UCSCBin 0.2.0

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  1. data/LICENSE +21 -0
  2. data/README.rdoc +46 -0
  3. data/Rakefile +51 -0
  4. data/UCSCBin.gemspec +92 -0
  5. data/VERSION +1 -0
  6. data/lib/UCSCBin.rb +144 -0
  7. data/rdoc/README_rdoc.html +170 -0
  8. data/rdoc/UCSCBin.html +185 -0
  9. data/rdoc/UCSCBin/BinRange.html +454 -0
  10. data/rdoc/UCSCBin/Utils.html +242 -0
  11. data/rdoc/created.rid +1 -0
  12. data/rdoc/images/brick.png +0 -0
  13. data/rdoc/images/brick_link.png +0 -0
  14. data/rdoc/images/bug.png +0 -0
  15. data/rdoc/images/bullet_black.png +0 -0
  16. data/rdoc/images/bullet_toggle_minus.png +0 -0
  17. data/rdoc/images/bullet_toggle_plus.png +0 -0
  18. data/rdoc/images/date.png +0 -0
  19. data/rdoc/images/find.png +0 -0
  20. data/rdoc/images/loadingAnimation.gif +0 -0
  21. data/rdoc/images/macFFBgHack.png +0 -0
  22. data/rdoc/images/package.png +0 -0
  23. data/rdoc/images/page_green.png +0 -0
  24. data/rdoc/images/page_white_text.png +0 -0
  25. data/rdoc/images/page_white_width.png +0 -0
  26. data/rdoc/images/plugin.png +0 -0
  27. data/rdoc/images/ruby.png +0 -0
  28. data/rdoc/images/tag_green.png +0 -0
  29. data/rdoc/images/wrench.png +0 -0
  30. data/rdoc/images/wrench_orange.png +0 -0
  31. data/rdoc/images/zoom.png +0 -0
  32. data/rdoc/index.html +79 -0
  33. data/rdoc/js/darkfish.js +116 -0
  34. data/rdoc/js/jquery.js +32 -0
  35. data/rdoc/js/quicksearch.js +114 -0
  36. data/rdoc/js/thickbox-compressed.js +10 -0
  37. data/rdoc/lib/UCSCBin_rb.html +82 -0
  38. data/rdoc/rdoc.css +696 -0
  39. data/sample/refseqgene.rb +35 -0
  40. data/spec/UCSCBin_BinRange_spec.rb +47 -0
  41. data/spec/UCSCBin_Utils_spec.rb +49 -0
  42. data/spec/spec.opts +1 -0
  43. data/spec/spec_helper.rb +9 -0
  44. metadata +132 -0
data/rdoc/UCSCBin/Utils.html ADDED
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+ <?xml version="1.0" encoding="utf-8"?>
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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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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+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
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+
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+ <title>Class: UCSCBin::Utils</title>
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+
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+ <link rel="stylesheet" href="../rdoc.css" type="text/css" media="screen" />
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+
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+ <script src="../js/jquery.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="../js/thickbox-compressed.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="../js/quicksearch.js" type="text/javascript"
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+ charset="utf-8"></script>
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+ <script src="../js/darkfish.js" type="text/javascript"
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+ charset="utf-8"></script>
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+
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+ </head>
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+ <body class="class">
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+
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+ <div id="metadata">
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+ <div id="file-metadata">
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+ <div id="file-list-section" class="section">
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+ <h3 class="section-header">In Files</h3>
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+ <div class="section-body">
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+ <ul>
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+
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+ <li><a href="../lib/UCSCBin_rb.html?TB_iframe=true&amp;height=550&amp;width=785"
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+ class="thickbox" title="lib/UCSCBin.rb">lib/UCSCBin.rb</a></li>
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+
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+ </ul>
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+ </div>
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+ </div>
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+
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+
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+ </div>
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+
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+ <div id="class-metadata">
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+
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+ <!-- Parent Class -->
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+
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+ <div id="parent-class-section" class="section">
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+ <h3 class="section-header">Parent</h3>
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+
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+ <p class="link">Object</p>
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+
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+ </div>
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+
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+
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+ <!-- Namespace Contents -->
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+
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+
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+ <!-- Method Quickref -->
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+
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+ <div id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+ <ul class="link-list">
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+
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+ <li><a href="#M000001">::one_to_zero</a></li>
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+
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+ <li><a href="#M000000">::zero_to_one</a></li>
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+
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+ </ul>
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+ </div>
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+
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+
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+ <!-- Included Modules -->
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+
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+ </div>
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+
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+ <div id="project-metadata">
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+
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+
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+ <div id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Files</h3>
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+ <ul>
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+
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+ <li class="file"><a href="../README_rdoc.html">README.rdoc</a></li>
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+
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+ </ul>
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+ </div>
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+
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+
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+ <div id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class Index
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+ <span class="search-toggle"><img src="../images/find.png"
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+ height="16" width="16" alt="[+]"
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+ title="show/hide quicksearch" /></span></h3>
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+ <form action="#" method="get" accept-charset="utf-8" class="initially-hidden">
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+ <fieldset>
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+ <legend>Quicksearch</legend>
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+ <input type="text" name="quicksearch" value=""
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+ class="quicksearch-field" />
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+ </fieldset>
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+ </form>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="../UCSCBin.html">UCSCBin</a></li>
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+
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+ <li><a href="../UCSCBin/BinRange.html">UCSCBin::BinRange</a></li>
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+
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+ <li><a href="../UCSCBin/Utils.html">UCSCBin::Utils</a></li>
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+
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+ </ul>
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+ <div id="no-class-search-results" style="display: none;">No matching classes.</div>
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+ </div>
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+
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+
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+ </div>
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+ </div>
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+
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+ <div id="documentation">
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+ <h1 class="class">UCSCBin::Utils</h1>
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+
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+ <div id="description">
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+
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+ </div>
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+
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+ <!-- Constants -->
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+
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+
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+ <!-- Attributes -->
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+
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+
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+ <!-- Methods -->
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+
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+ <div id="public-class-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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+
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+
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+ <div id="one-to-zero-method" class="method-detail ">
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+ <a name="M000001"></a>
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+
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+ <div class="method-heading">
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+
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+ <span class="method-name">one_to_zero</span><span
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+ class="method-args">(one_start, one_end)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+
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+ </div>
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+
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+ <div class="method-description">
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+
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+ <p>
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+ &#8216;one_start&#8217; and &#8216;one_end&#8217; are 1-based full-close
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+ used in UCSC genome browser&#8217;s human interface and most of other
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+ formats the first one base in a chromosome is [1, 1] Positions must be
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+ start<=end
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+ </p>
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+
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+
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+
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+ <div class="method-source-code"
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+ id="one-to-zero-source">
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+ <pre>
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+ <span class="ruby-comment cmt"># File lib/UCSCBin.rb, line 45</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">one_to_zero</span>(<span class="ruby-identifier">one_start</span>, <span class="ruby-identifier">one_end</span>)
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+ <span class="ruby-keyword kw">case</span>
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+ <span class="ruby-keyword kw">when</span> (<span class="ruby-identifier">one_start</span> <span class="ruby-operator">&lt;</span> <span class="ruby-value">1</span> <span class="ruby-operator">||</span> <span class="ruby-identifier">one_end</span> <span class="ruby-operator">&lt;</span> <span class="ruby-value">1</span>)
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+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-value str">&quot;positions must be &gt;=1&quot;</span>
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+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">one_start</span> <span class="ruby-operator">&gt;</span> <span class="ruby-identifier">one_end</span>
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+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-value str">&quot;positions must be start&lt;=end&quot;</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+ [<span class="ruby-identifier">one_start</span> <span class="ruby-operator">-</span> <span class="ruby-value">1</span> , <span class="ruby-identifier">one_end</span>]
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </div>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <div id="zero-to-one-method" class="method-detail ">
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+ <a name="M000000"></a>
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+
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+ <div class="method-heading">
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+
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+ <span class="method-name">zero_to_one</span><span
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+ class="method-args">(zero_start, zero_end)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+
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+ </div>
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+
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+ <div class="method-description">
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+
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+ <p>
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+ &#8216;zero_start&#8217; and &#8216;zero_end&#8217; are 0-based half-open
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+ used in UCSC MySQL database and the BED format. the first one base in a
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+ chromosome is [0, 1) Positions must be start<end
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+ </p>
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+
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+
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+
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+ <div class="method-source-code"
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+ id="zero-to-one-source">
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+ <pre>
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+ <span class="ruby-comment cmt"># File lib/UCSCBin.rb, line 30</span>
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+ <span class="ruby-keyword kw">def</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">zero_to_one</span>(<span class="ruby-identifier">zero_start</span>, <span class="ruby-identifier">zero_end</span>)
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+ <span class="ruby-keyword kw">case</span>
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+ <span class="ruby-keyword kw">when</span> (<span class="ruby-identifier">zero_start</span> <span class="ruby-operator">&lt;</span> <span class="ruby-value">0</span> <span class="ruby-operator">||</span> <span class="ruby-identifier">zero_end</span> <span class="ruby-operator">&lt;</span> <span class="ruby-value">0</span>)
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+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-value str">&quot;positions must be &gt;=0&quot;</span>
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+ <span class="ruby-keyword kw">when</span> <span class="ruby-identifier">zero_start</span> <span class="ruby-operator">&gt;=</span> <span class="ruby-identifier">zero_end</span>
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+ <span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-value str">&quot;positions must be start&lt;end&quot;</span>
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+ <span class="ruby-keyword kw">end</span>
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+
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+ [<span class="ruby-identifier">zero_start</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>, <span class="ruby-identifier">zero_end</span>]
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+ <span class="ruby-keyword kw">end</span></pre>
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+ </div>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <div id="rdoc-debugging-section-dump" class="debugging-section">
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+
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+ <p>Disabled; run with --debug to generate this.</p>
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+
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+ </div>
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
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+ Rdoc Generator</a> 1.1.6</small>.</p>
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+ </div>
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+
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+ </body>
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+ </html>
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+
data/rdoc/created.rid ADDED
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+ Thu, 28 Oct 2010 14:18:51 +0900
data/rdoc/images/brick.png ADDED
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data/rdoc/index.html ADDED
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
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+ "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
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+ <head>
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+ <meta content="text/html; charset=utf-8" http-equiv="Content-Type" />
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+
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+ <title>UCSCBin 0.2.0
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+ </title>
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+
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+ <link type="text/css" media="screen" href="rdoc.css" rel="stylesheet" />
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+
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+ <script src="js/jquery.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="js/thickbox-compressed.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="js/quicksearch.js" type="text/javascript" charset="utf-8"></script>
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+ <script src="js/darkfish.js" type="text/javascript" charset="utf-8"></script>
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+
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+ </head>
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+ <body class="indexpage">
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+
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+
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+ <h1>UCSCBin 0.2.0
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+ </h1>
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+
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+
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+ <p>This is the API documentation for 'UCSCBin 0.2.0
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+ '.</p>
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+
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+
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+
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+
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+ <h2>Files</h2>
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+ <ul>
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+
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+ <li class="file"><a href="README_rdoc.html">README.rdoc</a></li>
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+
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+ </ul>
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+
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+
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+ <h2>Classes/Modules</h2>
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+ <ul>
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+
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+ <li class="module"><a href="UCSCBin.html">UCSCBin</a></li>
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+
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+ <li class="class"><a href="UCSCBin/BinRange.html">UCSCBin::BinRange</a></li>
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+
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+ <li class="class"><a href="UCSCBin/Utils.html">UCSCBin::Utils</a></li>
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+
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+ </ul>
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+
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+ <h2>Methods</h2>
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+ <ul>
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+
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+ <li><a href="UCSCBin/BinRange.html#M000003">::bin_all &mdash; UCSCBin::BinRange</a></li>
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+
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+ <li><a href="UCSCBin/BinRange.html#M000007">::bin_all_extended &mdash; UCSCBin::BinRange</a></li>
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+
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+ <li><a href="UCSCBin/BinRange.html#M000006">::bin_all_standard &mdash; UCSCBin::BinRange</a></li>
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+
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+ <li><a href="UCSCBin/BinRange.html#M000002">::bin_from_range &mdash; UCSCBin::BinRange</a></li>
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+
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+ <li><a href="UCSCBin/BinRange.html#M000005">::bin_from_range_extended &mdash; UCSCBin::BinRange</a></li>
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+
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+ <li><a href="UCSCBin/BinRange.html#M000004">::bin_from_range_standard &mdash; UCSCBin::BinRange</a></li>
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+
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+ <li><a href="UCSCBin/Utils.html#M000001">::one_to_zero &mdash; UCSCBin::Utils</a></li>
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+
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+ <li><a href="UCSCBin/Utils.html#M000000">::zero_to_one &mdash; UCSCBin::Utils</a></li>
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+
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+ </ul>
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ <p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
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+ Rdoc Generator</a> 1.1.6</small>.</p>
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+ </div>
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+ </body>
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+ </html>
data/rdoc/js/darkfish.js ADDED
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+ /**
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+ *
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+ * Darkfish Page Functions
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+ * $Id: darkfish.js 53 2009-01-07 02:52:03Z deveiant $
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+ *
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+ * Author: Michael Granger <mgranger@laika.com>
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+ *
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+ */
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+
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+ /* Provide console simulation for firebug-less environments */
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+ if (!("console" in window) || !("firebug" in console)) {
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+ var names = ["log", "debug", "info", "warn", "error", "assert", "dir", "dirxml",
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+ "group", "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd"];
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+
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+ window.console = {};
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+ for (var i = 0; i < names.length; ++i)
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+ window.console[names[i]] = function() {};
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+ };
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+
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+
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+ /**
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+ * Unwrap the first element that matches the given @expr@ from the targets and return them.
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+ */
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+ $.fn.unwrap = function( expr ) {
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+ return this.each( function() {
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+ $(this).parents( expr ).eq( 0 ).after( this ).remove();
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+ });
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+ };
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+
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+
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+ function showSource( e ) {
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+ var target = e.target;
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+ var codeSections = $(target).
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+ parents('.method-detail').
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+ find('.method-source-code');
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+
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+ $(target).
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+ parents('.method-detail').
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+ find('.method-source-code').
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+ slideToggle();
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+ };
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+
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+ function hookSourceViews() {
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+ $('.method-description,.method-heading').click( showSource );
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+ };
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+
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+ function toggleDebuggingSection() {
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+ $('.debugging-section').slideToggle();
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+ };
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+
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+ function hookDebuggingToggle() {
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+ $('#debugging-toggle img').click( toggleDebuggingSection );
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+ };
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+
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+ function hookQuickSearch() {
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+ $('.quicksearch-field').each( function() {
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+ var searchElems = $(this).parents('.section').find( 'li' );
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+ var toggle = $(this).parents('.section').find('h3 .search-toggle');
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+ // console.debug( "Toggle is: %o", toggle );
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+ var qsbox = $(this).parents('form').get( 0 );
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+
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+ $(this).quicksearch( this, searchElems, {
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+ noSearchResultsIndicator: 'no-class-search-results',
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+ focusOnLoad: false
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+ });
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+ $(toggle).click( function() {
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+ // console.debug( "Toggling qsbox: %o", qsbox );
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+ $(qsbox).toggle();
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+ });
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+ });
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+ };
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+
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+ function highlightTarget( anchor ) {
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+ console.debug( "Highlighting target '%s'.", anchor );
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+
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+ $("a[name=" + anchor + "]").each( function() {
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+ if ( !$(this).parent().parent().hasClass('target-section') ) {
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+ console.debug( "Wrapping the target-section" );
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+ $('div.method-detail').unwrap( 'div.target-section' );
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+ $(this).parent().wrap( '<div class="target-section"></div>' );
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+ } else {
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+ console.debug( "Already wrapped." );
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+ }
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+ });
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+ };
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+
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+ function highlightLocationTarget() {
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+ console.debug( "Location hash: %s", window.location.hash );
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+ if ( ! window.location.hash || window.location.hash.length == 0 ) return;
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+
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+ var anchor = window.location.hash.substring(1);
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+ console.debug( "Found anchor: %s; matching %s", anchor, "a[name=" + anchor + "]" );
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+
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+ highlightTarget( anchor );
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+ };
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+
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+ function highlightClickTarget( event ) {
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+ console.debug( "Highlighting click target for event %o", event.target );
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+ try {
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+ var anchor = $(event.target).attr( 'href' ).substring(1);
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+ console.debug( "Found target anchor: %s", anchor );
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+ highlightTarget( anchor );
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+ } catch ( err ) {
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+ console.error( "Exception while highlighting: %o", err );
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+ };
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+ };
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+
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+
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+ $(document).ready( function() {
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+ hookSourceViews();
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+ hookDebuggingToggle();
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+ hookQuickSearch();
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+ highlightLocationTarget();
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+
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+ $('ul.link-list a').bind( "click", highlightClickTarget );
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+ });