manually writing up JavaScript API

docs/_build_html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 6d951a9cf5925d085b5d376fd31212d6
+config: e22f7d2efb6cf8a09998f298823ed2eb
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build_html/_sources/clustergrammer_js.rst.txt

@@ -55,6 +55,23 @@ Clustergrammer-JS API
 =====================
 Clustergrammer-JS' API allows users to pass options to the front-end visualization, such as optional callback functions.
 
+
+.. js:class:: Clustergrammer(args)
+
+  The Clusterrammer JavaScript object.
+
+  :args: The visualization JSON as well as optional arguments will be passed here.
+
+  Clustergrammer functions:
+
+  .. js:function:: update_cats(row_data)
+
+    Update the visualization row categories.
+
+    :param row_data: The row category data that will be used to ...
+
+
+
 .. _visualization_json:
 
 Visualization-JSON

docs/_build_html/_sources/clustergrammer_py.rst.txt

@@ -61,7 +61,6 @@ When a matrix is loaded into an instance of ``Network`` (e.g. ``net``) it is sto
     :members:
 
 
-
 .. _clustergrammer_py_dev:
 
 Clustergrammer-PY Development

docs/_build_html/_static/basic.css

@@ -85,10 +85,6 @@ div.sphinxsidebar #searchbox input[type="text"] {
     width: 170px;
 }
 
-div.sphinxsidebar #searchbox input[type="submit"] {
-    width: 30px;
-}
-
 img {
     border: 0;
     max-width: 100%;
@@ -126,6 +122,8 @@ ul.keywordmatches li.goodmatch a {
 
 table.contentstable {
     width: 90%;
+    margin-left: auto;
+    margin-right: auto;
 }
 
 table.contentstable p.biglink {
@@ -153,9 +151,14 @@ table.indextable td {
     vertical-align: top;
 }
 
-table.indextable dl, table.indextable dd {
+table.indextable ul {
     margin-top: 0;
     margin-bottom: 0;
+    list-style-type: none;
+}
+
+table.indextable > tbody > tr > td > ul {
+    padding-left: 0em;
 }
 
 table.indextable tr.pcap {
@@ -187,6 +190,13 @@ div.genindex-jumpbox {
     padding: 0.4em;
 }
 
+/* -- domain module index --------------------------------------------------- */
+
+table.modindextable td {
+    padding: 2px;
+    border-collapse: collapse;
+}
+
 /* -- general body styles --------------------------------------------------- */
 
 div.body p, div.body dd, div.body li, div.body blockquote {
@@ -221,10 +231,6 @@ div.body td {
     text-align: left;
 }
 
-.field-list ul {
-    padding-left: 1em;
-}
-
 .first {
     margin-top: 0 !important;
 }
@@ -341,10 +347,6 @@ table.docutils td, table.docutils th {
     border-bottom: 1px solid #aaa;
 }
 
-table.field-list td, table.field-list th {
-    border: 0 !important;
-}
-
 table.footnote td, table.footnote th {
     border: 0 !important;
 }
@@ -381,6 +383,20 @@ div.figure p.caption span.caption-number {
 div.figure p.caption span.caption-text {
 }
 
+/* -- field list styles ----------------------------------------------------- */
+
+table.field-list td, table.field-list th {
+    border: 0 !important;
+}
+
+.field-list ul {
+    margin: 0;
+    padding-left: 1em;
+}
+
+.field-list p {
+    margin: 0;
+}
 
 /* -- other body styles ----------------------------------------------------- */
 
@@ -431,15 +447,6 @@ dl.glossary dt {
     font-size: 1.1em;
 }
 
-.field-list ul {
-    margin: 0;
-    padding-left: 1em;
-}
-
-.field-list p {
-    margin: 0;
-}
-
 .optional {
     font-size: 1.3em;
 }
@@ -498,6 +505,13 @@ pre {
     overflow-y: hidden;  /* fixes display issues on Chrome browsers */
 }
 
+span.pre {
+    -moz-hyphens: none;
+    -ms-hyphens: none;
+    -webkit-hyphens: none;
+    hyphens: none;
+}
+
 td.linenos pre {
     padding: 5px 0px;
     border: 0;
@@ -589,6 +603,16 @@ span.eqno {
     float: right;
 }
 
+span.eqno a.headerlink {
+    position: relative;
+    left: 0px;
+    z-index: 1;
+}
+
+div.math:hover a.headerlink {
+    visibility: visible;
+}
+
 /* -- printout stylesheet --------------------------------------------------- */
 
 @media print {

docs/_build_html/_static/searchtools.js

@@ -226,6 +226,106 @@ var Scorer = {
 };
 
 
+
+
+
+var splitChars = (function() {
+    var result = {};
+    var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
+         1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
+         2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
+         2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
+         3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
+         3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
+         4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
+         8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
+         11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
+         43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
+    var i, j, start, end;
+    for (i = 0; i < singles.length; i++) {
+        result[singles[i]] = true;
+    }
+    var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
+         [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
+         [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
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+         [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
+         [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
+         [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
+    for (i = 0; i < ranges.length; i++) {
+        start = ranges[i][0];
+        end = ranges[i][1];
+        for (j = start; j <= end; j++) {
+            result[j] = true;
+        }
+    }
+    return result;
+})();
+
+function splitQuery(query) {
+    var result = [];
+    var start = -1;
+    for (var i = 0; i < query.length; i++) {
+        if (splitChars[query.charCodeAt(i)]) {
+            if (start !== -1) {
+                result.push(query.slice(start, i));
+                start = -1;
+            }
+        } else if (start === -1) {
+            start = i;
+        }
+    }
+    if (start !== -1) {
+        result.push(query.slice(start));
+    }
+    return result;
+}
+
+
+
+
 /**
  * Search Module
  */
@@ -324,7 +424,7 @@ var Search = {
     var searchterms = [];
     var excluded = [];
     var hlterms = [];
-    var tmp = query.split(/\s+/);
+    var tmp = splitQuery(query);
     var objectterms = [];
     for (i = 0; i < tmp.length; i++) {
       if (tmp[i] !== "") {
@@ -338,6 +438,10 @@ var Search = {
       }
       // stem the word
       var word = stemmer.stemWord(tmp[i].toLowerCase());
+      // prevent stemmer from cutting word smaller than two chars
+      if(word.length < 3 && tmp[i].length >= 3) {
+        word = tmp[i];
+      }
       var toAppend;
       // select the correct list
       if (word[0] == '-') {
@@ -435,7 +539,8 @@ var Search = {
             displayNextItem();
           });
         } else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
-          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
+          var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
+          $.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
                   dataType: "text",
                   complete: function(jqxhr, textstatus) {
                     var data = jqxhr.responseText;
@@ -474,6 +579,7 @@ var Search = {
    */
   performObjectSearch : function(object, otherterms) {
     var filenames = this._index.filenames;
+    var docnames = this._index.docnames;
     var objects = this._index.objects;
     var objnames = this._index.objnames;
     var titles = this._index.titles;
@@ -527,7 +633,7 @@ var Search = {
           } else {
             score += Scorer.objPrioDefault;
           }
-          results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
+          results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
         }
       }
     }
@@ -539,6 +645,7 @@ var Search = {
    * search for full-text terms in the index
    */
   performTermsSearch : function(searchterms, excluded, terms, titleterms) {
+    var docnames = this._index.docnames;
     var filenames = this._index.filenames;
     var titles = this._index.titles;
 
@@ -613,7 +720,7 @@ var Search = {
         // 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]);
+        results.push([docnames[file], titles[file], '', null, score, filenames[file]]);
       }
     }
     return results;

docs/_build_html/app_integration.html

@@ -30,6 +30,9 @@
 
 
 
+        <link rel="index" title="Index"
+              href="genindex.html"/>
+        <link rel="search" title="Search" href="search.html"/>
     <link rel="top" title="Clustergrammer 1.0.0 documentation" href="index.html"/>
         <link rel="next" title="Developing Clustergrammer" href="developing_with_clustergrammer.html"/>
         <link rel="prev" title="Clustergrammer-PY" href="clustergrammer_py.html"/> 
@@ -135,7 +138,7 @@
       <li class="wy-breadcrumbs-aside">
 
 
-            <a href="_sources/app_integration.txt" rel="nofollow"> View page source</a>
+            <a href="_sources/app_integration.rst.txt" rel="nofollow"> View page source</a>
 
 
       </li>

docs/_build_html/biology_specific_features.html

@@ -30,6 +30,9 @@
 
 
 
+        <link rel="index" title="Index"
+              href="genindex.html"/>
+        <link rel="search" title="Search" href="search.html"/>
     <link rel="top" title="Clustergrammer 1.0.0 documentation" href="index.html"/>
         <link rel="next" title="Case Studies" href="case_studies.html"/>
         <link rel="prev" title="Interacting with the Visualization" href="interacting_with_viz.html"/> 
@@ -133,7 +136,7 @@
       <li class="wy-breadcrumbs-aside">
 
 
-            <a href="_sources/biology_specific_features.txt" rel="nofollow"> View page source</a>
+            <a href="_sources/biology_specific_features.rst.txt" rel="nofollow"> View page source</a>
 
 
       </li>