args</code> - an Array of Bio::Graphics::Primitive …\n\n"],["from_json","Bio::Graphics::Page","Bio/Graphics/Page.html#method-c-from_json","(args)","<p>Takes a custom-written json file and writes an svg page to file which will\ncontain the given features …\n"],["generic","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-generic","(args)","<p>Creates a generic glyph, which is a rectangle\n<p><code>args</code>\n<p>height = the height of the Glyph (10)\n"],["get_limits","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-get_limits","()","<p>Calculates the Page scale-start and scale-stop position and the nucleotides\nper pixel for the current …\n"],["get_markup","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-get_markup","()","<p>Pulls together all track information to create svg text which will draw all\nthe features on the page …\n"],["get_rows","Bio::Graphics::Track","Bio/Graphics/Track.html#method-i-get_rows","()","<p>Calculates how many rows are needed per track for overlapping features and\nwhich row each feature should …\n"],["gradient","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-gradient","(gradient)","<p>Sets the the type (linear or radial) and colour of gradient for a\npre-defined gradient along with the …\n"],["gradient","Bio::Graphics::SVGEE","Bio/Graphics/SVGEE.html#method-i-gradient","(a)","<p>Takes the gradient information from a Glyph, which must be of type\n‘radial’ or ‘linear’ and creates the …\n"],["gradients","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-gradients","()","<p>The list of pre-defined gradients\n"],["label","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-label","(args)","<p>Creates a label Glyph to write text\n<p><code>args</code>\n<p>text = the text to write\n"],["new","Bio::Graphics::MiniFeature","Bio/Graphics/MiniFeature.html#method-c-new","(args)","<p>Creates a new MiniFeature\n<p><em>Arguments</em>\n<p>start = the start position of the feature\n"],["new","Bio::Graphics::Page","Bio/Graphics/Page.html#method-c-new","(args)","<p>Creates a new Page object.\n<p>A new Page contains the following arguments:\n<p>height = the height of the page …\n"],["new","Bio::Graphics::Primitive","Bio/Graphics/Primitive.html#method-c-new","(primitive,args)","<p>Creates a new Primitive and initialises the Hash keys into instance\nvariables\n<p><code>args</code>\n<p>primitive = the Primitive …\n"],["new","Bio::Graphics::SVGEE","Bio/Graphics/SVGEE.html#method-c-new","(args)","<p>Creates a new SVGEE object which will contain all the necessary objects to\ndisplay all the features on …\n"],["new","Bio::Graphics::Track","Bio/Graphics/Track.html#method-c-new","(args)","<p>Creates a new Track\n"],["open_tag","Bio::Graphics::SVGEE","Bio/Graphics/SVGEE.html#method-i-open_tag","()","<p>Produces the opening text for an svg file\n"],["overlaps","Bio::Graphics::Track","Bio/Graphics/Track.html#method-i-overlaps","(f1, f2)","<p>Calculates if two MiniFeature objects overlap by examining their start and\nend positions. If two features …\n"],["parse_gff","Bio::Graphics::Page","Bio/Graphics/Page.html#method-c-parse_gff","(gff_file)","<p>Parses a GFF file into an Array of Bio::GFF::GFF3::Record objects\n<p><code>gff_file</code> - a GFF-formatted file\n<p><code>returns</code> …\n"],["scale","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-scale","(args)","<p>Creates the scale across the top of the SVG page\n<p><code>args</code>\n<p>start = the start of the scale\n"],["span","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-span","(args)","<p>Creates a span glyph, which is a line\n<p><code>args</code>\n<p>height = the height of the Glyph (10)\n"],["to_px","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-to_px","(num)","<p>Provides the number of pixels required for a given number of nucleotides,\ne.g the length of a certain …\n"],["transcript","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-transcript","(args)","<p>Creates a transcript glyph, which is a number of different types of Glyph,\ndepending on the features …\n"],["up_triangle","Bio::Graphics::Glyph","Bio/Graphics/Glyph.html#method-c-up_triangle","(args)","<p>Creates a polygon Glyph for an upward-pointing triangle <code>args</code>\n<p>height = the height of the Glyph (10)\n<p>fill_color …\n"],["update","Bio::Graphics::Primitive","Bio/Graphics/Primitive.html#method-i-update","(args)","<p>Updates a Primitive and initialises any new parameters into instance\nvariables\n<p><code>args</code>\n<p>args = a hash of new …\n"],["write","Bio::Graphics::Page","Bio/Graphics/Page.html#method-i-write","(file)","<p>Writes the svg text to a file\n<p><code>file</code> - the file to which the svg text should be written\n\n"],["LICENSE","","LICENSE_txt.html","","<p>Copyright © 2012 Dan MacLean\n<p>Permission is hereby granted, free of charge, to any person obtaining a …\n"]],"searchIndex":["bio","graphics","glyph","minifeature","page","primitive","svgee","track","add()","add_primitive()","add_track()","circle()","close_tag()","directed()","down_triangle()","draw()","draw()","draw_circle()","draw_directed()","draw_down_triangle()","draw_features()","draw_generic()","draw_histogram()","draw_label()","draw_scale()","draw_span()","draw_transcript()","draw_up_triangle()","from_json()","generic()","get_limits()","get_markup()","get_rows()","gradient()","gradient()","gradients()","label()","new()","new()","new()","new()","new()","open_tag()","overlaps()","parse_gff()","scale()","span()","to_px()","transcript()","up_triangle()","update()","write()","license"],"longSearchIndex":["bio","bio::graphics","bio::graphics::glyph","bio::graphics::minifeature","bio::graphics::page","bio::graphics::primitive","bio::graphics::svgee","bio::graphics::track","bio::graphics::track#add()","bio::graphics::svgee#add_primitive()","bio::graphics::page#add_track()","bio::graphics::glyph::circle()","bio::graphics::svgee#close_tag()","bio::graphics::glyph::directed()","bio::graphics::glyph::down_triangle()","bio::graphics::page#draw()","bio::graphics::svgee#draw()","bio::graphics::page#draw_circle()","bio::graphics::page#draw_directed()","bio::graphics::page#draw_down_triangle()","bio::graphics::page#draw_features()","bio::graphics::page#draw_generic()","bio::graphics::page#draw_histogram()","bio::graphics::page#draw_label()","bio::graphics::page#draw_scale()","bio::graphics::page#draw_span()","bio::graphics::page#draw_transcript()","bio::graphics::page#draw_up_triangle()","bio::graphics::page::from_json()","bio::graphics::glyph::generic()","bio::graphics::page#get_limits()","bio::graphics::page#get_markup()","bio::graphics::track#get_rows()","bio::graphics::glyph::gradient()","bio::graphics::svgee#gradient()","bio::graphics::glyph::gradients()","bio::graphics::glyph::label()","bio::graphics::minifeature::new()","bio::graphics::page::new()","bio::graphics::primitive::new()","bio::graphics::svgee::new()","bio::graphics::track::new()","bio::graphics::svgee#open_tag()","bio::graphics::track#overlaps()","bio::graphics::page::parse_gff()","bio::graphics::glyph::scale()","bio::graphics::glyph::span()","bio::graphics::page#to_px()","bio::graphics::glyph::transcript()","bio::graphics::glyph::up_triangle()","bio::graphics::primitive#update()","bio::graphics::page#write()",""]}}

data/doc/js/searcher.js

@@ -0,0 +1,228 @@
+Searcher = function(data) {
+  this.data = data;
+  this.handlers = [];
+}
+
+Searcher.prototype = new function() {
+  // search is performed in chunks of 1000 for non-blocking user input
+  var CHUNK_SIZE = 1000;
+  // do not try to find more than 100 results
+  var MAX_RESULTS = 100;
+  var huid = 1;
+  var suid = 1;
+  var runs = 0;
+
+  this.find = function(query) {
+    var queries = splitQuery(query);
+    var regexps = buildRegexps(queries);
+    var highlighters = buildHilighters(queries);
+    var state = { from: 0, pass: 0, limit: MAX_RESULTS, n: suid++};
+    var _this = this;
+
+    this.currentSuid = state.n;
+
+    if (!query) return;
+
+    var run = function() {
+      // stop current search thread if new search started
+      if (state.n != _this.currentSuid) return;
+
+      var results =
+        performSearch(_this.data, regexps, queries, highlighters, state);
+      var hasMore = (state.limit > 0 && state.pass < 4);
+
+      triggerResults.call(_this, results, !hasMore);
+      if (hasMore) {
+        setTimeout(run, 2);
+      }
+      runs++;
+    };
+    runs = 0;
+
+    // start search thread
+    run();
+  }
+
+  /*  ----- Events ------  */
+  this.ready = function(fn) {
+    fn.huid = huid;
+    this.handlers.push(fn);
+  }
+
+  /*  ----- Utilities ------  */
+  function splitQuery(query) {
+    return jQuery.grep(query.split(/(\s+|::?|\(\)?)/), function(string) {
+      return string.match(/\S/)
+    });
+  }
+
+  function buildRegexps(queries) {
+    return jQuery.map(queries, function(query) {
+      return new RegExp(query.replace(/(.)/g, '([$1])([^$1]*?)'), 'i')
+    });
+  }
+
+  function buildHilighters(queries) {
+    return jQuery.map(queries, function(query) {
+      return jQuery.map(query.split(''), function(l, i) {
+        return '\u0001$' + (i*2+1) + '\u0002$' + (i*2+2);
+      }).join('');
+    });
+  }
+
+  // function longMatchRegexp(index, longIndex, regexps) {
+  //     for (var i = regexps.length - 1; i >= 0; i--){
+  //         if (!index.match(regexps[i]) && !longIndex.match(regexps[i])) return false;
+  //     };
+  //     return true;
+  // }
+
+
+  /*  ----- Mathchers ------  */
+
+  /*
+   * This record matches if the index starts with queries[0] and the record
+   * matches all of the regexps
+   */
+  function matchPassBeginning(index, longIndex, queries, regexps) {
+    if (index.indexOf(queries[0]) != 0) return false;
+    for (var i=1, l = regexps.length; i < l; i++) {
+      if (!index.match(regexps[i]) && !longIndex.match(regexps[i]))
+        return false;
+    };
+    return true;
+  }
+
+  /*
+   * This record matches if the longIndex starts with queries[0] and the
+   * longIndex matches all of the regexps
+   */
+  function matchPassLongIndex(index, longIndex, queries, regexps) {
+    if (longIndex.indexOf(queries[0]) != 0) return false;
+    for (var i=1, l = regexps.length; i < l; i++) {
+      if (!longIndex.match(regexps[i]))
+        return false;
+    };
+    return true;
+  }
+
+  /*
+   * This record matches if the index contains queries[0] and the record
+   * matches all of the regexps
+   */
+  function matchPassContains(index, longIndex, queries, regexps) {
+    if (index.indexOf(queries[0]) == -1) return false;
+    for (var i=1, l = regexps.length; i < l; i++) {
+      if (!index.match(regexps[i]) && !longIndex.match(regexps[i]))
+        return false;
+    };
+    return true;
+  }
+
+  /*
+   * This record matches if regexps[0] matches the index and the record
+   * matches all of the regexps
+   */
+  function matchPassRegexp(index, longIndex, queries, regexps) {
+    if (!index.match(regexps[0])) return false;
+    for (var i=1, l = regexps.length; i < l; i++) {
+      if (!index.match(regexps[i]) && !longIndex.match(regexps[i]))
+        return false;
+    };
+    return true;
+  }
+
+
+  /*  ----- Highlighters ------  */
+  function highlightRegexp(info, queries, regexps, highlighters) {
+    var result = createResult(info);
+    for (var i=0, l = regexps.length; i < l; i++) {
+      result.title = result.title.replace(regexps[i], highlighters[i]);
+      result.namespace = result.namespace.replace(regexps[i], highlighters[i]);
+    };
+    return result;
+  }
+
+  function hltSubstring(string, pos, length) {
+    return string.substring(0, pos) + '\u0001' + string.substring(pos, pos + length) + '\u0002' + string.substring(pos + length);
+  }
+
+  function highlightQuery(info, queries, regexps, highlighters) {
+    var result = createResult(info);
+    var pos = 0;
+    var lcTitle = result.title.toLowerCase();
+
+    pos = lcTitle.indexOf(queries[0]);
+    if (pos != -1) {
+      result.title = hltSubstring(result.title, pos, queries[0].length);
+    }
+
+    result.namespace = result.namespace.replace(regexps[0], highlighters[0]);
+    for (var i=1, l = regexps.length; i < l; i++) {
+      result.title = result.title.replace(regexps[i], highlighters[i]);
+      result.namespace = result.namespace.replace(regexps[i], highlighters[i]);
+    };
+    return result;
+  }
+
+  function createResult(info) {
+    var result = {};
+    result.title = info[0];
+    result.namespace = info[1];
+    result.path = info[2];
+    result.params = info[3];
+    result.snippet = info[4];
+    return result;
+  }
+
+  /*  ----- Searching ------  */
+  function performSearch(data, regexps, queries, highlighters, state) {
+    var searchIndex = data.searchIndex;
+    var longSearchIndex = data.longSearchIndex;
+    var info = data.info;
+    var result = [];
+    var i = state.from;
+    var l = searchIndex.length;
+    var togo = CHUNK_SIZE;
+    var matchFunc, hltFunc;
+
+    while (state.pass < 4 && state.limit > 0 && togo > 0) {
+      if (state.pass == 0) {
+        matchFunc = matchPassBeginning;
+        hltFunc = highlightQuery;
+      } else if (state.pass == 1) {
+        matchFunc = matchPassLongIndex;
+        hltFunc = highlightQuery;
+      } else if (state.pass == 2) {
+        matchFunc = matchPassContains;
+        hltFunc = highlightQuery;
+      } else if (state.pass == 3) {
+        matchFunc = matchPassRegexp;
+        hltFunc = highlightRegexp;
+      }
+
+      for (; togo > 0 && i < l && state.limit > 0; i++, togo--) {
+        if (info[i].n == state.n) continue;
+        if (matchFunc(searchIndex[i], longSearchIndex[i], queries, regexps)) {
+          info[i].n = state.n;
+          result.push(hltFunc(info[i], queries, regexps, highlighters));
+          state.limit--;
+        }
+      };
+      if (searchIndex.length <= i) {
+        state.pass++;
+        i = state.from = 0;
+      } else {
+        state.from = i;
+      }
+    }
+    return result;
+  }
+
+  function triggerResults(results, isLast) {
+    jQuery.each(this.handlers, function(i, fn) {
+      fn.call(this, results, isLast)
+    })
+  }
+}
+