simple_bioc 0.0.1 → 0.0.2
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- checksums.yaml +4 -4
- data/README.md +73 -3
- data/Rakefile +5 -0
- data/html/BioCReader.html +657 -0
- data/html/BioCWriter.html +556 -0
- data/html/README_md.html +231 -0
- data/html/SimpleBioC.html +255 -0
- data/html/SimpleBioC/Annotation.html +279 -0
- data/html/SimpleBioC/Collection.html +316 -0
- data/html/SimpleBioC/Document.html +426 -0
- data/html/SimpleBioC/Location.html +288 -0
- data/html/SimpleBioC/Node.html +334 -0
- data/html/SimpleBioC/NodeBase.html +281 -0
- data/html/SimpleBioC/Passage.html +418 -0
- data/html/SimpleBioC/Relation.html +301 -0
- data/html/SimpleBioC/Sentence.html +399 -0
- data/html/created.rid +15 -0
- data/html/images/add.png +0 -0
- data/html/images/arrow_up.png +0 -0
- data/html/images/brick.png +0 -0
- data/html/images/brick_link.png +0 -0
- data/html/images/bug.png +0 -0
- data/html/images/bullet_black.png +0 -0
- data/html/images/bullet_toggle_minus.png +0 -0
- data/html/images/bullet_toggle_plus.png +0 -0
- data/html/images/date.png +0 -0
- data/html/images/delete.png +0 -0
- data/html/images/find.png +0 -0
- data/html/images/loadingAnimation.gif +0 -0
- data/html/images/macFFBgHack.png +0 -0
- data/html/images/package.png +0 -0
- data/html/images/page_green.png +0 -0
- data/html/images/page_white_text.png +0 -0
- data/html/images/page_white_width.png +0 -0
- data/html/images/plugin.png +0 -0
- data/html/images/ruby.png +0 -0
- data/html/images/tag_blue.png +0 -0
- data/html/images/tag_green.png +0 -0
- data/html/images/transparent.png +0 -0
- data/html/images/wrench.png +0 -0
- data/html/images/wrench_orange.png +0 -0
- data/html/images/zoom.png +0 -0
- data/html/index.html +212 -0
- data/html/js/darkfish.js +155 -0
- data/html/js/jquery.js +18 -0
- data/html/js/navigation.js +142 -0
- data/html/js/search.js +94 -0
- data/html/js/search_index.js +1 -0
- data/html/js/searcher.js +228 -0
- data/html/rdoc.css +595 -0
- data/html/table_of_contents.html +199 -0
- data/lib/simple_bioc.rb +4 -0
- data/lib/simple_bioc/annotation.rb +10 -6
- data/lib/simple_bioc/bioc_reader.rb +2 -2
- data/lib/simple_bioc/collection.rb +13 -11
- data/lib/simple_bioc/document.rb +31 -22
- data/lib/simple_bioc/location.rb +13 -7
- data/lib/simple_bioc/node.rb +14 -8
- data/lib/simple_bioc/node_base.rb +13 -10
- data/lib/simple_bioc/passage.rb +26 -23
- data/lib/simple_bioc/relation.rb +13 -8
- data/lib/simple_bioc/sentence.rb +21 -15
- data/lib/simple_bioc/version.rb +2 -2
- data/samples/print_annotation.rb +18 -0
- data/samples/sample1.rb +31 -0
- data/simple_bioc.gemspec +1 -1
- metadata +52 -2
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<h1 class="module">module BioCWriter</h1>
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 6</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">write</span>(<span class="ruby-identifier">collection</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-identifier">write_collection</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>)
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<span class="ruby-keyword">end</span></pre>
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class="method-args">(xml, annotation)</span>
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 61</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-identifier">attribute</span> = {<span class="ruby-identifier">id</span><span class="ruby-operator">:</span> <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">id</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">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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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 21</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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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 31</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">write_infon</span>(<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">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">write_passage</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">p</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 13</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">xml</span>.<span class="ruby-identifier">infon</span>(<span class="ruby-value">:key</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">k</span>) {
|
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<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">text</span> <span class="ruby-identifier">v</span>
|
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}
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<span class="ruby-keyword">end</span></pre>
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</div><!-- write_infon-method -->
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<div id="method-i-write_location" class="method-detail ">
|
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<div class="method-heading">
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<span class="method-name">write_location</span><span
|
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|
+
class="method-args">(xml, location)</span>
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|
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|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 86</span>
|
|
378
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">write_location</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">location</span>)
|
|
379
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">location</span>(<span class="ruby-value">:offset</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">location</span>.<span class="ruby-identifier">offset</span>, <span class="ruby-value">:length</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">location</span>.<span class="ruby-identifier">length</span>)
|
|
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|
+
<span class="ruby-keyword">end</span></pre>
|
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|
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</div><!-- write_location-source -->
|
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|
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|
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|
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|
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|
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|
+
</div><!-- write_location-method -->
|
|
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|
+
|
|
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|
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|
|
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|
+
<div id="method-i-write_node" class="method-detail ">
|
|
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|
+
|
|
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|
+
<div class="method-heading">
|
|
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|
+
<span class="method-name">write_node</span><span
|
|
395
|
+
class="method-args">(xml, node)</span>
|
|
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|
+
|
|
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|
+
<span class="method-click-advice">click to toggle source</span>
|
|
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|
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|
+
</div>
|
|
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|
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|
|
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|
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|
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|
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|
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|
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|
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|
+
|
|
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|
+
<div class="method-source-code" id="write_node-source">
|
|
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|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 90</span>
|
|
411
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">write_node</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">node</span>)
|
|
412
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">node_</span>(<span class="ruby-value">:refid</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">node</span>.<span class="ruby-identifier">refid</span>, <span class="ruby-value">:role</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">node</span>.<span class="ruby-identifier">role</span>)
|
|
413
|
+
<span class="ruby-keyword">end</span></pre>
|
|
414
|
+
</div><!-- write_node-source -->
|
|
415
|
+
|
|
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|
+
</div>
|
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|
+
|
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|
+
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|
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|
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</div><!-- write_node-method -->
|
|
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|
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|
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|
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<div id="method-i-write_passage" class="method-detail ">
|
|
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|
+
|
|
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|
+
<div class="method-heading">
|
|
427
|
+
<span class="method-name">write_passage</span><span
|
|
428
|
+
class="method-args">(xml, passage)</span>
|
|
429
|
+
|
|
430
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
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|
+
|
|
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|
+
</div>
|
|
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|
+
|
|
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|
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|
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|
+
<div class="method-description">
|
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|
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|
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|
+
|
|
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|
+
|
|
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|
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|
|
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|
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|
|
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|
+
<div class="method-source-code" id="write_passage-source">
|
|
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|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 40</span>
|
|
444
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">write_passage</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>)
|
|
445
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">passage</span> {
|
|
446
|
+
<span class="ruby-identifier">write_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>)
|
|
447
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">offset</span> <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">offset</span>
|
|
448
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">text_</span> <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">text</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">text</span>.<span class="ruby-identifier">nil?</span>
|
|
449
|
+
<span class="ruby-identifier">passage</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_sentence</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">s</span>)}
|
|
450
|
+
<span class="ruby-identifier">passage</span>.<span class="ruby-identifier">annotations</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_annotation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">a</span>)}
|
|
451
|
+
<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>)}
|
|
452
|
+
}
|
|
453
|
+
<span class="ruby-keyword">end</span></pre>
|
|
454
|
+
</div><!-- write_passage-source -->
|
|
455
|
+
|
|
456
|
+
</div>
|
|
457
|
+
|
|
458
|
+
|
|
459
|
+
|
|
460
|
+
|
|
461
|
+
</div><!-- write_passage-method -->
|
|
462
|
+
|
|
463
|
+
|
|
464
|
+
<div id="method-i-write_relation" class="method-detail ">
|
|
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|
+
|
|
466
|
+
<div class="method-heading">
|
|
467
|
+
<span class="method-name">write_relation</span><span
|
|
468
|
+
class="method-args">(xml, relation)</span>
|
|
469
|
+
|
|
470
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
471
|
+
|
|
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|
+
</div>
|
|
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|
+
|
|
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|
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|
|
475
|
+
<div class="method-description">
|
|
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|
+
|
|
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|
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|
|
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|
+
|
|
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|
+
|
|
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|
+
|
|
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|
+
|
|
482
|
+
<div class="method-source-code" id="write_relation-source">
|
|
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|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 74</span>
|
|
484
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">write_relation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">relation</span>)
|
|
485
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">relation</span>.<span class="ruby-identifier">id</span>.<span class="ruby-identifier">nil?</span>
|
|
486
|
+
<span class="ruby-identifier">attribute</span> = <span class="ruby-keyword">nil</span>
|
|
487
|
+
<span class="ruby-keyword">else</span>
|
|
488
|
+
<span class="ruby-identifier">attribute</span> = {<span class="ruby-identifier">id</span><span class="ruby-operator">:</span> <span class="ruby-identifier">relation</span>.<span class="ruby-identifier">id</span>}
|
|
489
|
+
<span class="ruby-keyword">end</span>
|
|
490
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">relation</span>(<span class="ruby-identifier">attribute</span>) {
|
|
491
|
+
<span class="ruby-identifier">write_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">relation</span>)
|
|
492
|
+
<span class="ruby-identifier">relation</span>.<span class="ruby-identifier">nodes</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-identifier">write_node</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">n</span>)}
|
|
493
|
+
}
|
|
494
|
+
<span class="ruby-keyword">end</span></pre>
|
|
495
|
+
</div><!-- write_relation-source -->
|
|
496
|
+
|
|
497
|
+
</div>
|
|
498
|
+
|
|
499
|
+
|
|
500
|
+
|
|
501
|
+
|
|
502
|
+
</div><!-- write_relation-method -->
|
|
503
|
+
|
|
504
|
+
|
|
505
|
+
<div id="method-i-write_sentence" class="method-detail ">
|
|
506
|
+
|
|
507
|
+
<div class="method-heading">
|
|
508
|
+
<span class="method-name">write_sentence</span><span
|
|
509
|
+
class="method-args">(xml, sentence)</span>
|
|
510
|
+
|
|
511
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
512
|
+
|
|
513
|
+
</div>
|
|
514
|
+
|
|
515
|
+
|
|
516
|
+
<div class="method-description">
|
|
517
|
+
|
|
518
|
+
|
|
519
|
+
|
|
520
|
+
|
|
521
|
+
|
|
522
|
+
|
|
523
|
+
<div class="method-source-code" id="write_sentence-source">
|
|
524
|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_writer.rb, line 51</span>
|
|
525
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">write_sentence</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>)
|
|
526
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">sentence</span> {
|
|
527
|
+
<span class="ruby-identifier">write_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>)
|
|
528
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">offset</span> <span class="ruby-identifier">sentence</span>.<span class="ruby-identifier">offset</span>
|
|
529
|
+
<span class="ruby-identifier">xml</span>.<span class="ruby-identifier">text_</span> <span class="ruby-identifier">sentence</span>.<span class="ruby-identifier">text</span> <span class="ruby-keyword">unless</span> <span class="ruby-identifier">sentence</span>.<span class="ruby-identifier">text</span>.<span class="ruby-identifier">nil?</span>
|
|
530
|
+
<span class="ruby-identifier">sentence</span>.<span class="ruby-identifier">annotations</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span> <span class="ruby-identifier">write_annotation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">a</span>)}
|
|
531
|
+
<span class="ruby-identifier">sentence</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>)}
|
|
532
|
+
}
|
|
533
|
+
<span class="ruby-keyword">end</span></pre>
|
|
534
|
+
</div><!-- write_sentence-source -->
|
|
535
|
+
|
|
536
|
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</div>
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</section><!-- 5Buntitled-5D -->
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</div><!-- documentation -->
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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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