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/Relation.html CHANGED
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+ <script src="../js/jquery.js"></script>
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+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
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+ <a href="../index.html" rel="home">Home</a>
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+ </h2>
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- <nav id="metadata">
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- <nav id="home-section" class="section">
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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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- </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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+ </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="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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- <ul class="link-list">
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- <li><a href="../BioCReader.html">BioCReader</a>
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- <li><a href="../BioCWriter.html">BioCWriter</a>
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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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-
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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/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::Relation</h1>
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+ <main role="main" aria-labelledby="class-SimpleBioC::Relation">
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+ <h1 id="class-SimpleBioC::Relation" class="class">
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+ class SimpleBioC::Relation
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+ </h1>
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+ <span class="method-name">original</span><span
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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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+ <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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data/html/SimpleBioC/Sentence.html CHANGED
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- <h1 class="class">class SimpleBioC::Sentence</h1>
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+ <main role="main" aria-labelledby="class-SimpleBioC::Sentence">
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+ <h1 id="class-SimpleBioC::Sentence" class="class">
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+ class SimpleBioC::Sentence
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+ </h1>
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- <!-- Attributes -->
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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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  <span class="ruby-ivar">@relations</span> = []
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  <span class="ruby-ivar">@passage</span> = <span class="ruby-identifier">parent</span>
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  <span class="ruby-keyword">end</span></pre>
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+ <header>
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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">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-keyword">nil</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;Sentence @#{offset}: #{text}&quot;</span>
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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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