simple_bioc 0.0.5 → 0.0.6

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Files changed (46) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +13 -0
  3. data/html/BioCMerger.html +748 -0
  4. data/html/BioCReader.html +138 -146
  5. data/html/BioCWriter.html +84 -131
  6. data/html/README_md.html +79 -100
  7. data/html/SimpleBioC/Annotation.html +70 -113
  8. data/html/SimpleBioC/Collection.html +70 -113
  9. data/html/SimpleBioC/Document.html +76 -119
  10. data/html/SimpleBioC/Location.html +70 -113
  11. data/html/SimpleBioC/Node.html +72 -115
  12. data/html/SimpleBioC/NodeBase.html +63 -108
  13. data/html/SimpleBioC/Passage.html +74 -117
  14. data/html/SimpleBioC/Relation.html +85 -115
  15. data/html/SimpleBioC/Sentence.html +74 -117
  16. data/html/SimpleBioC.html +221 -129
  17. data/html/created.rid +16 -15
  18. data/html/css/fonts.css +167 -0
  19. data/html/css/rdoc.css +590 -0
  20. data/html/fonts/Lato-Light.ttf +0 -0
  21. data/html/fonts/Lato-LightItalic.ttf +0 -0
  22. data/html/fonts/Lato-Regular.ttf +0 -0
  23. data/html/fonts/Lato-RegularItalic.ttf +0 -0
  24. data/html/fonts/SourceCodePro-Bold.ttf +0 -0
  25. data/html/fonts/SourceCodePro-Regular.ttf +0 -0
  26. data/html/index.html +71 -53
  27. data/html/js/darkfish.js +32 -26
  28. data/html/js/jquery.js +4 -18
  29. data/html/js/navigation.js.gz +0 -0
  30. data/html/js/search.js +20 -5
  31. data/html/js/search_index.js +1 -1
  32. data/html/js/search_index.js.gz +0 -0
  33. data/html/js/searcher.js.gz +0 -0
  34. data/html/table_of_contents.html +379 -136
  35. data/lib/simple_bioc/bioc_merger.rb +209 -0
  36. data/lib/simple_bioc/relation.rb +1 -1
  37. data/lib/simple_bioc/version.rb +1 -1
  38. data/lib/simple_bioc.rb +8 -4
  39. data/spec/file_check_spec.rb +14 -1
  40. data/xml/PMC2133144.xml +3 -0
  41. data/xml/merge/9864355.xml +1 -0
  42. data/xml/merge/9864355_1.xml +1 -0
  43. data/xml/merge/9864355_2.xml +1974 -0
  44. data/xml/merge/9864355_3.xml +1 -0
  45. data/xml/merge/output.xml +6742 -0
  46. metadata +21 -2
data/html/SimpleBioC/NodeBase.html CHANGED
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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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+ <script src="../js/jquery.js"></script>
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+ <script src="../js/darkfish.js"></script>
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+ <link href="../css/fonts.css" rel="stylesheet">
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+ <link href="../css/rdoc.css" rel="stylesheet">
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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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+ <body id="top" role="document" class="class">
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+ <nav role="navigation">
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+ <div id="project-navigation">
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+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
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+ <h2>
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+ <a href="../index.html" rel="home">Home</a>
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+ </h2>
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+ <div id="table-of-contents-navigation">
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+ <a href="../table_of_contents.html#pages">Pages</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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+ <div id="search-section" role="search" class="project-section initially-hidden">
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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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+ <div id="search-field-wrapper">
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+ <input id="search-field" role="combobox" aria-label="Search"
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+ aria-autocomplete="list" aria-controls="search-results"
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+ type="text" name="search" placeholder="Search" spellcheck="false"
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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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+ </div>
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- <ul id="search-results" class="initially-hidden"></ul>
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- </nav>
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+ <ul id="search-results" aria-label="Search Results"
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+ aria-busy="false" aria-expanded="false"
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+ aria-atomic="false" class="initially-hidden"></ul>
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+ </form>
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+ </div>
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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/node_base.rb
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- </ul>
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+ <div id="parent-class-section" class="nav-section">
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+ <h3>Parent</h3>
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- <nav id="method-list-section" class="section">
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+ <div id="method-list-section" class="nav-section">
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+ <h3>Methods</h3>
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- <ul class="link-list">
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+ <ul class="link-list" role="directory">
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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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- <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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+ <main role="main" aria-labelledby="class-SimpleBioC::NodeBase">
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+ <h1 id="class-SimpleBioC::NodeBase" class="class">
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+ class SimpleBioC::NodeBase
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+ </h1>
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- <ul class="link-list">
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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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- <li><a href="../SimpleBioC/Passage.html">SimpleBioC::Passage</a>
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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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- </nav>
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- <div id="documentation">
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- <h1 class="class">class SimpleBioC::NodeBase</h1>
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+ <section class="description">
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  <p><a href="NodeBase.html">NodeBase</a> is not a BioC DTD entity. This is a
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  super class of <a href="Annotation.html">Annotation</a> &amp; <a
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  href="Relation.html">Relation</a>.</p>
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+ <header>
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+ <section id="public-class-5Buntitled-5D-method-details" class="method-section">
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+ <header>
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+ <h3>Public Class Methods</h3>
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+ </header>
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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 id="validator-badges" role="contentinfo">
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+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
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+ <p>Generated by <a href="http://docs.seattlerb.org/rdoc/">RDoc</a> 4.2.0.
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+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-RDoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
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data/html/SimpleBioC/Passage.html CHANGED
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  <span class="ruby-keyword">end</span></pre>
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+ </div>
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- </div><!-- new-method -->
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+ </div>
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- </section><!-- public-class-method-details -->
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+ </section>
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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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+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section">
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+ <header>
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+ <h3>Public Instance Methods</h3>
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+ </header>
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  <div id="method-i-each_relation" class="method-detail ">
@@ -322,14 +280,14 @@
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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>
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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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  <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-method -->
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  <div id="method-i-to_s" class="method-detail ">
@@ -393,26 +351,25 @@
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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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+ </section>
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- </section><!-- 5Buntitled-5D -->
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- </div><!-- documentation -->
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+ </section>
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+ </main>
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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 id="validator-badges" role="contentinfo">
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+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
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+ <p>Generated by <a href="http://docs.seattlerb.org/rdoc/">RDoc</a> 4.2.0.
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+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-RDoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
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  </footer>
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