diff doc/_build/html/_static/searchtools.js @ 20:40469b265ddb draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/doc/_build/html/_static/searchtools.js	Fri Jan 20 17:12:03 2017 -0500
@@ -0,0 +1,651 @@
+/*
+ * searchtools.js_t
+ * ~~~~~~~~~~~~~~~~
+ *
+ * Sphinx JavaScript utilities for the full-text search.
+ *
+ * :copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+
+/* Non-minified version JS is _stemmer.js if file is provided */ 
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+
+
+
+/**
+ * Simple result scoring code.
+ */
+var Scorer = {
+  // Implement the following function to further tweak the score for each result
+  // The function takes a result array [filename, title, anchor, descr, score]
+  // and returns the new score.
+  /*
+  score: function(result) {
+    return result[4];
+  },
+  */
+
+  // query matches the full name of an object
+  objNameMatch: 11,
+  // or matches in the last dotted part of the object name
+  objPartialMatch: 6,
+  // Additive scores depending on the priority of the object
+  objPrio: {0:  15,   // used to be importantResults
+            1:  5,   // used to be objectResults
+            2: -5},  // used to be unimportantResults
+  //  Used when the priority is not in the mapping.
+  objPrioDefault: 0,
+
+  // query found in title
+  title: 15,
+  // query found in terms
+  term: 5
+};
+
+
+/**
+ * Search Module
+ */
+var Search = {
+
+  _index : null,
+  _queued_query : null,
+  _pulse_status : -1,
+
+  init : function() {
+      var params = $.getQueryParameters();
+      if (params.q) {
+          var query = params.q[0];
+          $('input[name="q"]')[0].value = query;
+          this.performSearch(query);
+      }
+  },
+
+  loadIndex : function(url) {
+    $.ajax({type: "GET", url: url, data: null,
+            dataType: "script", cache: true,
+            complete: function(jqxhr, textstatus) {
+              if (textstatus != "success") {
+                document.getElementById("searchindexloader").src = url;
+              }
+            }});
+  },
+
+  setIndex : function(index) {
+    var q;
+    this._index = index;
+    if ((q = this._queued_query) !== null) {
+      this._queued_query = null;
+      Search.query(q);
+    }
+  },
+
+  hasIndex : function() {
+      return this._index !== null;
+  },
+
+  deferQuery : function(query) {
+      this._queued_query = query;
+  },
+
+  stopPulse : function() {
+      this._pulse_status = 0;
+  },
+
+  startPulse : function() {
+    if (this._pulse_status >= 0)
+        return;
+    function pulse() {
+      var i;
+      Search._pulse_status = (Search._pulse_status + 1) % 4;
+      var dotString = '';
+      for (i = 0; i < Search._pulse_status; i++)
+        dotString += '.';
+      Search.dots.text(dotString);
+      if (Search._pulse_status > -1)
+        window.setTimeout(pulse, 500);
+    }
+    pulse();
+  },
+
+  /**
+   * perform a search for something (or wait until index is loaded)
+   */
+  performSearch : function(query) {
+    // create the required interface elements
+    this.out = $('#search-results');
+    this.title = $('<h2>' + _('Searching') + '</h2>').appendTo(this.out);
+    this.dots = $('<span></span>').appendTo(this.title);
+    this.status = $('<p style="display: none"></p>').appendTo(this.out);
+    this.output = $('<ul class="search"/>').appendTo(this.out);
+
+    $('#search-progress').text(_('Preparing search...'));
+    this.startPulse();
+
+    // index already loaded, the browser was quick!
+    if (this.hasIndex())
+      this.query(query);
+    else
+      this.deferQuery(query);
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  query : function(query) {
+    var i;
+    var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+
+    // stem the searchterms and add them to the correct list
+    var stemmer = new Stemmer();
+    var searchterms = [];
+    var excluded = [];
+    var hlterms = [];
+    var tmp = query.split(/\W+/);
+    var objectterms = [];
+    for (i = 0; i < tmp.length; i++) {
+      if (tmp[i] !== "") {
+          objectterms.push(tmp[i].toLowerCase());
+      }
+
+      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
+          tmp[i] === "") {
+        // skip this "word"
+        continue;
+      }
+      // stem the word
+      var word = stemmer.stemWord(tmp[i].toLowerCase());
+      var toAppend;
+      // select the correct list
+      if (word[0] == '-') {
+        toAppend = excluded;
+        word = word.substr(1);
+      }
+      else {
+        toAppend = searchterms;
+        hlterms.push(tmp[i].toLowerCase());
+      }
+      // only add if not already in the list
+      if (!$u.contains(toAppend, word))
+        toAppend.push(word);
+    }
+    var highlightstring = '?highlight=' + $.urlencode(hlterms.join(" "));
+
+    // console.debug('SEARCH: searching for:');
+    // console.info('required: ', searchterms);
+    // console.info('excluded: ', excluded);
+
+    // prepare search
+    var terms = this._index.terms;
+    var titleterms = this._index.titleterms;
+
+    // array of [filename, title, anchor, descr, score]
+    var results = [];
+    $('#search-progress').empty();
+
+    // lookup as object
+    for (i = 0; i < objectterms.length; i++) {
+      var others = [].concat(objectterms.slice(0, i),
+                             objectterms.slice(i+1, objectterms.length));
+      results = results.concat(this.performObjectSearch(objectterms[i], others));
+    }
+
+    // lookup as search terms in fulltext
+    results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
+
+    // let the scorer override scores with a custom scoring function
+    if (Scorer.score) {
+      for (i = 0; i < results.length; i++)
+        results[i][4] = Scorer.score(results[i]);
+    }
+
+    // now sort the results by score (in opposite order of appearance, since the
+    // display function below uses pop() to retrieve items) and then
+    // alphabetically
+    results.sort(function(a, b) {
+      var left = a[4];
+      var right = b[4];
+      if (left > right) {
+        return 1;
+      } else if (left < right) {
+        return -1;
+      } else {
+        // same score: sort alphabetically
+        left = a[1].toLowerCase();
+        right = b[1].toLowerCase();
+        return (left > right) ? -1 : ((left < right) ? 1 : 0);
+      }
+    });
+
+    // for debugging
+    //Search.lastresults = results.slice();  // a copy
+    //console.info('search results:', Search.lastresults);
+
+    // print the results
+    var resultCount = results.length;
+    function displayNextItem() {
+      // results left, load the summary and display it
+      if (results.length) {
+        var item = results.pop();
+        var listItem = $('<li style="display:none"></li>');
+        if (DOCUMENTATION_OPTIONS.FILE_SUFFIX === '') {
+          // dirhtml builder
+          var dirname = item[0] + '/';
+          if (dirname.match(/\/index\/$/)) {
+            dirname = dirname.substring(0, dirname.length-6);
+          } else if (dirname == 'index/') {
+            dirname = '';
+          }
+          listItem.append($('<a/>').attr('href',
+            DOCUMENTATION_OPTIONS.URL_ROOT + dirname +
+            highlightstring + item[2]).html(item[1]));
+        } else {
+          // normal html builders
+          listItem.append($('<a/>').attr('href',
+            item[0] + DOCUMENTATION_OPTIONS.FILE_SUFFIX +
+            highlightstring + item[2]).html(item[1]));
+        }
+        if (item[3]) {
+          listItem.append($('<span> (' + item[3] + ')</span>'));
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
+          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
+                  dataType: "text",
+                  complete: function(jqxhr, textstatus) {
+                    var data = jqxhr.responseText;
+                    if (data !== '' && data !== undefined) {
+                      listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
+                    }
+                    Search.output.append(listItem);
+                    listItem.slideDown(5, function() {
+                      displayNextItem();
+                    });
+                  }});
+        } else {
+          // no source available, just display title
+          Search.output.append(listItem);
+          listItem.slideDown(5, function() {
+            displayNextItem();
+          });
+        }
+      }
+      // search finished, update title and status message
+      else {
+        Search.stopPulse();
+        Search.title.text(_('Search Results'));
+        if (!resultCount)
+          Search.status.text(_('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.'));
+        else
+            Search.status.text(_('Search finished, found %s page(s) matching the search query.').replace('%s', resultCount));
+        Search.status.fadeIn(500);
+      }
+    }
+    displayNextItem();
+  },
+
+  /**
+   * search for object names
+   */
+  performObjectSearch : function(object, otherterms) {
+    var filenames = this._index.filenames;
+    var objects = this._index.objects;
+    var objnames = this._index.objnames;
+    var titles = this._index.titles;
+
+    var i;
+    var results = [];
+
+    for (var prefix in objects) {
+      for (var name in objects[prefix]) {
+        var fullname = (prefix ? prefix + '.' : '') + name;
+        if (fullname.toLowerCase().indexOf(object) > -1) {
+          var score = 0;
+          var parts = fullname.split('.');
+          // check for different match types: exact matches of full name or
+          // "last name" (i.e. last dotted part)
+          if (fullname == object || parts[parts.length - 1] == object) {
+            score += Scorer.objNameMatch;
+          // matches in last name
+          } else if (parts[parts.length - 1].indexOf(object) > -1) {
+            score += Scorer.objPartialMatch;
+          }
+          var match = objects[prefix][name];
+          var objname = objnames[match[1]][2];
+          var title = titles[match[0]];
+          // If more than one term searched for, we require other words to be
+          // found in the name/title/description
+          if (otherterms.length > 0) {
+            var haystack = (prefix + ' ' + name + ' ' +
+                            objname + ' ' + title).toLowerCase();
+            var allfound = true;
+            for (i = 0; i < otherterms.length; i++) {
+              if (haystack.indexOf(otherterms[i]) == -1) {
+                allfound = false;
+                break;
+              }
+            }
+            if (!allfound) {
+              continue;
+            }
+          }
+          var descr = objname + _(', in ') + title;
+
+          var anchor = match[3];
+          if (anchor === '')
+            anchor = fullname;
+          else if (anchor == '-')
+            anchor = objnames[match[1]][1] + '-' + fullname;
+          // add custom score for some objects according to scorer
+          if (Scorer.objPrio.hasOwnProperty(match[2])) {
+            score += Scorer.objPrio[match[2]];
+          } else {
+            score += Scorer.objPrioDefault;
+          }
+          results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
+        }
+      }
+    }
+
+    return results;
+  },
+
+  /**
+   * search for full-text terms in the index
+   */
+  performTermsSearch : function(searchterms, excluded, terms, titleterms) {
+    var filenames = this._index.filenames;
+    var titles = this._index.titles;
+
+    var i, j, file;
+    var fileMap = {};
+    var scoreMap = {};
+    var results = [];
+
+    // perform the search on the required terms
+    for (i = 0; i < searchterms.length; i++) {
+      var word = searchterms[i];
+      var files = [];
+      var _o = [
+        {files: terms[word], score: Scorer.term},
+        {files: titleterms[word], score: Scorer.title}
+      ];
+
+      // no match but word was a required one
+      if ($u.every(_o, function(o){return o.files === undefined;})) {
+        break;
+      }
+      // found search word in contents
+      $u.each(_o, function(o) {
+        var _files = o.files;
+        if (_files === undefined)
+          return
+
+        if (_files.length === undefined)
+          _files = [_files];
+        files = files.concat(_files);
+
+        // set score for the word in each file to Scorer.term
+        for (j = 0; j < _files.length; j++) {
+          file = _files[j];
+          if (!(file in scoreMap))
+            scoreMap[file] = {}
+          scoreMap[file][word] = o.score;
+        }
+      });
+
+      // create the mapping
+      for (j = 0; j < files.length; j++) {
+        file = files[j];
+        if (file in fileMap)
+          fileMap[file].push(word);
+        else
+          fileMap[file] = [word];
+      }
+    }
+
+    // now check if the files don't contain excluded terms
+    for (file in fileMap) {
+      var valid = true;
+
+      // check if all requirements are matched
+      if (fileMap[file].length != searchterms.length)
+          continue;
+
+      // ensure that none of the excluded terms is in the search result
+      for (i = 0; i < excluded.length; i++) {
+        if (terms[excluded[i]] == file ||
+            titleterms[excluded[i]] == file ||
+            $u.contains(terms[excluded[i]] || [], file) ||
+            $u.contains(titleterms[excluded[i]] || [], file)) {
+          valid = false;
+          break;
+        }
+      }
+
+      // if we have still a valid result we can add it to the result list
+      if (valid) {
+        // select one (max) score for the file.
+        // for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
+        var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
+        results.push([filenames[file], titles[file], '', null, score]);
+      }
+    }
+    return results;
+  },
+
+  /**
+   * helper function to return a node containing the
+   * search summary for a given text. keywords is a list
+   * of stemmed words, hlwords is the list of normal, unstemmed
+   * words. the first one is used to find the occurrence, the
+   * latter for highlighting it.
+   */
+  makeSearchSummary : function(text, keywords, hlwords) {
+    var textLower = text.toLowerCase();
+    var start = 0;
+    $.each(keywords, function() {
+      var i = textLower.indexOf(this.toLowerCase());
+      if (i > -1)
+        start = i;
+    });
+    start = Math.max(start - 120, 0);
+    var excerpt = ((start > 0) ? '...' : '') +
+      $.trim(text.substr(start, 240)) +
+      ((start + 240 - text.length) ? '...' : '');
+    var rv = $('<div class="context"></div>').text(excerpt);
+    $.each(hlwords, function() {
+      rv = rv.highlightText(this, 'highlighted');
+    });
+    return rv;
+  }
+};
+
+$(document).ready(function() {
+  Search.init();
+});
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