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/Collection.html CHANGED
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- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
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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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+ <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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- <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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- </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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- <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/collection.rb
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- </ul>
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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" role="directory">
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  <li ><a href="#method-c-new">::new</a>
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- </nav>
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- </div>
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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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- </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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- <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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-
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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/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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- </ul>
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- </nav>
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+ </div>
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- <div id="documentation">
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- <h1 class="class">class SimpleBioC::Collection</h1>
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+ <main role="main" aria-labelledby="class-SimpleBioC::Collection">
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+ <h1 id="class-SimpleBioC::Collection" class="class">
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+ class SimpleBioC::Collection
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+ </h1>
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+ <section class="description">
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- <h3 class="section-header">Attributes</h3>
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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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- <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 class="section-header">Public Instance Methods</h3>
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+ <header>
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+ </main>
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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/Document.html CHANGED
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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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+ <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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  <div id="method-c-new" class="method-detail ">
@@ -257,20 +213,22 @@
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  <span class="ruby-ivar">@relations</span> = []
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  <span class="ruby-ivar">@collection</span> = <span class="ruby-identifier">parent</span>
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  <span class="ruby-keyword">end</span></pre>
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- <h3 class="section-header">Public Instance Methods</h3>
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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-adjust_ref" class="method-detail ">
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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">each_relation</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">r</span><span class="ruby-operator">|</span> <span class="ruby-identifier">r</span>.<span class="ruby-identifier">adjust_ref</span>}
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  <div id="method-i-each_relation" class="method-detail ">
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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">passages</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">p</span><span class="ruby-operator">|</span> <span class="ruby-identifier">p</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 id="method-i-find_node" class="method-detail ">
@@ -368,14 +326,14 @@
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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 id="method-i-to_s" class="method-detail ">
@@ -401,26 +359,25 @@
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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;Document:#{id}&quot;</span>
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  <span class="ruby-keyword">end</span></pre>
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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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