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/table_of_contents.html CHANGED
@@ -2,40 +2,38 @@
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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>Table of Contents - RDoc Documentation</title>
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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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+ <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 class="indexpage">
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- <h1>Table of Contents - RDoc Documentation</h1>
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+ <body id="top" class="table-of-contents">
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+ <main role="main">
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+ <h1 class="class">Table of Contents - RDoc Documentation</h1>
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- <h2>Pages</h2>
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+ <h2 id="pages">Pages</h2>
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  <ul>
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  <li class="file">
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  <a href="README_md.html">README</a>
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- <img class="toc-toggle" src="images/transparent.png" alt="" title="toggle headings">
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- <ul class="initially-hidden">
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+ <ul>
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  <li><a href="README_md.html#label-SimpleBioC">SimpleBioC</a>
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- <li><a href="README_md.html#label-Feature%3A">Feature:</a>
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+ <li><a href="README_md.html#label-Feature-3A">Feature:</a>
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  <li><a href="README_md.html#label-Installation">Installation</a>
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  <li><a href="README_md.html#label-Simple+Usages">Simple Usages</a>
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  <li><a href="README_md.html#label-Options">Options</a>
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- <li><a href="README_md.html#label-Specify+set+of+%3Cdocument%3Es+to+parse">Specify set of &lt;document&gt;s to parse</a>
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+ <li><a href="README_md.html#label-Specify+set+of+-3Cdocument-3Es+to+parse">Specify set of &lt;document&gt;s to parse</a>
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  <li><a href="README_md.html#label-No+whitespace+in+output">No whitespace in output</a>
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  <li><a href="README_md.html#label-Sample">Sample</a>
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  <li><a href="README_md.html#label-Contributing">Contributing</a>
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  </ul>
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- <h2 id="classes">Classes/Modules</h2>
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+ <h2 id="classes">Classes and Modules</h2>
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  <ul>
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+ <li class="module">
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+ <a href="BioCMerger.html">BioCMerger</a>
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+ </li>
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  <li class="module">
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  <a href="BioCReader.html">BioCReader</a>
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  </li>
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+ <li class="module">
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  <a href="BioCWriter.html">BioCWriter</a>
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  </li>
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- <li class="module">
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+ <li class="module">
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  <a href="SimpleBioC.html">SimpleBioC</a>
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  </li>
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- <li class="class">
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+ <li class="class">
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  <a href="SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
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  </li>
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- <li class="class">
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+ <li class="class">
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  <a href="SimpleBioC/Collection.html">SimpleBioC::Collection</a>
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  </li>
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- <li class="class">
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+ <li class="class">
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  <a href="SimpleBioC/Document.html">SimpleBioC::Document</a>
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  </li>
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- <li class="class">
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+ <li class="class">
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  <a href="SimpleBioC/Location.html">SimpleBioC::Location</a>
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  </li>
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- <li class="class">
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  <a href="SimpleBioC/Node.html">SimpleBioC::Node</a>
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  </li>
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- <li class="class">
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+ <li class="class">
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  <a href="SimpleBioC/NodeBase.html">SimpleBioC::NodeBase</a>
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  </li>
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- <li class="class">
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+ <li class="class">
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  <a href="SimpleBioC/Passage.html">SimpleBioC::Passage</a>
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  </li>
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- <li class="class">
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+ <li class="class">
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  <a href="SimpleBioC/Relation.html">SimpleBioC::Relation</a>
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  </li>
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- <li class="class">
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  <a href="SimpleBioC/Sentence.html">SimpleBioC::Sentence</a>
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  </li>
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-
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  </ul>
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  <h2 id="methods">Methods</h2>
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  <ul>
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-
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- <li class="method"><a href="SimpleBioC/Annotation.html#method-c-new">::new &mdash; SimpleBioC::Annotation</a>
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-
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- <li class="method"><a href="SimpleBioC/Passage.html#method-c-new">::new &mdash; SimpleBioC::Passage</a>
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- <li class="method"><a href="SimpleBioC/Collection.html#method-c-new">::new &mdash; SimpleBioC::Collection</a>
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- <li class="method"><a href="SimpleBioC/NodeBase.html#method-c-new">::new &mdash; SimpleBioC::NodeBase</a>
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- <li class="method"><a href="SimpleBioC/Document.html#method-c-new">::new &mdash; SimpleBioC::Document</a>
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- <li class="method"><a href="SimpleBioC/Relation.html#method-c-new">::new &mdash; SimpleBioC::Relation</a>
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- <li class="method"><a href="SimpleBioC/Node.html#method-c-new">::new &mdash; SimpleBioC::Node</a>
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- <li class="method"><a href="SimpleBioC/Location.html#method-c-new">::new &mdash; SimpleBioC::Location</a>
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- <li class="method"><a href="SimpleBioC/Sentence.html#method-c-new">::new &mdash; SimpleBioC::Sentence</a>
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- <li class="method"><a href="SimpleBioC/Document.html#method-i-adjust_ref">#adjust_ref &mdash; SimpleBioC::Document</a>
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- <li class="method"><a href="SimpleBioC/Relation.html#method-i-adjust_ref">#adjust_ref &mdash; SimpleBioC::Relation</a>
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- <li class="method"><a href="SimpleBioC/Node.html#method-i-adjust_ref">#adjust_ref &mdash; SimpleBioC::Node</a>
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- <li class="method"><a href="SimpleBioC/Document.html#method-i-each_relation">#each_relation &mdash; SimpleBioC::Document</a>
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- <li class="method"><a href="SimpleBioC/Sentence.html#method-i-each_relation">#each_relation &mdash; SimpleBioC::Sentence</a>
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- <li class="method"><a href="SimpleBioC/Passage.html#method-i-each_relation">#each_relation &mdash; SimpleBioC::Passage</a>
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- <li class="method"><a href="SimpleBioC/Sentence.html#method-i-find_node">#find_node &mdash; SimpleBioC::Sentence</a>
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- <li class="method"><a href="SimpleBioC/Document.html#method-i-find_node">#find_node &mdash; SimpleBioC::Document</a>
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- <li class="method"><a href="SimpleBioC/Passage.html#method-i-find_node">#find_node &mdash; SimpleBioC::Passage</a>
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- <li class="method"><a href="SimpleBioC.html#method-i-from_xml">#from_xml &mdash; SimpleBioC</a>
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- <li class="method"><a href="BioCReader.html#method-i-read">#read &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_annotation">#read_annotation &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_collection">#read_collection &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_document">#read_document &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_infon">#read_infon &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_int">#read_int &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_location">#read_location &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_node">#read_node &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_passage">#read_passage &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_recursive">#read_recursive &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_relation">#read_relation &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_sentence">#read_sentence &mdash; BioCReader</a>
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- <li class="method"><a href="BioCReader.html#method-i-read_text">#read_text &mdash; BioCReader</a>
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- <li class="method"><a href="SimpleBioC/Node.html#method-i-to_c">#to_c &mdash; SimpleBioC::Node</a>
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- <li class="method"><a href="SimpleBioC/Collection.html#method-i-to_c">#to_c &mdash; SimpleBioC::Collection</a>
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- <li class="method"><a href="SimpleBioC/Relation.html#method-i-to_c">#to_c &mdash; SimpleBioC::Relation</a>
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- <li class="method"><a href="SimpleBioC/Sentence.html#method-i-to_c">#to_c &mdash; SimpleBioC::Sentence</a>
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- <li class="method"><a href="SimpleBioC/Document.html#method-i-to_s">#to_s &mdash; SimpleBioC::Document</a>
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- <li class="method"><a href="SimpleBioC/Location.html#method-i-to_s">#to_s &mdash; SimpleBioC::Location</a>
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+ <li class="method">
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+ <a href="SimpleBioC/Passage.html#method-i-find_node">#find_node</a>
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+ <span class="container">SimpleBioC::Passage</span>
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+ <li class="method">
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+ <a href="SimpleBioC.html#method-i-from_xml">#from_xml</a>
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+ <span class="container">SimpleBioC</span>
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+ <span class="container">SimpleBioC</span>
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+ <span class="container">SimpleBioC</span>
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+ <span class="container">BioCReader</span>
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+ <span class="container">BioCReader</span>
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+ <a href="SimpleBioC/Passage.html#method-i-to_s">#to_s</a>
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+ <li class="method">
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+ <li class="method">
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+ <a href="SimpleBioC.html#method-i-to_xml">#to_xml</a>
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+ &mdash;
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+ <span class="container">BioCWriter</span>
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+ <li class="method">
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+ <li class="method">
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+ <a href="BioCWriter.html#method-i-write_collection">#write_collection</a>
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+ <span class="container">BioCWriter</span>
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+ <li class="method">
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+ <a href="BioCWriter.html#method-i-write_document">#write_document</a>
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+ <span class="container">BioCWriter</span>
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+ <li class="method">
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+ <a href="BioCWriter.html#method-i-write_infon">#write_infon</a>
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+ <span class="container">BioCWriter</span>
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+ <li class="method">
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+ <a href="BioCWriter.html#method-i-write_location">#write_location</a>
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+ <span class="container">BioCWriter</span>
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+ <li class="method">
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+ <a href="BioCWriter.html#method-i-write_node">#write_node</a>
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+ <li class="method">
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+ <a href="BioCWriter.html#method-i-write_passage">#write_passage</a>
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+ <li class="method">
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+ <a href="BioCWriter.html#method-i-write_relation">#write_relation</a>
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+ &mdash;
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+ <span class="container">BioCWriter</span>
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+ <a href="BioCWriter.html#method-i-write_sentence">#write_sentence</a>
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