simple_bioc 0.0.5 → 0.0.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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/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="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#methods">Methods</a>
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+ <div id="search-section" role="search" class="project-section 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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+ <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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- </ul>
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+ <div id="parent-class-section" class="nav-section">
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+ <h3>Methods</h3>
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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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- <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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-
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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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- </ul>
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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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- <div id="description" class="description">
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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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+ </section>
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+ <section class="attribute-method-details" class="method-section">
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+ <header>
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+ <h3>Attributes</h3>
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+ </header>
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- <h3 class="section-header">Public Class Methods</h3>
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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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@@ -256,26 +212,25 @@ href="Relation.html">Relation</a>.</p>
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  <span class="ruby-ivar">@passage</span> = <span class="ruby-ivar">@sentence</span>.<span class="ruby-identifier">passage</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@sentence</span>.<span class="ruby-identifier">nil?</span>
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  <span class="ruby-ivar">@document</span> = <span class="ruby-ivar">@passage</span>.<span class="ruby-identifier">document</span> <span class="ruby-keyword">unless</span> <span class="ruby-ivar">@passage</span>.<span class="ruby-identifier">nil?</span>
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  <span class="ruby-keyword">end</span></pre>
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- </div><!-- new-source -->
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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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data/html/SimpleBioC/Passage.html CHANGED
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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>
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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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