simple_bioc 0.0.1 → 0.0.2

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Files changed (67) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +73 -3
  3. data/Rakefile +5 -0
  4. data/html/BioCReader.html +657 -0
  5. data/html/BioCWriter.html +556 -0
  6. data/html/README_md.html +231 -0
  7. data/html/SimpleBioC.html +255 -0
  8. data/html/SimpleBioC/Annotation.html +279 -0
  9. data/html/SimpleBioC/Collection.html +316 -0
  10. data/html/SimpleBioC/Document.html +426 -0
  11. data/html/SimpleBioC/Location.html +288 -0
  12. data/html/SimpleBioC/Node.html +334 -0
  13. data/html/SimpleBioC/NodeBase.html +281 -0
  14. data/html/SimpleBioC/Passage.html +418 -0
  15. data/html/SimpleBioC/Relation.html +301 -0
  16. data/html/SimpleBioC/Sentence.html +399 -0
  17. data/html/created.rid +15 -0
  18. data/html/images/add.png +0 -0
  19. data/html/images/arrow_up.png +0 -0
  20. data/html/images/brick.png +0 -0
  21. data/html/images/brick_link.png +0 -0
  22. data/html/images/bug.png +0 -0
  23. data/html/images/bullet_black.png +0 -0
  24. data/html/images/bullet_toggle_minus.png +0 -0
  25. data/html/images/bullet_toggle_plus.png +0 -0
  26. data/html/images/date.png +0 -0
  27. data/html/images/delete.png +0 -0
  28. data/html/images/find.png +0 -0
  29. data/html/images/loadingAnimation.gif +0 -0
  30. data/html/images/macFFBgHack.png +0 -0
  31. data/html/images/package.png +0 -0
  32. data/html/images/page_green.png +0 -0
  33. data/html/images/page_white_text.png +0 -0
  34. data/html/images/page_white_width.png +0 -0
  35. data/html/images/plugin.png +0 -0
  36. data/html/images/ruby.png +0 -0
  37. data/html/images/tag_blue.png +0 -0
  38. data/html/images/tag_green.png +0 -0
  39. data/html/images/transparent.png +0 -0
  40. data/html/images/wrench.png +0 -0
  41. data/html/images/wrench_orange.png +0 -0
  42. data/html/images/zoom.png +0 -0
  43. data/html/index.html +212 -0
  44. data/html/js/darkfish.js +155 -0
  45. data/html/js/jquery.js +18 -0
  46. data/html/js/navigation.js +142 -0
  47. data/html/js/search.js +94 -0
  48. data/html/js/search_index.js +1 -0
  49. data/html/js/searcher.js +228 -0
  50. data/html/rdoc.css +595 -0
  51. data/html/table_of_contents.html +199 -0
  52. data/lib/simple_bioc.rb +4 -0
  53. data/lib/simple_bioc/annotation.rb +10 -6
  54. data/lib/simple_bioc/bioc_reader.rb +2 -2
  55. data/lib/simple_bioc/collection.rb +13 -11
  56. data/lib/simple_bioc/document.rb +31 -22
  57. data/lib/simple_bioc/location.rb +13 -7
  58. data/lib/simple_bioc/node.rb +14 -8
  59. data/lib/simple_bioc/node_base.rb +13 -10
  60. data/lib/simple_bioc/passage.rb +26 -23
  61. data/lib/simple_bioc/relation.rb +13 -8
  62. data/lib/simple_bioc/sentence.rb +21 -15
  63. data/lib/simple_bioc/version.rb +2 -2
  64. data/samples/print_annotation.rb +18 -0
  65. data/samples/sample1.rb +31 -0
  66. data/simple_bioc.gemspec +1 -1
  67. metadata +52 -2
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+ <!DOCTYPE html>
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+ <html>
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+ <head>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <title>class SimpleBioC::Passage - RDoc Documentation</title>
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+ <link type="text/css" media="screen" href="../rdoc.css" rel="stylesheet">
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+ <script type="text/javascript">
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+ var rdoc_rel_prefix = "../";
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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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+ <script type="text/javascript" charset="utf-8" src="../js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/darkfish.js"></script>
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+ <body id="top" class="class">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../index.html">Home</a>
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+ <a href="../table_of_contents.html#classes">Classes</a>
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+ <a href="../table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+ <div id="file-metadata">
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+ <nav id="file-list-section" class="section">
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+ <h3 class="section-header">Defined In</h3>
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+ <ul>
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+ <li>lib/simple_bioc/passage.rb
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+ </ul>
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+ </nav>
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+ </div>
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+ <div id="class-metadata">
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+ <nav 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
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+ </nav>
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+
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+
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+
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+ <!-- Method Quickref -->
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+ <nav id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+
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+ <ul class="link-list">
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+
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+ <li ><a href="#method-c-new">::new</a>
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+
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+ <li ><a href="#method-i-each_relation">#each_relation</a>
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+
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+ <li ><a href="#method-i-find_node">#find_node</a>
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+ <li ><a href="#method-i-to_s">#to_s</a>
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+ </ul>
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+ </nav>
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+ </div>
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+
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+ <div id="project-metadata">
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+ <nav id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Pages</h3>
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+ <ul>
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+ <li class="file"><a href="../README_md.html">README</a>
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+ </ul>
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+ </nav>
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+ <ul class="link-list">
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+
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+ <li><a href="../BioCReader.html">BioCReader</a>
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+
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+ <li><a href="../BioCWriter.html">BioCWriter</a>
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+
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+ <li><a href="../SimpleBioC.html">SimpleBioC</a>
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+ <li><a href="../SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
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+ <li><a href="../SimpleBioC/Collection.html">SimpleBioC::Collection</a>
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+ <li><a href="../SimpleBioC/Document.html">SimpleBioC::Document</a>
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+ <li><a href="../SimpleBioC/Location.html">SimpleBioC::Location</a>
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+ <li><a href="../SimpleBioC/Node.html">SimpleBioC::Node</a>
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+ <li><a href="../SimpleBioC/NodeBase.html">SimpleBioC::NodeBase</a>
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+
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+ <li><a href="../SimpleBioC/Passage.html">SimpleBioC::Passage</a>
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+
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+ <li><a href="../SimpleBioC/Relation.html">SimpleBioC::Relation</a>
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+ <li><a href="../SimpleBioC/Sentence.html">SimpleBioC::Sentence</a>
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+
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+ </ul>
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+ </nav>
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+
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+ </div>
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+ </nav>
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+
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+ <div id="documentation">
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+ <h1 class="class">class SimpleBioC::Passage</h1>
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+
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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+ <section id="5Buntitled-5D" class="documentation-section">
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+ <!-- Attributes -->
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+ <section id="attribute-method-details" class="method-section section">
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+ <h3 class="section-header">Attributes</h3>
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+ <div id="attribute-i-annotations" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">annotations</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ </div>
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+ <div id="attribute-i-document" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">document</span><span
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+ class="attribute-access-type">[R]</span>
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+ </div>
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">infons</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div id="attribute-i-offset" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">offset</span><span
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+ class="attribute-access-type">[RW]</span>
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+ <div id="attribute-i-relations" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">relations</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ </div>
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+ <div id="attribute-i-sentences" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">sentences</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ </div>
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+ <div id="attribute-i-text" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">text</span><span
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+ class="attribute-access-type">[RW]</span>
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+ </div>
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+ <div class="method-description">
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+ </div>
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+ </div>
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+
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+ </section><!-- attribute-method-details -->
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+
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+
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+ <!-- Methods -->
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+
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+ <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Class Methods</h3>
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+ <div id="method-c-new" class="method-detail ">
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+ <div class="method-heading">
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+ <span class="method-name">new</span><span
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+ class="method-args">(parent)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+ <div class="method-description">
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+ <div class="method-source-code" id="new-source">
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/passage.rb, line 6</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">parent</span>)
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+ <span class="ruby-ivar">@infons</span> = {}
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+ <span class="ruby-ivar">@sentences</span> = []
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+ <span class="ruby-ivar">@annotations</span> = []
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+ <span class="ruby-ivar">@relations</span> = []
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+ <span class="ruby-ivar">@document</span> = <span class="ruby-identifier">parent</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- new-source -->
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+ </div><!-- new-method -->
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+ </section><!-- public-class-method-details -->
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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Instance Methods</h3>
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+ <div id="method-i-each_relation" class="method-detail ">
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+ <div class="method-heading">
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+ <span class="method-name">each_relation</span><span
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+ class="method-args">() { |r| ... }</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+ <div class="method-description">
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+ <div class="method-source-code" id="each_relation-source">
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/passage.rb, line 27</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">each_relation</span>
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+ <span class="ruby-identifier">relations</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">r</span><span class="ruby-operator">|</span> <span class="ruby-keyword">yield</span> <span class="ruby-identifier">r</span>}
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+ <span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span> <span class="ruby-identifier">s</span>.<span class="ruby-identifier">each_relation</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">r</span><span class="ruby-operator">|</span> <span class="ruby-keyword">yield</span> <span class="ruby-identifier">r</span>}}
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- each_relation-source -->
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+ </div><!-- each_relation-method -->
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+ <div id="method-i-find_node" class="method-detail ">
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+ <div class="method-heading">
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+ <span class="method-name">find_node</span><span
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+ class="method-args">(id)</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+ <div class="method-source-code" id="find_node-source">
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/passage.rb, line 18</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">find_node</span>(<span class="ruby-identifier">id</span>)
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+ (<span class="ruby-identifier">relations</span><span class="ruby-operator">+</span><span class="ruby-identifier">annotations</span>).<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span> <span class="ruby-keyword">return</span> <span class="ruby-identifier">n</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">n</span>.<span class="ruby-identifier">id</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">id</span>}
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+ <span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
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+ <span class="ruby-identifier">ret</span> = <span class="ruby-identifier">s</span>.<span class="ruby-identifier">find_node</span>(<span class="ruby-identifier">id</span>)
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+ <span class="ruby-keyword">return</span> <span class="ruby-identifier">ret</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">ret</span>.<span class="ruby-identifier">nil?</span>
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+ <span class="ruby-keyword">end</span>
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+ <span class="ruby-keyword">nil</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- find_node-source -->
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+ <div id="method-i-to_s" class="method-detail ">
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+ <div class="method-heading">
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+ <span class="method-name">to_s</span><span
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+ class="method-args">()</span>
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+ <span class="method-click-advice">click to toggle source</span>
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+ </div>
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+ <div class="method-description">
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+ <div class="method-source-code" id="to_s-source">
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/passage.rb, line 14</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_s</span>
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+ <span class="ruby-node">&quot;Passage @#{offset}: #{text}&quot;</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- to_s-source -->
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+ </div><!-- to_s-method -->
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+ </section><!-- public-instance-method-details -->
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+ </section><!-- 5Buntitled-5D -->
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+ </div><!-- documentation -->
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+ <footer id="validator-badges">
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+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
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+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.
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+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
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+ </footer>
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+ <html>
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+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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+ <title>class SimpleBioC::Relation - RDoc Documentation</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 type="text/javascript">
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+ var rdoc_rel_prefix = "../";
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+ </script>
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+
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+ <script type="text/javascript" charset="utf-8" src="../js/jquery.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/navigation.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/search_index.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/search.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/searcher.js"></script>
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+ <script type="text/javascript" charset="utf-8" src="../js/darkfish.js"></script>
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+
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+
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+ <body id="top" class="class">
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+ <nav id="metadata">
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+ <nav id="home-section" class="section">
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+ <h3 class="section-header">
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+ <a href="../index.html">Home</a>
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+ <a href="../table_of_contents.html#classes">Classes</a>
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+ <a href="../table_of_contents.html#methods">Methods</a>
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+ </h3>
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+ </nav>
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+
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+
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+ <nav id="search-section" class="section project-section" class="initially-hidden">
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+ <form action="#" method="get" accept-charset="utf-8">
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+ <h3 class="section-header">
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+ <input type="text" name="search" placeholder="Search" id="search-field"
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+ title="Type to search, Up and Down to navigate, Enter to load">
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+ </h3>
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+ </form>
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+ <ul id="search-results" class="initially-hidden"></ul>
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+ </nav>
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+ <div id="file-metadata">
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+ <nav id="file-list-section" class="section">
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+ <h3 class="section-header">Defined In</h3>
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+ <ul>
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+ <li>lib/simple_bioc/relation.rb
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+ </ul>
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+ </nav>
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+ </div>
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+ <div id="class-metadata">
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+
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+ <nav 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"><a href="NodeBase.html">SimpleBioC::NodeBase</a>
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+
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+ </nav>
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+
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+
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+
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+ <!-- Method Quickref -->
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+ <nav id="method-list-section" class="section">
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+ <h3 class="section-header">Methods</h3>
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+
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+ <ul class="link-list">
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+
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+ <li class="calls-super" ><a href="#method-c-new">::new</a>
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+
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+ <li ><a href="#method-i-adjust_ref">#adjust_ref</a>
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+
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+ <li ><a href="#method-i-to_c">#to_c</a>
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+
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+ </ul>
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+ </nav>
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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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+ <nav id="fileindex-section" class="section project-section">
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+ <h3 class="section-header">Pages</h3>
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+ <li class="file"><a href="../README_md.html">README</a>
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+
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+ </ul>
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+ </nav>
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+
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+ <nav id="classindex-section" class="section project-section">
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+ <h3 class="section-header">Class and Module Index</h3>
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+
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+ <ul class="link-list">
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+
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+ <li><a href="../BioCReader.html">BioCReader</a>
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+
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+ <li><a href="../BioCWriter.html">BioCWriter</a>
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+
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+ <li><a href="../SimpleBioC.html">SimpleBioC</a>
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+
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+ <li><a href="../SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
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+
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+ <li><a href="../SimpleBioC/Collection.html">SimpleBioC::Collection</a>
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+
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+ <li><a href="../SimpleBioC/Document.html">SimpleBioC::Document</a>
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+
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+ <li><a href="../SimpleBioC/Location.html">SimpleBioC::Location</a>
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+
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+ <li><a href="../SimpleBioC/Node.html">SimpleBioC::Node</a>
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+
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+ <li><a href="../SimpleBioC/NodeBase.html">SimpleBioC::NodeBase</a>
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+
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+ <li><a href="../SimpleBioC/Passage.html">SimpleBioC::Passage</a>
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+
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+ <li><a href="../SimpleBioC/Relation.html">SimpleBioC::Relation</a>
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+
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+ <li><a href="../SimpleBioC/Sentence.html">SimpleBioC::Sentence</a>
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+
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+ </ul>
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+ </nav>
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+
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+ </div>
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+ </nav>
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+
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+ <div id="documentation">
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+ <h1 class="class">class SimpleBioC::Relation</h1>
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+
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+ <div id="description" class="description">
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+
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+ </div><!-- description -->
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+
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+
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+
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+
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+ <section id="5Buntitled-5D" class="documentation-section">
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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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+ <!-- Attributes -->
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+ <section id="attribute-method-details" class="method-section section">
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+ <h3 class="section-header">Attributes</h3>
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+
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+
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+ <div id="attribute-i-nodes" class="method-detail">
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+ <div class="method-heading attribute-method-heading">
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+ <span class="method-name">nodes</span><span
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+ class="attribute-access-type">[RW]</span>
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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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+
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+
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+ </div>
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+ </div>
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+
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+ </section><!-- attribute-method-details -->
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+
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+
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+ <!-- Methods -->
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+
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+ <section id="public-class-5Buntitled-5D-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="method-c-new" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">new</span><span
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+ class="method-args">(parent)</span>
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+
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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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+
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+ <div class="method-description">
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+
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+
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+
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+
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+ <div class="method-calls-super">
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+ Calls superclass method
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+ <a href="NodeBase.html#method-c-new">SimpleBioC::NodeBase.new</a>
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+ </div>
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+
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+
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+
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+ <div class="method-source-code" id="new-source">
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/relation.rb, line 6</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">parent</span>)
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+ <span class="ruby-keyword">super</span>(<span class="ruby-identifier">parent</span>)
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+ <span class="ruby-ivar">@nodes</span> = []
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- new-source -->
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+
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+ </div>
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+
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+
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+
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+
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+ </div><!-- new-method -->
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+
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+
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+ </section><!-- public-class-method-details -->
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+
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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
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+ <h3 class="section-header">Public Instance Methods</h3>
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+
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+
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+ <div id="method-i-adjust_ref" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">adjust_ref</span><span
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+ class="method-args">()</span>
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+
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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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+
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+ <div class="method-description">
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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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+ <div class="method-source-code" id="adjust_ref-source">
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/relation.rb, line 11</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">adjust_ref</span>
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+ <span class="ruby-identifier">nodes</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span> <span class="ruby-identifier">n</span>.<span class="ruby-identifier">adjust_ref</span>}
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- adjust_ref-source -->
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+
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+ </div>
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+
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+
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+
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+
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+ </div><!-- adjust_ref-method -->
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+
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+
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+ <div id="method-i-to_c" class="method-detail ">
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+
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+ <div class="method-heading">
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+ <span class="method-name">to_c</span><span
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+ class="method-args">()</span>
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+
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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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+
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+ <div class="method-description">
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+
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+
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+
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+
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+
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+ <div class="method-source-code" id="to_c-source">
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+ <pre><span class="ruby-comment"># File lib/simple_bioc/relation.rb, line 15</span>
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+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_c</span>
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+ <span class="ruby-node">&quot;Relation:#{id}&quot;</span>
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+ <span class="ruby-keyword">end</span></pre>
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+ </div><!-- to_c-source -->
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+
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+ </div>
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+ </div><!-- to_c-method -->
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+
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+
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+ </section><!-- public-instance-method-details -->
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+
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+ </section><!-- 5Buntitled-5D -->
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+
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+ </div><!-- documentation -->
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+
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+
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