simple_bioc 0.0.5 → 0.0.6
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- checksums.yaml +4 -4
- data/.gitignore +13 -0
- data/html/BioCMerger.html +748 -0
- data/html/BioCReader.html +138 -146
- data/html/BioCWriter.html +84 -131
- data/html/README_md.html +79 -100
- data/html/SimpleBioC/Annotation.html +70 -113
- data/html/SimpleBioC/Collection.html +70 -113
- data/html/SimpleBioC/Document.html +76 -119
- data/html/SimpleBioC/Location.html +70 -113
- data/html/SimpleBioC/Node.html +72 -115
- data/html/SimpleBioC/NodeBase.html +63 -108
- data/html/SimpleBioC/Passage.html +74 -117
- data/html/SimpleBioC/Relation.html +85 -115
- data/html/SimpleBioC/Sentence.html +74 -117
- data/html/SimpleBioC.html +221 -129
- data/html/created.rid +16 -15
- data/html/css/fonts.css +167 -0
- data/html/css/rdoc.css +590 -0
- data/html/fonts/Lato-Light.ttf +0 -0
- data/html/fonts/Lato-LightItalic.ttf +0 -0
- data/html/fonts/Lato-Regular.ttf +0 -0
- data/html/fonts/Lato-RegularItalic.ttf +0 -0
- data/html/fonts/SourceCodePro-Bold.ttf +0 -0
- data/html/fonts/SourceCodePro-Regular.ttf +0 -0
- data/html/index.html +71 -53
- data/html/js/darkfish.js +32 -26
- data/html/js/jquery.js +4 -18
- data/html/js/navigation.js.gz +0 -0
- data/html/js/search.js +20 -5
- data/html/js/search_index.js +1 -1
- data/html/js/search_index.js.gz +0 -0
- data/html/js/searcher.js.gz +0 -0
- data/html/table_of_contents.html +379 -136
- data/lib/simple_bioc/bioc_merger.rb +209 -0
- data/lib/simple_bioc/relation.rb +1 -1
- data/lib/simple_bioc/version.rb +1 -1
- data/lib/simple_bioc.rb +8 -4
- data/spec/file_check_spec.rb +14 -1
- data/xml/PMC2133144.xml +3 -0
- data/xml/merge/9864355.xml +1 -0
- data/xml/merge/9864355_1.xml +1 -0
- data/xml/merge/9864355_2.xml +1974 -0
- data/xml/merge/9864355_3.xml +1 -0
- data/xml/merge/output.xml +6742 -0
- metadata +21 -2
data/html/BioCWriter.html
CHANGED
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<h3 class="section-header">Defined In</h3>
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<li>lib/simple_bioc/bioc_writer.rb
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<!-- Method Quickref -->
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<h3>Methods</h3>
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<li ><a href="#method-i-write">#write</a>
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<li ><a href="#method-i-write_sentence">#write_sentence</a>
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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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<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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<main role="main" aria-labelledby="module-BioCWriter">
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<h1 id="module-BioCWriter" class="module">
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module BioCWriter
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</h1>
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<section class="description">
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<!-- Methods -->
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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-write" class="method-detail ">
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<div class="method-source-code" id="write-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 8</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">write</span>(<span class="ruby-identifier">collection</span>, <span class="ruby-identifier">options</span> = {})
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<span class="ruby-identifier">options</span>[<span class="ruby-value">:save_with</span>] = <span class="ruby-value">1</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:save_with</span>].<span class="ruby-identifier">nil?</span>
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<span class="ruby-identifier">builder</span> = <span class="ruby-constant">Nokogiri</span><span class="ruby-operator">::</span><span class="ruby-constant">XML</span><span class="ruby-operator">::</span><span class="ruby-constant">Builder</span>.<span class="ruby-identifier">new</span>(<span class="ruby-value">:encoding</span> =<span class="ruby-operator">></span> <span class="ruby-string">'UTF-8'</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">xml</span><span class="ruby-operator">|</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-identifier">builder</span>.<span class="ruby-identifier">to_xml</span>(<span class="ruby-identifier">options</span>)
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<span class="ruby-keyword">end</span></pre>
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<div id="method-i-write_annotation" class="method-detail ">
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<div class="method-source-code" id="write_annotation-source">
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 65</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">write_annotation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">annotation</span>)
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<span class="ruby-keyword">end</span>
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<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">annotation</span>(<span class="ruby-identifier">attribute</span>) {
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<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">text_</span> <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">text</span>
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<span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_location</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">l</span>)}
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<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">text_</span> <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">text</span>
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}
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 25</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">write_collection</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>)
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<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">collection</span> {
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<span class="ruby-identifier">collection</span>.<span class="ruby-identifier">documents</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">d</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_document</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">d</span>)}
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}
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 35</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">write_document</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">document</span>)
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<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">document</span> {
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<span class="ruby-identifier">document</span>.<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-identifier">write_relation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">r</span>)}
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}
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 17</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">write_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">obj</span>)
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<span class="ruby-identifier">obj</span>.<span class="ruby-identifier">infons</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>, <span class="ruby-identifier">v</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">passage</span>.<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-identifier">write_relation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">r</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="http://docs.seattlerb.org/rdoc/">RDoc</a> 4.2.0.
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