parse_fasta 1.0.0 → 1.0.1

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  1. checksums.yaml +4 -4
  2. data/.gitignore +1 -0
  3. data/lib/parse_fasta/version.rb +1 -1
  4. metadata +1 -19
  5. data/doc/FastaFile.html +0 -292
  6. data/doc/File.html +0 -212
  7. data/doc/ParseFasta.html +0 -144
  8. data/doc/Sequence.html +0 -361
  9. data/doc/_index.html +0 -136
  10. data/doc/class_list.html +0 -54
  11. data/doc/css/common.css +0 -1
  12. data/doc/css/full_list.css +0 -57
  13. data/doc/css/style.css +0 -339
  14. data/doc/file.README.html +0 -161
  15. data/doc/file_list.html +0 -56
  16. data/doc/frames.html +0 -26
  17. data/doc/index.html +0 -161
  18. data/doc/js/app.js +0 -219
  19. data/doc/js/full_list.js +0 -178
  20. data/doc/js/jquery.js +0 -4
  21. data/doc/method_list.html +0 -71
  22. data/doc/top-level-namespace.html +0 -114
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- document.getElementById('base_target').target = 'main';
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- document.body.className = 'frames';
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- }
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- </script>
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- <div id="content">
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- <h1 id="full_list_header">File List</h1>
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- <li class="r1"><span class="object_link"><a href="index.html" title="README">README</a></a></li>
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- </div>
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- </body>
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- </html>
data/doc/frames.html DELETED
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- <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN"
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- <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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- <head>
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- <title>Documentation by YARD 0.8.7.4</title>
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- </head>
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- <script type="text/javascript" charset="utf-8">
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- window.onload = function() {
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- File: README
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- &mdash; Documentation by YARD 0.8.7.4
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- <body>
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- <a href="_index.html">Index</a> &raquo;
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- <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
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- </div>
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- <div id="search">
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- <a class="full_list_link" id="class_list_link"
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- href="class_list.html">
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- Class List
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- <a class="full_list_link" id="method_list_link"
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- href="method_list.html">
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- Method List
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- <a class="full_list_link" id="file_list_link"
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- href="file_list.html">
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- File List
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- </a>
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- </div>
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- <div class="clear"></div>
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-
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- <iframe id="search_frame"></iframe>
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-
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- <div id="content"><div id='filecontents'>
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- <h1 id="label-parse_fasta">parse_fasta</h1>
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-
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- <p>So you want to parse a fasta file…</p>
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-
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- <h2 id="label-Installation">Installation</h2>
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-
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- <p>Add this line to your application&#39;s Gemfile:</p>
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-
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- <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_gem'>gem</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>&#39;</span></span></code></pre>
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-
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- <p>And then execute:</p>
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-
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- <pre class="code ruby"><code class="ruby">$ bundle</code></pre>
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-
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- <p>Or install it yourself as:</p>
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-
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- <pre class="code ruby"><code class="ruby">$ gem install parse_fasta</code></pre>
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-
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- <h2 id="label-Overview">Overview</h2>
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-
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- <p>Provides the method <code>#each_record</code> for the <code>File</code>
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- class.</p>
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-
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- <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_each_record'>each_record</span> <span class='lbrace'>{</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span> <span class='id identifier rubyid_block'>block</span> <span class='rbrace'>}</span>
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- </code></pre>
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-
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- <p>The whole file is not loaded into memory, so have no fear of giant fasta
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- files!</p>
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-
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- <h2 id="label-Usage">Usage</h2>
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-
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- <h3 id="label-Version+1.0.0+%28current%29">Version 1.0.0 (current)</h3>
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-
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- <p>The monkey patch of the <code>File</code> class is no more! Here is the new
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- print length example:</p>
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-
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- <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_require'>require</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>&#39;</span></span>
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-
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- <span class='const'>FastaFile</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='const'>ARGV</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_record'>each_record</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span>
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- <span class='id identifier rubyid_puts'>puts</span> <span class='lbracket'>[</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
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- <span class='kw'>end</span>
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- </code></pre>
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-
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- <p>And here, a script to calculate GC content:</p>
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-
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- <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_require'>require</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>&#39;</span></span>
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-
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- <span class='const'>FastaFile</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='const'>ARGV</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_record'>each_record</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span>
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- <span class='id identifier rubyid_puts'>puts</span> <span class='lbracket'>[</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='period'>.</span><span class='id identifier rubyid_gc'>gc</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
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- <span class='kw'>end</span>
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- </code></pre>
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-
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- <h3 id="label-Version+0.0.5+%28old%29">Version 0.0.5 (old)</h3>
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-
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- <p>An example that lists the length for each sequence. (Won&#39;t work in
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- version 1.0.0)</p>
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-
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- <pre class="code ruby"><code class="ruby"><span class='id identifier rubyid_require'>require</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>parse_fasta</span><span class='tstring_end'>&#39;</span></span>
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-
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- <span class='const'>File</span><span class='period'>.</span><span class='id identifier rubyid_open'>open</span><span class='lparen'>(</span><span class='const'>ARGV</span><span class='period'>.</span><span class='id identifier rubyid_first'>first</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&#39;</span><span class='tstring_content'>r</span><span class='tstring_end'>&#39;</span></span><span class='rparen'>)</span><span class='period'>.</span><span class='id identifier rubyid_each_record'>each_record</span> <span class='kw'>do</span> <span class='op'>|</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='op'>|</span>
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- <span class='id identifier rubyid_puts'>puts</span> <span class='lbracket'>[</span><span class='id identifier rubyid_header'>header</span><span class='comma'>,</span> <span class='id identifier rubyid_sequence'>sequence</span><span class='period'>.</span><span class='id identifier rubyid_length'>length</span><span class='rbracket'>]</span><span class='period'>.</span><span class='id identifier rubyid_join'>join</span><span class='lparen'>(</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>\t</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
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- <span class='kw'>end</span>
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- </code></pre>
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-
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- <h2 id="label-Benchmark">Benchmark</h2>
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-
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- <p>Just for fun, I wanted to compare the execution time to that of BioRuby. I
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- calculated sequence length for each fasta record with both the
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- <code>each_record</code> method from this gem and using the
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- <code>FastaFormat</code> class from BioRuby. You can see the test script in
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- <code>benchmark.rb</code>.</p>
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-
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- <p>The test file contained 2,009,897 illumina reads and the file size was 1.1
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- gigabytes. Here are the results from Ruby&#39;s <code>Benchmark</code>
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- class:</p>
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-
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- <pre class="code ruby"><code class="ruby"> user system total real
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- parse_fasta 64.530000 1.740000 66.270000 ( 67.081502)
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- bioruby 116.250000 2.260000 118.510000 (120.223710)</code></pre>
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-
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- <p>I just wanted a nice, clean way to parse fasta files, but being nearly
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- twice as fasta as BioRuby doesn&#39;t hurt either!</p>
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-
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- <h2 id="label-Notes">Notes</h2>
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-
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- <p>Currently in doesn&#39;t check whether your file is actually a fasta file
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- or anything, so watch out.</p>
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- </div></div>
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-
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- <div id="footer">
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- Generated on Tue Jun 3 22:55:41 2014 by
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- <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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- 0.8.7.4 (ruby-2.1.1).
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data/doc/js/app.js DELETED
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- if ($('#' + proposedId).length > 0) { proposedId += counter; counter++; }
171
- this.id = proposedId;
172
- }
173
- }
174
- if (thisTag > lastTag) {
175
- for (i = 0; i < thisTag - lastTag; i++) {
176
- var tmp = $('<ol/>'); toc.append(tmp); toc = tmp;
177
- }
178
- }
179
- if (thisTag < lastTag) {
180
- for (i = 0; i < lastTag - thisTag; i++) toc = toc.parent();
181
- }
182
- var title = $(this).attr('toc-title');
183
- if (typeof(title) == "undefined") title = $(this).text();
184
- toc.append('<li><a href="#' + this.id + '">' + title + '</a></li>');
185
- lastTag = thisTag;
186
- });
187
- if (!show) return;
188
- html = '<div id="toc"><p class="title"><a class="hide_toc" href="#"><strong>Table of Contents</strong></a> <small>(<a href="#" class="float_toc">left</a>)</small></p></div>';
189
- $('#content').prepend(html);
190
- $('#toc').append(_toc);
191
- $('#toc .hide_toc').toggle(function() {
192
- $('#toc .top').slideUp('fast');
193
- $('#toc').toggleClass('hidden');
194
- $('#toc .title small').toggle();
195
- }, function() {
196
- $('#toc .top').slideDown('fast');
197
- $('#toc').toggleClass('hidden');
198
- $('#toc .title small').toggle();
199
- });
200
- $('#toc .float_toc').toggle(function() {
201
- $(this).text('float');
202
- $('#toc').toggleClass('nofloat');
203
- }, function() {
204
- $(this).text('left');
205
- $('#toc').toggleClass('nofloat');
206
- });
207
- }
208
-
209
- $(framesInit);
210
- $(createSourceLinks);
211
- $(createDefineLinks);
212
- $(createFullTreeLinks);
213
- $(fixBoxInfoHeights);
214
- $(searchFrameLinks);
215
- $(linkSummaries);
216
- $(keyboardShortcuts);
217
- $(summaryToggle);
218
- $(fixOutsideWorldLinks);
219
- $(generateTOC);
data/doc/js/full_list.js DELETED
@@ -1,178 +0,0 @@
1
- var inSearch = null;
2
- var searchIndex = 0;
3
- var searchCache = [];
4
- var searchString = '';
5
- var regexSearchString = '';
6
- var caseSensitiveMatch = false;
7
- var ignoreKeyCodeMin = 8;
8
- var ignoreKeyCodeMax = 46;
9
- var commandKey = 91;
10
-
11
- RegExp.escape = function(text) {
12
- return text.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, "\\$&");
13
- }
14
-
15
- function fullListSearch() {
16
- // generate cache
17
- searchCache = [];
18
- $('#full_list li').each(function() {
19
- var link = $(this).find('.object_link a');
20
- if (link.length === 0) return;
21
- var fullName = link.attr('title').split(' ')[0];
22
- searchCache.push({name:link.text(), fullName:fullName, node:$(this), link:link});
23
- });
24
-
25
- $('#search input').keyup(function(event) {
26
- if ((event.keyCode > ignoreKeyCodeMin && event.keyCode < ignoreKeyCodeMax)
27
- || event.keyCode == commandKey)
28
- return;
29
- searchString = this.value;
30
- caseSensitiveMatch = searchString.match(/[A-Z]/) != null;
31
- regexSearchString = RegExp.escape(searchString);
32
- if (caseSensitiveMatch) {
33
- regexSearchString += "|" +
34
- $.map(searchString.split(''), function(e) { return RegExp.escape(e); }).
35
- join('.+?');
36
- }
37
- if (searchString === "") {
38
- clearTimeout(inSearch);
39
- inSearch = null;
40
- $('ul .search_uncollapsed').removeClass('search_uncollapsed');
41
- $('#full_list, #content').removeClass('insearch');
42
- $('#full_list li').removeClass('found').each(function() {
43
-
44
- var link = $(this).find('.object_link a');
45
- if (link.length > 0) link.text(link.text());
46
- });
47
- if (clicked) {
48
- clicked.parents('ul').each(function() {
49
- $(this).removeClass('collapsed').prev().removeClass('collapsed');
50
- });
51
- }
52
- highlight();
53
- }
54
- else {
55
- if (inSearch) clearTimeout(inSearch);
56
- searchIndex = 0;
57
- lastRowClass = '';
58
- $('#full_list, #content').addClass('insearch');
59
- $('#noresults').text('');
60
- searchItem();
61
- }
62
- });
63
-
64
- $('#search input').focus();
65
- $('#full_list').after("<div id='noresults'></div>");
66
- }
67
-
68
- var lastRowClass = '';
69
- function searchItem() {
70
- for (var i = 0; i < searchCache.length / 50; i++) {
71
- var item = searchCache[searchIndex];
72
- var searchName = (searchString.indexOf('::') != -1 ? item.fullName : item.name);
73
- var matchString = regexSearchString;
74
- var matchRegexp = new RegExp(matchString, caseSensitiveMatch ? "" : "i");
75
- if (searchName.match(matchRegexp) == null) {
76
- item.node.removeClass('found');
77
- }
78
- else {
79
- item.node.css('padding-left', '10px').addClass('found');
80
- item.node.parents().addClass('search_uncollapsed');
81
- item.node.removeClass(lastRowClass).addClass(lastRowClass == 'r1' ? 'r2' : 'r1');
82
- lastRowClass = item.node.hasClass('r1') ? 'r1' : 'r2';
83
- item.link.html(item.name.replace(matchRegexp, "<strong>$&</strong>"));
84
- }
85
-
86
- if (searchCache.length === searchIndex + 1) {
87
- searchDone();
88
- return;
89
- }
90
- else {
91
- searchIndex++;
92
- }
93
- }
94
- inSearch = setTimeout('searchItem()', 0);
95
- }
96
-
97
- function searchDone() {
98
- highlight(true);
99
- if ($('#full_list li:visible').size() === 0) {
100
- $('#noresults').text('No results were found.').hide().fadeIn();
101
- }
102
- else {
103
- $('#noresults').text('');
104
- }
105
- $('#content').removeClass('insearch');
106
- clearTimeout(inSearch);
107
- inSearch = null;
108
- }
109
-
110
- clicked = null;
111
- function linkList() {
112
- $('#full_list li, #full_list li a:last').click(function(evt) {
113
- if ($(this).hasClass('toggle')) return true;
114
- if (this.tagName.toLowerCase() == "li") {
115
- if ($(this).find('.object_link a').length === 0) {
116
- $(this).children('a.toggle').click();
117
- return false;
118
- }
119
- var toggle = $(this).children('a.toggle');
120
- if (toggle.size() > 0 && evt.pageX < toggle.offset().left) {
121
- toggle.click();
122
- return false;
123
- }
124
- }
125
- if (clicked) clicked.removeClass('clicked');
126
- var win = window.top.frames.main ? window.top.frames.main : window.parent;
127
- if (this.tagName.toLowerCase() == "a") {
128
- clicked = $(this).parents('li').addClass('clicked');
129
- win.location = this.href;
130
- }
131
- else {
132
- clicked = $(this).addClass('clicked');
133
- win.location = $(this).find('a:last').attr('href');
134
- }
135
- return false;
136
- });
137
- }
138
-
139
- function collapse() {
140
- if (!$('#full_list').hasClass('class')) return;
141
- $('#full_list.class a.toggle').click(function() {
142
- $(this).parent().toggleClass('collapsed').next().toggleClass('collapsed');
143
- highlight();
144
- return false;
145
- });
146
- $('#full_list.class ul').each(function() {
147
- $(this).addClass('collapsed').prev().addClass('collapsed');
148
- });
149
- $('#full_list.class').children().removeClass('collapsed');
150
- highlight();
151
- }
152
-
153
- function highlight(no_padding) {
154
- var n = 1;
155
- $('#full_list li:visible').each(function() {
156
- var next = n == 1 ? 2 : 1;
157
- $(this).removeClass("r" + next).addClass("r" + n);
158
- if (!no_padding && $('#full_list').hasClass('class')) {
159
- $(this).css('padding-left', (10 + $(this).parents('ul').size() * 15) + 'px');
160
- }
161
- n = next;
162
- });
163
- }
164
-
165
- function escapeShortcut() {
166
- $(document).keydown(function(evt) {
167
- if (evt.which == 27) {
168
- $('#search_frame', window.top.document).slideUp(100);
169
- $('#search a', window.top.document).removeClass('active inactive');
170
- $(window.top).focus();
171
- }
172
- });
173
- }
174
-
175
- $(escapeShortcut);
176
- $(fullListSearch);
177
- $(linkList);
178
- $(collapse);