bio-bwa 0.2.0

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Files changed (91) hide show
  1. data/.document +5 -0
  2. data/Gemfile +15 -0
  3. data/Gemfile.lock +28 -0
  4. data/LICENSE.txt +35 -0
  5. data/README.rdoc +33 -0
  6. data/Rakefile +56 -0
  7. data/VERSION +1 -0
  8. data/bio-bwa.gemspec +152 -0
  9. data/doc/Bio.html +93 -0
  10. data/doc/Bio/BWA.html +2884 -0
  11. data/doc/Bio/BWA/Library.html +229 -0
  12. data/doc/_index.html +119 -0
  13. data/doc/class_list.html +36 -0
  14. data/doc/css/common.css +1 -0
  15. data/doc/css/full_list.css +53 -0
  16. data/doc/css/style.css +310 -0
  17. data/doc/file.LICENSE.html +88 -0
  18. data/doc/file.README.html +119 -0
  19. data/doc/file_list.html +41 -0
  20. data/doc/frames.html +13 -0
  21. data/doc/index.html +119 -0
  22. data/doc/js/app.js +203 -0
  23. data/doc/js/full_list.js +149 -0
  24. data/doc/js/jquery.js +154 -0
  25. data/doc/method_list.html +171 -0
  26. data/doc/top-level-namespace.html +88 -0
  27. data/ext/COPYING +674 -0
  28. data/ext/ChangeLog +3864 -0
  29. data/ext/NEWS +555 -0
  30. data/ext/README +29 -0
  31. data/ext/bamlite.c +155 -0
  32. data/ext/bamlite.h +94 -0
  33. data/ext/bntseq.c +303 -0
  34. data/ext/bntseq.h +80 -0
  35. data/ext/bwa.1 +562 -0
  36. data/ext/bwape.c +807 -0
  37. data/ext/bwase.c +686 -0
  38. data/ext/bwase.h +27 -0
  39. data/ext/bwaseqio.c +222 -0
  40. data/ext/bwt.c +250 -0
  41. data/ext/bwt.h +105 -0
  42. data/ext/bwt_gen/Makefile +23 -0
  43. data/ext/bwt_gen/QSufSort.c +496 -0
  44. data/ext/bwt_gen/QSufSort.h +40 -0
  45. data/ext/bwt_gen/bwt_gen.c +1547 -0
  46. data/ext/bwt_gen/bwt_gen.h +105 -0
  47. data/ext/bwt_lite.c +94 -0
  48. data/ext/bwt_lite.h +29 -0
  49. data/ext/bwtaln.c +345 -0
  50. data/ext/bwtaln.h +150 -0
  51. data/ext/bwtgap.c +264 -0
  52. data/ext/bwtgap.h +38 -0
  53. data/ext/bwtindex.c +186 -0
  54. data/ext/bwtio.c +77 -0
  55. data/ext/bwtmisc.c +269 -0
  56. data/ext/bwtsw2.h +51 -0
  57. data/ext/bwtsw2_aux.c +650 -0
  58. data/ext/bwtsw2_chain.c +107 -0
  59. data/ext/bwtsw2_core.c +594 -0
  60. data/ext/bwtsw2_main.c +100 -0
  61. data/ext/cs2nt.c +191 -0
  62. data/ext/is.c +218 -0
  63. data/ext/khash.h +506 -0
  64. data/ext/kseq.h +208 -0
  65. data/ext/ksort.h +269 -0
  66. data/ext/kstring.c +35 -0
  67. data/ext/kstring.h +46 -0
  68. data/ext/kvec.h +90 -0
  69. data/ext/main.c +63 -0
  70. data/ext/main.h +29 -0
  71. data/ext/mkrf_conf.rb +49 -0
  72. data/ext/qualfa2fq.pl +27 -0
  73. data/ext/simple_dp.c +162 -0
  74. data/ext/simpletest.c +23 -0
  75. data/ext/solid2fastq.pl +111 -0
  76. data/ext/stdaln.c +1072 -0
  77. data/ext/stdaln.h +162 -0
  78. data/ext/utils.c +82 -0
  79. data/ext/utils.h +54 -0
  80. data/lib/bio-bwa.rb +7 -0
  81. data/lib/bio/bwa.rb +312 -0
  82. data/lib/bio/bwa/library.rb +42 -0
  83. data/test/data/testdata.fa +602 -0
  84. data/test/data/testdata.long.fa +175 -0
  85. data/test/data/testdata.short.fa +2 -0
  86. data/test/helper.rb +18 -0
  87. data/test/test_bio-bwa_basic.rb +62 -0
  88. data/test/test_bio-bwa_make_index.rb +42 -0
  89. data/test/test_bio-bwa_run_aln.rb +49 -0
  90. data/test/test_bio-bwa_sam_conversion.rb +49 -0
  91. metadata +218 -0
data/doc/Bio/BWA/Library.html ADDED
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+ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.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 name="Content-Type" content="text/html; charset=utf-8" />
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+ <title>Class: Bio::BWA::Library</title>
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+ <link rel="stylesheet" href="../../css/style.css" type="text/css" media="screen" charset="utf-8" />
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+ <link rel="stylesheet" href="../../css/common.css" type="text/css" media="screen" charset="utf-8" />
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+
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+ <script type="text/javascript" charset="utf-8">
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+ relpath = '../..';
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+ if (relpath != '') relpath += '/';
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+ </script>
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+ <script type="text/javascript" charset="utf-8" src="../../js/jquery.js"></script>
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+ <body>
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+ <script type="text/javascript" charset="utf-8">
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+ if (window.top.frames.main) document.body.className = 'frames';
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+ </script>
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+
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+ <div id="header">
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+ <div id="menu">
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+
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+ <a href="../../_index.html">Index (L)</a> &raquo;
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+ <span class='title'><span class='object_link'><a href="../../Bio.html" title="Bio (module)">Bio</a></span></span> &raquo; <span class='title'><span class='object_link'><a href="../BWA.html" title="Bio::BWA (class)">BWA</a></span></span>
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+ &raquo;
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+ <span class="title">Library</span>
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+
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+
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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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+
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+ <div id="search">
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+ <a id="class_list_link" href="#">Class List</a>
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+ <a id="method_list_link" href="#">Method List</a>
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+ <a id ="file_list_link" href="#">File List</a>
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+ </div>
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+
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+ <div class="clear"></div>
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+ </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"><h1>Class: Bio::BWA::Library
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+
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+
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+
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+ </h1>
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+
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+ <dl class="box">
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+
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+ <dt class="r1">Inherits:</dt>
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+ <dd class="r1">
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+ <span class="inheritName">Object</span>
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+
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+ <ul class="fullTree">
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+ <li>Object</li>
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+
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+ <li class="next">Bio::BWA::Library</li>
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+
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+ </ul>
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+ <a href="#" class="inheritanceTree">show all</a>
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+
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+ </dd>
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+ <dt class="r2 last">Defined in:</dt>
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+ <dd class="r2 last">lib/bio/bwa/library.rb</dd>
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+
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+ </dl>
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+ <div class="clear"></div>
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+
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+
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+
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+
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+
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+ <h2>
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+ Class Method Summary
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+ <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
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+ </h2>
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+
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+ <ul class="summary">
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+
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+ <li class="public ">
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+ <span class="summary_signature">
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+
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+ <a href="#load-class_method" title="load (class method)">+ (String) <strong>load</strong> </a>
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+
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+
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+
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+ </span>
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+
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+
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+
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+
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+
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+
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+
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+
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+ <span class="summary_desc"><div class='inline'><p>
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+ Load the correct library for the OS system in use.
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+ </p>
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+ </div></span>
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+
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+ </li>
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+
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+
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+ </ul>
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+
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+
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+
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+
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+ <div id="class_method_details" class="method_details_list">
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+ <h2>Class Method Details</h2>
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+
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+
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+ <div class="method_details first">
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+ <p class="signature first" id="load-class_method">
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+
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+ + (<tt>String</tt>) <strong>load</strong>
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+
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+
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+
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+ </p><div class="docstring">
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+ <div class="discussion">
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+
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+ <div class="note notetag">
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+ <strong>Note:</strong>
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+ <div class='inline'><p>
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+ this method is called automatically when the module is loaded
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+ </p>
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+ </div>
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+ </div>
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+
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+ <p>
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+ Load the correct library for the OS system in use
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+ </p>
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+
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+
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+ </div>
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+ </div>
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+ <div class="tags">
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+ <h3>Returns:</h3>
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+ <ul class="return">
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+
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+ <li>
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+
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+ <span class='type'>(<tt>String</tt>)</span>
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+
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+
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+
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+
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+ &mdash;
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+ <div class='inline'><p>
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+ the absolute path for the filename of the shared library
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+ </p>
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+ </div>
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+
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+ </li>
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+
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+ </ul>
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+ <h3>Raises:</h3>
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+ <ul class="raise">
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+
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+ <li>
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+
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+ <span class='type'>(<tt>RuntimeError</tt>)</span>
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+
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+
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+
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+
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+ </li>
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+
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+ </ul>
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+
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+ </div><table class="source_code">
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+ <tr>
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+ <td>
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+ <pre class="lines">
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+ 10
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+ 13
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+ 18</pre>
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+ </td>
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+ <td>
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+ <pre class="code"><span class="info file"># File 'lib/bio/bwa/library.rb', line 10</span>
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+
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+ <span class='kw'>def</span> <span class='kw'>self</span><span class='period'>.</span><span class='id load'>load</span>
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+ <span class='id raise'>raise</span> <span class='const'>RuntimeError</span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>Unable to load shared library! BWA is compiled for 64bit systems</span><span class='tstring_end'>&quot;</span></span> <span class='kw'>if</span> <span class='id arch_type'>arch_type</span> <span class='op'>==</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>32bit</span><span class='tstring_end'>&quot;</span></span>
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+ <span class='id lib_extension'>lib_extension</span> <span class='op'>=</span> <span class='kw'>case</span> <span class='const'>Config</span><span class='op'>::</span><span class='const'>CONFIG</span><span class='lbracket'>[</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>host_os</span><span class='tstring_end'>'</span></span><span class='rbracket'>]</span>
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+ <span class='kw'>when</span> <span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>linux</span><span class='regexp_end'>/</span></span> <span class='kw'>then</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>so</span><span class='tstring_end'>'</span></span>
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+ <span class='kw'>when</span> <span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>darwin</span><span class='regexp_end'>/</span></span> <span class='kw'>then</span> <span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>dylib</span><span class='tstring_end'>'</span></span>
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+ <span class='kw'>when</span> <span class='tstring'><span class='regexp_beg'>/</span><span class='tstring_content'>mswin|mingw</span><span class='regexp_end'>/</span></span> <span class='kw'>then</span> <span class='id raise'>raise</span> <span class='const'>NotImplementedError</span><span class='comma'>,</span> <span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>BWA library is not available for Windows platform</span><span class='tstring_end'>&quot;</span></span>
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+ <span class='kw'>end</span>
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+ <span class='const'>File</span><span class='period'>.</span><span class='id join'>join</span><span class='lparen'>(</span><span class='const'>File</span><span class='period'>.</span><span class='id expand_path'>expand_path</span><span class='lparen'>(</span><span class='const'>File</span><span class='period'>.</span><span class='id dirname'>dirname</span><span class='lparen'>(</span><span class='kw'>__FILE__</span><span class='rparen'>)</span><span class='rparen'>)</span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>'</span><span class='tstring_content'>ext</span><span class='tstring_end'>'</span></span><span class='comma'>,</span><span class='tstring'><span class='tstring_beg'>&quot;</span><span class='tstring_content'>libbwa.</span><span class='embexpr_beg'>#{</span><span class='id lib_extension'>lib_extension</span><span class='rbrace'>}</span><span class='tstring_end'>&quot;</span></span><span class='rparen'>)</span>
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+ <span class='kw'>end</span></pre>
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+
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+ </div>
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+
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+ </div>
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+
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+ <div id="footer">
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+ Generated on Thu Feb 10 16:31:17 2011 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.6.4 (ruby-1.9.2).
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/_index.html ADDED
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+ <title>Documentation by YARD 0.6.4</title>
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+ <h2>Namespace Listing A-Z</h2>
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+
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+ <table>
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+ <td valign='top' width="33%">
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+ <li class="letter">B</li>
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+ <ul>
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+
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+ <li>
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+ <span class='object_link'><a href="Bio/BWA.html" title="Bio::BWA (class)">BWA</a></span>
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+
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+ <small>(Bio)</small>
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+
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+
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+ <span class='object_link'><a href="Bio.html" title="Bio (module)">Bio</a></span>
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+ <ul id="alpha_L" class="alpha">
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+ <li class="letter">L</li>
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+ <ul>
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+
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+ <li>
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+ <span class='object_link'><a href="Bio/BWA/Library.html" title="Bio::BWA::Library (class)">Library</a></span>
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+
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+ <small>(Bio::BWA)</small>
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+
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+ </li>
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+
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+ </ul>
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+ </ul>
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+ Generated on Thu Feb 10 16:31:16 2011 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.6.4 (ruby-1.9.2).
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+ <div id="nav">
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+ <ul id="full_list" class="class">
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+ <li><span class='object_link'><a href="top-level-namespace.html" title=" (root)">Top Level Namespace</a></span></li>
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+ <li><a class='toggle'></a> <span class='object_link'><a href="Bio.html" title="Bio (module)">Bio</a></span><small class='search_info'>Top Level Namespace</small></li><ul><li><a class='toggle'></a> <span class='object_link'><a href="Bio/BWA.html" title="Bio::BWA (class)">BWA</a></span> &lt; Object<small class='search_info'>Bio</small></li><ul><li><span class='object_link'><a href="Bio/BWA/Library.html" title="Bio::BWA::Library (class)">Library</a></span> &lt; Object<small class='search_info'>Bio::BWA</small></li></ul></ul>
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+ #search { position: absolute; right: 5px; top: 9px; padding-left: 24px; }
12
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+ #full_list { padding: 0; list-style: none; margin-left: 0; }
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+ #full_list ul { padding: 0; }
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+ #full_list li { padding: 5px; padding-left: 12px; margin: 0; font-size: 1.1em; list-style: none; }
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+ #noresults { padding: 7px 12px; }
17
+ #content.insearch #noresults { margin-left: 7px; }
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+ ul.collapsed ul, ul.collapsed li { display: none; }
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+ li a.toggle { cursor: default; position: relative; left: -5px; top: 4px; text-indent: -999px; width: 10px; height: 9px; margin-left: -10px; display: block; float: left; background: url(data:image/png;base64,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) no-repeat bottom left; }
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+ li { color: #888; cursor: pointer; }
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+ li.deprecated { text-decoration: line-through; font-style: italic; }
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+ li.r1 { background: #f0f0f0; }
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+ li.r2 { background: #fafafa; }
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+ li:hover { background: #ddd; }
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+ li small:before { content: "("; }
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+ li small:after { content: ")"; }
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+ li small.search_info { display: none; }
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+ a:link, a:visited { text-decoration: none; color: #05a; }
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+ li.clicked { background: #05a; color: #ccc; }
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+ li.clicked a:link, li.clicked a:visited { color: #eee; }
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+ li.clicked a.toggle { opacity: 0.5; background-position: bottom right; }
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+ li.collapsed.clicked a.toggle { background-position: top right; }
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+ #search input { border: 1px solid #bbb; -moz-border-radius: 3px; -webkit-border-radius: 3px; }
35
+ #nav { margin-left: 10px; font-size: 0.9em; display: none; color: #aaa; }
36
+ #nav a:link, #nav a:visited { color: #358; }
37
+ #nav a:hover { background: transparent; color: #5af; }
38
+
39
+ .frames #content h1 { margin-top: 0; }
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+ .frames li { white-space: nowrap; cursor: normal; }
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+ .frames li small { display: block; font-size: 0.8em; }
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+ .frames li small:before { content: ""; }
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+ .frames li small:after { content: ""; }
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+ .frames li small.search_info { display: none; }
45
+ .frames #search { width: 170px; position: static; margin: 3px; margin-left: 10px; font-size: 0.9em; color: #888; padding-left: 0; padding-right: 24px; }
46
+ .frames #content.insearch #search { background-position: center right; }
47
+ .frames #search input { width: 110px; }
48
+ .frames #nav { display: block; }
49
+
50
+ #full_list.insearch li { display: none; }
51
+ #full_list.insearch li.found { display: list-item; padding-left: 10px; }
52
+ #full_list.insearch li a.toggle { display: none; }
53
+ #full_list.insearch li small.search_info { display: block; }
data/doc/css/style.css ADDED
@@ -0,0 +1,310 @@
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+ body {
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+ padding: 0 20px;
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+ font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
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+ font-size: 13px;
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+ }
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+ body.frames { padding: 0 5px; }
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+ h1 { font-size: 25px; margin: 1em 0 0.5em; padding-top: 4px; border-top: 1px dotted #d5d5d5; }
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+ h1.noborder { border-top: 0px; margin-top: 0; padding-top: 4px; }
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+ h1.title { margin-bottom: 10px; }
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+ h1.alphaindex { margin-top: 0; font-size: 22px; }
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+ h2 {
12
+ padding: 0;
13
+ padding-bottom: 3px;
14
+ border-bottom: 1px #aaa solid;
15
+ font-size: 1.4em;
16
+ margin: 1.8em 0 0.5em;
17
+ }
18
+ h2 small { font-weight: normal; font-size: 0.7em; display: block; float: right; }
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+ .clear { clear: both; }
20
+ .inline { display: inline; }
21
+ .inline p:first-child { display: inline; }
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+ .docstring h1, .docstring h2, .docstring h3, .docstring h4 { padding: 0; border: 0; border-bottom: 1px dotted #bbb; }
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+ .docstring h1 { font-size: 1.2em; }
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+ .docstring h2 { font-size: 1.1em; }
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+ .docstring h3, .docstring h4 { font-size: 1em; border-bottom: 0; padding-top: 10px; }
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+ .docstring .object_link { font-family: monospace; }
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+
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+ .note {
29
+ color: #222;
30
+ -moz-border-radius: 3px; -webkit-border-radius: 3px;
31
+ background: #e3e4e3; border: 1px solid #d5d5d5; padding: 7px 10px;
32
+ display: block;
33
+ }
34
+ .note.todo { background: #ffffc5; border-color: #ececaa; }
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+ .note.returns_void { background: #efefef; }
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+ .note.deprecated { background: #ffe5e5; border-color: #e9dada; }
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+ .note.private { background: #ffffc5; border-color: #ececaa; }
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+ .note.title { text-transform: lowercase; padding: 1px 5px; font-size: 0.9em; font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif; display: inline; }
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+ .summary_signature + .note.title { margin-left: 7px; }
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+ h1 .note.title { font-size: 0.5em; font-weight: normal; padding: 3px 5px; position: relative; top: -3px; text-transform: capitalize; }
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+ .note.title.constructor { color: #fff; background: #6a98d6; border-color: #6689d6; }
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+ .note.title.writeonly { color: #fff; background: #45a638; border-color: #2da31d; }
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+ .note.title.readonly { color: #fff; background: #6a98d6; border-color: #6689d6; }
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+ .note.title.private { background: #d5d5d5; border-color: #c5c5c5; }
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+ .discussion .note { margin-top: 6px; }
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+ .discussion .note:first-child { margin-top: 0; }
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+
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+ h3.inherited {
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+ font-style: italic;
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+ font-family: "Lucida Sans", "Lucida Grande", Verdana, Arial, sans-serif;
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+ font-weight: normal;
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+ padding: 0;
53
+ margin: 0;
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+ margin-top: 12px;
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+ margin-bottom: 3px;
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+ font-size: 13px;
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+ }
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+ p.inherited {
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+ padding: 0;
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+ margin: 0;
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+ margin-left: 25px;
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+ }
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+
64
+ dl.box {
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+ width: 520px;
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+ font-size: 1em;
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+ }
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+ dl.box dt {
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+ float: left;
70
+ display: block;
71
+ width: 100px;
72
+ margin: 0;
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+ text-align: right;
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+ font-weight: bold;
75
+ border: 1px solid #aaa;
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+ border-width: 1px 0px 0px 1px;
77
+ padding: 6px 0;
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+ padding-right: 10px;
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+ }
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+ dl.box dd {
81
+ float: left;
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+ display: block;
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+ width: 380px;
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+ margin: 0;
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+ padding: 6px 0;
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+ padding-right: 20px;
87
+ border: 1px solid #aaa;
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+ border-width: 1px 1px 0 0;
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+ }
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+ dl.box .last {
91
+ border-bottom: 1px solid #aaa;
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+ }
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+ dl.box .r1 { background: #eee; }
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+
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+ ul.toplevel { list-style: none; padding-left: 0; font-size: 1.1em; }
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+ #files { padding-left: 15px; font-size: 1.1em; }
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+
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+ #files { padding: 0; }
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+ #files li { list-style: none; display: inline; padding: 7px 12px; line-height: 35px; }
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+
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+ dl.constants { margin-left: 40px; }
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+ dl.constants dt { font-weight: bold; font-size: 1.1em; margin-bottom: 5px; }
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+ dl.constants dd { width: 75%; white-space: pre; font-family: monospace; margin-bottom: 18px; }
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+
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+ .summary_desc { margin-left: 32px; display: block; font-family: sans-serif; }
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+ .summary_desc tt { font-size: 0.9em; }
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+ dl.constants .note { padding: 2px 6px; padding-right: 12px; margin-top: 6px; }
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+ dl.constants .docstring { margin-left: 32px; font-size: 0.9em; font-weight: normal; }
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+ dl.constants .tags { padding-left: 32px; font-size: 0.9em; line-height: 0.8em; }
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+ dl.constants .discussion *:first-child { margin-top: 0; }
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+ dl.constants .discussion *:last-child { margin-bottom: 0; }
112
+
113
+ .method_details { border-top: 1px dotted #aaa; margin-top: 15px; padding-top: 0; }
114
+ .method_details.first { border: 0; }
115
+ p.signature {
116
+ font-size: 1.1em; font-weight: normal; font-family: Monaco, Consolas, Courier, monospace;
117
+ padding: 6px 10px; margin-top: 18px;
118
+ background: #e5e8ff; border: 1px solid #d8d8e5; -moz-border-radius: 3px; -webkit-border-radius: 3px;
119
+ }
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+ p.signature tt { font-family: Monaco, Consolas, Courier, monospace; }
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+ p.signature .overload { display: block; }
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+ p.signature .extras { font-weight: normal; font-family: sans-serif; color: #444; font-size: 1em; }
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+ p.signature .aliases { display: block; font-weight: normal; font-size: 0.9em; font-family: sans-serif; margin-top: 0px; color: #555; }
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+ p.signature .aliases .names { font-family: Monaco, Consolas, Courier, monospace; font-weight: bold; color: #000; font-size: 1.2em; }
125
+
126
+ .tags h3 { font-size: 1em; margin-bottom: 0; }
127
+ .tags ul { margin-top: 5px; padding-left: 30px; list-style: square; }
128
+ .tags ul li { margin-bottom: 3px; }
129
+ .tags ul .name { font-family: monospace; font-weight: bold; }
130
+ .tags ul .note { padding: 3px 6px; }
131
+ .tags { margin-bottom: 12px; }
132
+
133
+ .tags .examples h3 { margin-bottom: 10px; }
134
+ .tags .examples h4 { padding: 0; margin: 0; margin-left: 15px; font-weight: bold; font-size: 0.9em; }
135
+
136
+ .tags .overload .overload_item { list-style: none; margin-bottom: 25px; }
137
+ .tags .overload .overload_item .signature {
138
+ padding: 2px 8px;
139
+ background: #e5e8ff; border: 1px solid #d8d8e5; -moz-border-radius: 3px; -webkit-border-radius: 3px;
140
+ }
141
+ .tags .overload .signature { margin-left: -15px; font-family: monospace; display: block; font-size: 1.1em; }
142
+ .tags .overload .docstring { margin-top: 15px; }
143
+
144
+ .defines { display: none; }
145
+
146
+ #method_missing_details .notice.this { position: relative; top: -8px; color: #888; padding: 0; margin: 0; }
147
+
148
+ .showSource { font-size: 0.9em; }
149
+ .showSource a:link, .showSource a:visited { text-decoration: none; color: #666; }
150
+
151
+ #content a:link, #content a:visited { text-decoration: none; color: #05a; }
152
+ #content a:hover { background: #ffffa5; }
153
+ .docstring { margin-right: 6em; }
154
+
155
+ ul.summary {
156
+ list-style: none;
157
+ font-family: monospace;
158
+ font-size: 1em;
159
+ line-height: 1.5em;
160
+ }
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+ ul.summary a:link, ul.summary a:visited {
162
+ text-decoration: none; font-size: 1.1em;
163
+ }
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+ ul.summary li { margin-bottom: 5px; }
165
+ .summary .summary_signature {
166
+ padding: 1px 10px;
167
+ background: #eaeaff; border: 1px solid #dfdfe5;
168
+ -moz-border-radius: 3px; -webkit-border-radius: 3px;
169
+ }
170
+ .summary_signature:hover { background: #eeeeff; cursor: pointer; }
171
+ ul.summary.compact li { display: inline-block; margin: 0px 5px 0px 0px; line-height: 2.6em;}
172
+ ul.summary.compact .summary_signature { padding: 5px 7px; padding-right: 4px; }
173
+ #content .summary_signature:hover a:link,
174
+ #content .summary_signature:hover a:visited {
175
+ background: transparent;
176
+ color: #48f;
177
+ }
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+
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+ p.inherited a { font-family: monospace; font-size: 0.9em; }
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+ p.inherited { word-spacing: 5px; font-size: 1.2em; }
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+
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+ p.children { font-size: 1.2em; }
183
+ p.children a { font-size: 0.9em; }
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+ p.children strong { font-size: 0.8em; }
185
+ p.children strong.modules { padding-left: 5px; }
186
+
187
+ ul.fullTree { display: none; padding-left: 0; list-style: none; margin-left: 0; margin-bottom: 10px; }
188
+ ul.fullTree ul { margin-left: 0; padding-left: 0; list-style: none; }
189
+ ul.fullTree li { text-align: center; padding-top: 18px; padding-bottom: 12px; background: url(data:image/gif;base64,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) no-repeat top center; }
190
+ ul.fullTree li:first-child { padding-top: 0; background: transparent; }
191
+ ul.fullTree li:last-child { padding-bottom: 0; }
192
+ .showAll ul.fullTree { display: block; }
193
+ .showAll .inheritName { display: none; }
194
+
195
+ #search { position: absolute; right: 14px; top: 0px; }
196
+ #search a:link, #search a:visited {
197
+ display: block; float: left; margin-right: 4px;
198
+ padding: 8px 10px; text-decoration: none; color: #05a;
199
+ border: 1px solid #d8d8e5;
200
+ -moz-border-radius-bottomleft: 3px; -moz-border-radius-bottomright: 3px;
201
+ -webkit-border-bottom-left-radius: 3px; -webkit-border-bottom-right-radius: 3px;
202
+ background: #eaf0ff;
203
+ -webkit-box-shadow: -1px 1px 3px #ddd;
204
+ }
205
+ #search a:hover { background: #f5faff; color: #06b; }
206
+ #search a.active {
207
+ background: #568; padding-bottom: 20px; color: #fff; border: 1px solid #457;
208
+ -moz-border-radius-topleft: 5px; -moz-border-radius-topright: 5px;
209
+ -webkit-border-top-left-radius: 5px; -webkit-border-top-right-radius: 5px;
210
+ }
211
+ #search a.inactive { color: #999; }
212
+ .frames #search { display: none; }
213
+ .inheritanceTree, .toggleDefines { float: right; }
214
+
215
+ #menu { font-size: 1.3em; color: #bbb; top: -5px; position: relative; }
216
+ #menu .title, #menu a { font-size: 0.7em; }
217
+ #menu .title a { font-size: 1em; }
218
+ #menu .title { color: #555; }
219
+ #menu a:link, #menu a:visited { color: #333; text-decoration: none; border-bottom: 1px dotted #bbd; }
220
+ #menu a:hover { color: #05a; }
221
+ #menu .noframes { display: none; }
222
+ .frames #menu .noframes { display: inline; float: right; }
223
+
224
+ #footer { margin-top: 15px; border-top: 1px solid #ccc; text-align: center; padding: 7px 0; color: #999; }
225
+ #footer a:link, #footer a:visited { color: #444; text-decoration: none; border-bottom: 1px dotted #bbd; }
226
+ #footer a:hover { color: #05a; }
227
+
228
+ #listing ul.alpha { font-size: 1.1em; }
229
+ #listing ul.alpha { margin: 0; padding: 0; padding-bottom: 10px; list-style: none; }
230
+ #listing ul.alpha li.letter { font-size: 1.4em; padding-bottom: 10px; }
231
+ #listing ul.alpha ul { margin: 0; padding-left: 15px; }
232
+ #listing ul small { color: #666; font-size: 0.7em; }
233
+
234
+ li.r1 { background: #f0f0f0; }
235
+ li.r2 { background: #fafafa; }
236
+
237
+ #search_frame {
238
+ z-index: 9999;
239
+ background: #fff;
240
+ display: none;
241
+ position: absolute;
242
+ top: 36px;
243
+ right: 18px;
244
+ width: 500px;
245
+ height: 80%;
246
+ overflow-y: scroll;
247
+ border: 1px solid #999;
248
+ border-collapse: collapse;
249
+ -webkit-box-shadow: -7px 5px 25px #aaa;
250
+ -moz-box-shadow: -7px 5px 25px #aaa;
251
+ -moz-border-radius: 2px;
252
+ -webkit-border-radius: 2px;
253
+ }
254
+
255
+ #content ul.summary li.deprecated a:link,
256
+ #content ul.summary li.deprecated a:visited { text-decoration: line-through; font-style: italic; }
257
+
258
+ #toc {
259
+ padding: 20px; padding-right: 30px; border: 1px solid #ddd; float: right; background: #fff; margin-left: 20px; margin-bottom: 20px;
260
+ max-width: 300px;
261
+ -webkit-box-shadow: -2px 2px 6px #bbb;
262
+ -moz-box-shadow: -2px 2px 6px #bbb;
263
+ z-index: 5000;
264
+ position: relative;
265
+ }
266
+ #toc.nofloat { float: none; max-width: none; border: none; padding: 0; margin: 20px 0; -webkit-box-shadow: none; -moz-box-shadow: none; }
267
+ #toc.nofloat.hidden { padding: 0; background: 0; margin-bottom: 5px; }
268
+ #toc .title { margin: 0; }
269
+ #toc ol { padding-left: 1.8em; }
270
+ #toc li { font-size: 1.1em; line-height: 1.7em; }
271
+ #toc > ol > li { font-size: 1.1em; font-weight: bold; }
272
+ #toc ol > ol { font-size: 0.9em; }
273
+ #toc ol ol > ol { padding-left: 2.3em; }
274
+ #toc ol + li { margin-top: 0.3em; }
275
+ #toc.hidden { padding: 10px; background: #f6f6f6; -webkit-box-shadow: none; -moz-box-shadow: none; }
276
+ #filecontents h1 + #toc.nofloat { margin-top: 0; }
277
+
278
+ /* syntax highlighting */
279
+ .source_code { display: none; padding: 3px 8px; border-left: 8px solid #ddd; margin-top: 5px; }
280
+ #filecontents pre.code, .docstring pre.code, .source_code pre { font-family: monospace; }
281
+ #filecontents pre.code, .docstring pre.code { display: block; }
282
+ .source_code .lines { padding-right: 12px; color: #555; text-align: right; }
283
+ #filecontents pre.code, .docstring pre.code,
284
+ .tags .example { padding: 5px 12px; margin-top: 4px; border: 1px solid #eef; background: #f5f5ff; }
285
+ pre.code { color: #000; }
286
+ pre.code .info.file { color: #555; }
287
+ pre.code .val { color: #036A07; }
288
+ pre.code .tstring_content,
289
+ pre.code .heredoc_beg, pre.code .heredoc_end,
290
+ pre.code .qwords_beg, pre.code .qwords_end,
291
+ pre.code .tstring, pre.code .dstring { color: #036A07; }
292
+ pre.code .fid, pre.code .id.new, pre.code .id.to_s,
293
+ pre.code .id.to_sym, pre.code .id.to_f,
294
+ pre.code .dot + pre.code .id,
295
+ pre.code .id.to_i pre.code .id.each { color: #0085FF; }
296
+ pre.code .comment { color: #0066FF; }
297
+ pre.code .const, pre.code .constant { color: #585CF6; }
298
+ pre.code .symbol { color: #C5060B; }
299
+ pre.code .kw,
300
+ pre.code .label,
301
+ pre.code .id.require,
302
+ pre.code .id.extend,
303
+ pre.code .id.include { color: #0000FF; }
304
+ pre.code .ivar { color: #318495; }
305
+ pre.code .gvar,
306
+ pre.code .id.backref,
307
+ pre.code .id.nth_ref { color: #6D79DE; }
308
+ pre.code .regexp, .dregexp { color: #036A07; }
309
+ pre.code a { border-bottom: 1px dotted #bbf; }
310
+