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/README_md.html CHANGED
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+ <a href="./index.html" rel="home">Home</a>
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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" aria-label="Search Results"
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- <li><a href="#label-SimpleBioC">SimpleBioC</a>
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- <li><a href="#label-Feature%3A">Feature:</a>
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- <li><a href="#label-Installation">Installation</a>
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- <li><a href="#label-Simple+Usages">Simple Usages</a>
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- <li><a href="#label-Options">Options</a>
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- <li><a href="#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="#label-No+whitespace+in+output">No whitespace in output</a>
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- <li><a href="#label-Sample">Sample</a>
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- <li><a href="#label-Contributing">Contributing</a>
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+ <h3>Table of Contents</h3>
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+ <ul class="link-list" role="directory">
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+ <li><a href="#label-SimpleBioC">SimpleBioC</a>
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+ <li><a href="#label-Feature-3A">Feature:</a>
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+ <li><a href="#label-Installation">Installation</a>
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+ <li><a href="#label-Simple+Usages">Simple Usages</a>
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+ <li><a href="#label-Options">Options</a>
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+ <li><a href="#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="#label-No+whitespace+in+output">No whitespace in output</a>
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+ <li><a href="#label-Sample">Sample</a>
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+ <li><a href="#label-Contributing">Contributing</a>
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- <nav id="classindex-section" class="section project-section">
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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/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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+ <li><a href="./README_md.html">README</a>
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- <div id="documentation" class="description">
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- <h1 id="label-SimpleBioC"><a href="SimpleBioC.html">SimpleBioC</a><span><a href="#label-SimpleBioC">&para;</a> <a href="#documentation">&uarr;</a></span></h1>
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+ <main role="main" aria-label="Page README.md">
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+ <h1 id="label-SimpleBioC"><a href="SimpleBioC.html">SimpleBioC</a><span><a href="#label-SimpleBioC">&para;</a> <a href="#top">&uarr;</a></span></h1>
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  <p><a href="SimpleBioC.html">SimpleBioC</a> is a simple parser / builder for
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  BioC data format. BioC is a simple XML format to share text documents and
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  href="http://www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/">www.ncbi.nlm.nih.gov/CBBresearch/Dogan/BioC/</a>)</p>
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  <ul><li>
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  <p>Parse &amp; convert a BioC document to an object instance compatible to
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  <p>Build a BioC document from an object instance</p>
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- <h2 id="label-Installation">Installation<span><a href="#label-Installation">&para;</a> <a href="#documentation">&uarr;</a></span></h2>
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  <p>Add this line to your application&#39;s Gemfile:</p>
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- <pre>gem &#39;simple_bioc&#39;</pre>
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  <p>Traverse &amp; Manipulate Data. Data structure are almost the same as the
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  <p>You can parse only a set of document elements in a large xml document
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  <ol><li>
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  <p>Fork it</p>
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  <p>Copyright © 2013, Dongseop Kwon</p>
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  <p>Released under the MIT License.</p>
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