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.
- 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
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module BioCMerger
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 83</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">adjust_annotation_offset</span>(<span class="ruby-identifier">obj</span>)
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<span class="ruby-identifier">obj</span>.<span class="ruby-identifier">annotations</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span>
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<span class="ruby-identifier">positions</span> = <span class="ruby-identifier">find_all_locations</span>(<span class="ruby-identifier">obj</span>, <span class="ruby-identifier">a</span>.<span class="ruby-identifier">text</span>)
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<span class="ruby-identifier">l</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">choose_offset_candidate</span>(<span class="ruby-identifier">l</span>.<span class="ruby-identifier">offset</span>, <span class="ruby-identifier">positions</span>)
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 102</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">adjust_relation_refid</span>(<span class="ruby-identifier">obj</span>, <span class="ruby-identifier">id_map</span>)
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 92</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">adjust_relation_refids</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">id_map</span>)
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 172</span>
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 151</span>
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">choose_id</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">id</span>, <span class="ruby-identifier">id_map</span>)
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<span class="ruby-identifier">new_id</span> = <span class="ruby-identifier">id</span>
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<span class="ruby-keyword">until</span> <span class="ruby-identifier">node</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-keyword">do</span>
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<span class="ruby-identifier">new_id</span> = <span class="ruby-identifier">new_id</span> <span class="ruby-operator">+</span> <span class="ruby-string">"_c"</span>
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<span class="ruby-identifier">node</span> = <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find_node</span>(<span class="ruby-identifier">new_id</span>)
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<span class="ruby-keyword">end</span>
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<span class="ruby-identifier">id_map</span>[<span class="ruby-identifier">id</span>] = <span class="ruby-identifier">new_id</span>
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">return</span> <span class="ruby-identifier">new_id</span>
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 196</span>
|
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<span class="ruby-keyword">def</span> <span class="ruby-identifier">choose_offset_candidate</span>(<span class="ruby-identifier">offset</span>, <span class="ruby-identifier">positions</span>)
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<span class="ruby-identifier">min_diff</span> = <span class="ruby-value">99999</span>
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|
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<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">offset</span>.<span class="ruby-identifier">to_i</span>
|
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<span class="ruby-identifier">positions</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p</span><span class="ruby-operator">|</span>
|
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<span class="ruby-identifier">diff</span> = (<span class="ruby-identifier">offset</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">p</span>).<span class="ruby-identifier">abs</span>
|
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<span class="ruby-keyword">if</span> <span class="ruby-identifier">diff</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">min_diff</span>
|
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|
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<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">p</span>
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<span class="ruby-identifier">min_diff</span> = <span class="ruby-identifier">diff</span>
|
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<span class="ruby-keyword">end</span>
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<span class="ruby-keyword">end</span>
|
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<span class="ruby-keyword">return</span> <span class="ruby-identifier">ret</span>
|
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|
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<span class="ruby-keyword">end</span></pre>
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</div>
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<div id="method-i-copy_annotation" class="method-detail ">
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<div class="method-heading">
|
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|
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<span class="method-name">copy_annotation</span><span
|
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369
|
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class="method-args">(doc, dest, annotation, id_map)</span>
|
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|
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<span class="method-click-advice">click to toggle source</span>
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</div>
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|
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<div class="method-source-code" id="copy_annotation-source">
|
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|
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<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 137</span>
|
|
385
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">copy_annotation</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">dest</span>, <span class="ruby-identifier">annotation</span>, <span class="ruby-identifier">id_map</span>)
|
|
386
|
+
<span class="ruby-identifier">new_a</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-constant">Annotation</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">dest</span>)
|
|
387
|
+
<span class="ruby-identifier">new_a</span>.<span class="ruby-identifier">id</span> = <span class="ruby-identifier">choose_id</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">id</span>, <span class="ruby-identifier">id_map</span>)
|
|
388
|
+
<span class="ruby-identifier">new_a</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">text</span>
|
|
389
|
+
<span class="ruby-identifier">new_a</span>.<span class="ruby-identifier">locations</span> = []
|
|
390
|
+
<span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">locations</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span>
|
|
391
|
+
<span class="ruby-identifier">new_l</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-constant">Location</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">new_a</span>)
|
|
392
|
+
<span class="ruby-identifier">new_l</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">l</span>.<span class="ruby-identifier">offset</span>
|
|
393
|
+
<span class="ruby-identifier">new_l</span>.<span class="ruby-identifier">length</span> = <span class="ruby-identifier">l</span>.<span class="ruby-identifier">length</span>
|
|
394
|
+
<span class="ruby-identifier">new_a</span>.<span class="ruby-identifier">locations</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">new_l</span>
|
|
395
|
+
<span class="ruby-keyword">end</span>
|
|
396
|
+
<span class="ruby-identifier">dest</span>.<span class="ruby-identifier">annotations</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">new_a</span>
|
|
397
|
+
<span class="ruby-keyword">end</span></pre>
|
|
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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>
|
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|
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|
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|
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|
|
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|
+
<div id="method-i-copy_annotations" class="method-detail ">
|
|
409
|
+
|
|
410
|
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<div class="method-heading">
|
|
411
|
+
<span class="method-name">copy_annotations</span><span
|
|
412
|
+
class="method-args">(doc, dest, src, id_map)</span>
|
|
413
|
+
|
|
414
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
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|
+
|
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416
|
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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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|
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<div class="method-source-code" id="copy_annotations-source">
|
|
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|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 119</span>
|
|
428
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">copy_annotations</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">dest</span>, <span class="ruby-identifier">src</span>, <span class="ruby-identifier">id_map</span>)
|
|
429
|
+
<span class="ruby-identifier">src</span>.<span class="ruby-identifier">annotations</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span>
|
|
430
|
+
<span class="ruby-identifier">copy_annotation</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">dest</span>, <span class="ruby-identifier">a</span>, <span class="ruby-identifier">id_map</span>)
|
|
431
|
+
<span class="ruby-keyword">end</span>
|
|
432
|
+
<span class="ruby-keyword">end</span></pre>
|
|
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|
+
</div>
|
|
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|
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|
|
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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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|
+
|
|
440
|
+
</div>
|
|
441
|
+
|
|
442
|
+
|
|
443
|
+
<div id="method-i-copy_infons" class="method-detail ">
|
|
444
|
+
|
|
445
|
+
<div class="method-heading">
|
|
446
|
+
<span class="method-name">copy_infons</span><span
|
|
447
|
+
class="method-args">(dest, src, warnings)</span>
|
|
448
|
+
|
|
449
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
450
|
+
|
|
451
|
+
</div>
|
|
452
|
+
|
|
453
|
+
|
|
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|
+
<div class="method-description">
|
|
455
|
+
|
|
456
|
+
|
|
457
|
+
|
|
458
|
+
|
|
459
|
+
|
|
460
|
+
|
|
461
|
+
<div class="method-source-code" id="copy_infons-source">
|
|
462
|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 176</span>
|
|
463
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">copy_infons</span>(<span class="ruby-identifier">dest</span>, <span class="ruby-identifier">src</span>, <span class="ruby-identifier">warnings</span>)
|
|
464
|
+
<span class="ruby-identifier">src</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>
|
|
465
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">dest</span>.<span class="ruby-identifier">infons</span>[<span class="ruby-identifier">k</span>].<span class="ruby-identifier">nil?</span>
|
|
466
|
+
<span class="ruby-identifier">dest</span>.<span class="ruby-identifier">infons</span>[<span class="ruby-identifier">k</span>] = <span class="ruby-identifier">v</span>
|
|
467
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">dest</span>.<span class="ruby-identifier">infons</span>[<span class="ruby-identifier">k</span>] <span class="ruby-operator">!=</span> <span class="ruby-identifier">v</span>
|
|
468
|
+
<span class="ruby-identifier">warnings</span> <span class="ruby-operator"><<</span> <span class="ruby-node">"Failed to copy <#{k}:#{v}>. the key is already exist in infons."</span>
|
|
469
|
+
<span class="ruby-keyword">end</span>
|
|
470
|
+
<span class="ruby-keyword">end</span>
|
|
471
|
+
<span class="ruby-keyword">end</span></pre>
|
|
472
|
+
</div>
|
|
473
|
+
|
|
474
|
+
</div>
|
|
475
|
+
|
|
476
|
+
|
|
477
|
+
|
|
478
|
+
|
|
479
|
+
</div>
|
|
480
|
+
|
|
481
|
+
|
|
482
|
+
<div id="method-i-copy_relation" class="method-detail ">
|
|
483
|
+
|
|
484
|
+
<div class="method-heading">
|
|
485
|
+
<span class="method-name">copy_relation</span><span
|
|
486
|
+
class="method-args">(doc, dest, relation, id_map)</span>
|
|
487
|
+
|
|
488
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
489
|
+
|
|
490
|
+
</div>
|
|
491
|
+
|
|
492
|
+
|
|
493
|
+
<div class="method-description">
|
|
494
|
+
|
|
495
|
+
|
|
496
|
+
|
|
497
|
+
|
|
498
|
+
|
|
499
|
+
|
|
500
|
+
<div class="method-source-code" id="copy_relation-source">
|
|
501
|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 124</span>
|
|
502
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">copy_relation</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">dest</span>, <span class="ruby-identifier">relation</span>, <span class="ruby-identifier">id_map</span>)
|
|
503
|
+
<span class="ruby-identifier">new_r</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-constant">Relation</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">dest</span>)
|
|
504
|
+
<span class="ruby-identifier">new_r</span>.<span class="ruby-identifier">id</span> = <span class="ruby-identifier">choose_id</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">relation</span>.<span class="ruby-identifier">id</span>, <span class="ruby-identifier">id_map</span>)
|
|
505
|
+
<span class="ruby-identifier">relation</span>.<span class="ruby-identifier">nodes</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">n</span><span class="ruby-operator">|</span>
|
|
506
|
+
<span class="ruby-identifier">node</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-constant">Node</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">new_r</span>)
|
|
507
|
+
<span class="ruby-identifier">node</span>.<span class="ruby-identifier">refid</span> = <span class="ruby-identifier">relation</span>.<span class="ruby-identifier">refid</span>
|
|
508
|
+
<span class="ruby-identifier">node</span>.<span class="ruby-identifier">role</span> = <span class="ruby-identifier">relation</span>.<span class="ruby-identifier">role</span>
|
|
509
|
+
<span class="ruby-identifier">new_r</span>.<span class="ruby-identifier">nodes</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">node</span>
|
|
510
|
+
<span class="ruby-keyword">end</span>
|
|
511
|
+
<span class="ruby-identifier">new_r</span>.<span class="ruby-identifier">original</span> = <span class="ruby-identifier">relation</span>
|
|
512
|
+
<span class="ruby-identifier">dest</span>.<span class="ruby-identifier">relations</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">new_r</span>
|
|
513
|
+
<span class="ruby-keyword">end</span></pre>
|
|
514
|
+
</div>
|
|
515
|
+
|
|
516
|
+
</div>
|
|
517
|
+
|
|
518
|
+
|
|
519
|
+
|
|
520
|
+
|
|
521
|
+
</div>
|
|
522
|
+
|
|
523
|
+
|
|
524
|
+
<div id="method-i-copy_relations" class="method-detail ">
|
|
525
|
+
|
|
526
|
+
<div class="method-heading">
|
|
527
|
+
<span class="method-name">copy_relations</span><span
|
|
528
|
+
class="method-args">(doc, dest, src, id_map)</span>
|
|
529
|
+
|
|
530
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
531
|
+
|
|
532
|
+
</div>
|
|
533
|
+
|
|
534
|
+
|
|
535
|
+
<div class="method-description">
|
|
536
|
+
|
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537
|
+
|
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538
|
+
|
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539
|
+
|
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540
|
+
|
|
541
|
+
|
|
542
|
+
<div class="method-source-code" id="copy_relations-source">
|
|
543
|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 113</span>
|
|
544
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">copy_relations</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">dest</span>, <span class="ruby-identifier">src</span>, <span class="ruby-identifier">id_map</span>)
|
|
545
|
+
<span class="ruby-identifier">src</span>.<span class="ruby-identifier">relations</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">r</span><span class="ruby-operator">|</span>
|
|
546
|
+
<span class="ruby-identifier">copy_relation</span>(<span class="ruby-identifier">doc</span>, <span class="ruby-identifier">dest</span>, <span class="ruby-identifier">r</span>, <span class="ruby-identifier">id_map</span>)
|
|
547
|
+
<span class="ruby-keyword">end</span>
|
|
548
|
+
<span class="ruby-keyword">end</span></pre>
|
|
549
|
+
</div>
|
|
550
|
+
|
|
551
|
+
</div>
|
|
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|
+
|
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553
|
+
|
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554
|
+
|
|
555
|
+
|
|
556
|
+
</div>
|
|
557
|
+
|
|
558
|
+
|
|
559
|
+
<div id="method-i-copy_text" class="method-detail ">
|
|
560
|
+
|
|
561
|
+
<div class="method-heading">
|
|
562
|
+
<span class="method-name">copy_text</span><span
|
|
563
|
+
class="method-args">(dest, src)</span>
|
|
564
|
+
|
|
565
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
566
|
+
|
|
567
|
+
</div>
|
|
568
|
+
|
|
569
|
+
|
|
570
|
+
<div class="method-description">
|
|
571
|
+
|
|
572
|
+
|
|
573
|
+
|
|
574
|
+
|
|
575
|
+
|
|
576
|
+
|
|
577
|
+
<div class="method-source-code" id="copy_text-source">
|
|
578
|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 166</span>
|
|
579
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">copy_text</span>(<span class="ruby-identifier">dest</span>, <span class="ruby-identifier">src</span>)
|
|
580
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">blank?</span>(<span class="ruby-identifier">dest</span>.<span class="ruby-identifier">text</span>) <span class="ruby-operator">&&</span> <span class="ruby-operator">!</span><span class="ruby-identifier">blank?</span>(<span class="ruby-identifier">src</span>.<span class="ruby-identifier">text</span>)
|
|
581
|
+
<span class="ruby-identifier">dest</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">src</span>.<span class="ruby-identifier">text</span>
|
|
582
|
+
<span class="ruby-keyword">end</span>
|
|
583
|
+
<span class="ruby-keyword">end</span></pre>
|
|
584
|
+
</div>
|
|
585
|
+
|
|
586
|
+
</div>
|
|
587
|
+
|
|
588
|
+
|
|
589
|
+
|
|
590
|
+
|
|
591
|
+
</div>
|
|
592
|
+
|
|
593
|
+
|
|
594
|
+
<div id="method-i-find_all_locations" class="method-detail ">
|
|
595
|
+
|
|
596
|
+
<div class="method-heading">
|
|
597
|
+
<span class="method-name">find_all_locations</span><span
|
|
598
|
+
class="method-args">(obj, text)</span>
|
|
599
|
+
|
|
600
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
601
|
+
|
|
602
|
+
</div>
|
|
603
|
+
|
|
604
|
+
|
|
605
|
+
<div class="method-description">
|
|
606
|
+
|
|
607
|
+
|
|
608
|
+
|
|
609
|
+
|
|
610
|
+
|
|
611
|
+
|
|
612
|
+
<div class="method-source-code" id="find_all_locations-source">
|
|
613
|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 186</span>
|
|
614
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">find_all_locations</span>(<span class="ruby-identifier">obj</span>, <span class="ruby-identifier">text</span>)
|
|
615
|
+
<span class="ruby-identifier">positions</span> = []
|
|
616
|
+
<span class="ruby-identifier">pos</span> = <span class="ruby-identifier">obj</span>.<span class="ruby-identifier">text</span>.<span class="ruby-identifier">index</span>(<span class="ruby-identifier">text</span>)
|
|
617
|
+
<span class="ruby-keyword">until</span> <span class="ruby-identifier">pos</span>.<span class="ruby-identifier">nil?</span>
|
|
618
|
+
<span class="ruby-identifier">positions</span> <span class="ruby-operator"><<</span> (<span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">obj</span>.<span class="ruby-identifier">offset</span>)
|
|
619
|
+
<span class="ruby-identifier">pos</span> = <span class="ruby-identifier">obj</span>.<span class="ruby-identifier">text</span>.<span class="ruby-identifier">index</span>(<span class="ruby-identifier">text</span>, <span class="ruby-identifier">pos</span> <span class="ruby-operator">+</span> <span class="ruby-value">1</span>)
|
|
620
|
+
<span class="ruby-keyword">end</span>
|
|
621
|
+
<span class="ruby-keyword">return</span> <span class="ruby-identifier">positions</span>
|
|
622
|
+
<span class="ruby-keyword">end</span></pre>
|
|
623
|
+
</div>
|
|
624
|
+
|
|
625
|
+
</div>
|
|
626
|
+
|
|
627
|
+
|
|
628
|
+
|
|
629
|
+
|
|
630
|
+
</div>
|
|
631
|
+
|
|
632
|
+
|
|
633
|
+
<div id="method-i-merge" class="method-detail ">
|
|
634
|
+
|
|
635
|
+
<div class="method-heading">
|
|
636
|
+
<span class="method-name">merge</span><span
|
|
637
|
+
class="method-args">(dest_collection, src_collection)</span>
|
|
638
|
+
|
|
639
|
+
<span class="method-click-advice">click to toggle source</span>
|
|
640
|
+
|
|
641
|
+
</div>
|
|
642
|
+
|
|
643
|
+
|
|
644
|
+
<div class="method-description">
|
|
645
|
+
|
|
646
|
+
|
|
647
|
+
|
|
648
|
+
|
|
649
|
+
|
|
650
|
+
|
|
651
|
+
<div class="method-source-code" id="merge-source">
|
|
652
|
+
<pre><span class="ruby-comment"># File lib/simple_bioc/bioc_merger.rb, line 8</span>
|
|
653
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">merge</span>(<span class="ruby-identifier">dest_collection</span>, <span class="ruby-identifier">src_collection</span>)
|
|
654
|
+
<span class="ruby-identifier">errors</span> = []
|
|
655
|
+
<span class="ruby-identifier">warnings</span> = []
|
|
656
|
+
<span class="ruby-identifier">id_map</span> = {}
|
|
657
|
+
|
|
658
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">documents</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-value">1</span> <span class="ruby-operator">||</span> <span class="ruby-identifier">src_collection</span>.<span class="ruby-identifier">documents</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-value">1</span>
|
|
659
|
+
<span class="ruby-identifier">warnings</span> <span class="ruby-operator"><<</span> <span class="ruby-string">'Only the first documents will be merged'</span>
|
|
660
|
+
<span class="ruby-keyword">end</span>
|
|
661
|
+
|
|
662
|
+
<span class="ruby-identifier">doc_d</span> = <span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">documents</span>[<span class="ruby-value">0</span>]
|
|
663
|
+
<span class="ruby-identifier">doc_s</span> = <span class="ruby-identifier">src_collection</span>.<span class="ruby-identifier">documents</span>[<span class="ruby-value">0</span>]
|
|
664
|
+
|
|
665
|
+
<span class="ruby-identifier">copy_infons</span>(<span class="ruby-identifier">dest_collection</span>, <span class="ruby-identifier">src_collection</span>, <span class="ruby-identifier">warnings</span>)
|
|
666
|
+
<span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">source</span> = <span class="ruby-identifier">src_collection</span>.<span class="ruby-identifier">source</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">source</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">source</span>.<span class="ruby-identifier">empty?</span>
|
|
667
|
+
<span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">date</span> = <span class="ruby-identifier">src_collection</span>.<span class="ruby-identifier">date</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">date</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">date</span>.<span class="ruby-identifier">empty?</span>
|
|
668
|
+
<span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">key</span> = <span class="ruby-identifier">src_collection</span>.<span class="ruby-identifier">key</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">key</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-operator">||</span> <span class="ruby-identifier">dest_collection</span>.<span class="ruby-identifier">key</span>.<span class="ruby-identifier">empty?</span>
|
|
669
|
+
|
|
670
|
+
<span class="ruby-identifier">copy_infons</span>(<span class="ruby-identifier">doc_d</span>, <span class="ruby-identifier">doc_s</span>, <span class="ruby-identifier">warnings</span>)
|
|
671
|
+
<span class="ruby-identifier">copy_relations</span>(<span class="ruby-identifier">doc_d</span>, <span class="ruby-identifier">doc_d</span>, <span class="ruby-identifier">doc_s</span>, <span class="ruby-identifier">id_map</span>)
|
|
672
|
+
|
|
673
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">doc_d</span>.<span class="ruby-identifier">passages</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">doc_s</span>.<span class="ruby-identifier">passages</span>.<span class="ruby-identifier">size</span>
|
|
674
|
+
<span class="ruby-identifier">warnings</span> <span class="ruby-operator"><<</span> <span class="ruby-string">'Passages will not be merged because the numbers of passages in documents are different'</span>
|
|
675
|
+
<span class="ruby-keyword">end</span>
|
|
676
|
+
|
|
677
|
+
<span class="ruby-identifier">doc_d</span>.<span class="ruby-identifier">passages</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p_d</span>, <span class="ruby-identifier">index</span><span class="ruby-operator">|</span>
|
|
678
|
+
<span class="ruby-identifier">p_s</span> = <span class="ruby-identifier">doc_s</span>.<span class="ruby-identifier">passages</span>[<span class="ruby-identifier">index</span>]
|
|
679
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">blank?</span>(<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">text</span>) <span class="ruby-operator">&&</span> <span class="ruby-identifier">blank?</span>(<span class="ruby-identifier">p_s</span>.<span class="ruby-identifier">text</span>) <span class="ruby-operator">&&</span> <span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">p_s</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">size</span>
|
|
680
|
+
<span class="ruby-identifier">warnings</span> <span class="ruby-operator"><<</span> <span class="ruby-string">'The number of sentences in pages should be the same'</span>
|
|
681
|
+
<span class="ruby-keyword">end</span>
|
|
682
|
+
<span class="ruby-keyword">end</span>
|
|
683
|
+
|
|
684
|
+
<span class="ruby-identifier">doc_d</span>.<span class="ruby-identifier">passages</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">p_d</span>, <span class="ruby-identifier">index</span><span class="ruby-operator">|</span>
|
|
685
|
+
<span class="ruby-identifier">p_s</span> = <span class="ruby-identifier">doc_s</span>.<span class="ruby-identifier">passages</span>[<span class="ruby-identifier">index</span>]
|
|
686
|
+
<span class="ruby-identifier">copy_relations</span>(<span class="ruby-identifier">doc_d</span>, <span class="ruby-identifier">p_d</span>, <span class="ruby-identifier">p_s</span>, <span class="ruby-identifier">id_map</span>)
|
|
687
|
+
|
|
688
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">p_s</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">size</span>
|
|
689
|
+
<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">each_with_index</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s_d</span>, <span class="ruby-identifier">index</span><span class="ruby-operator">|</span>
|
|
690
|
+
<span class="ruby-identifier">s_s</span> = <span class="ruby-identifier">p_s</span>.<span class="ruby-identifier">sentences</span>[<span class="ruby-identifier">index</span>]
|
|
691
|
+
<span class="ruby-identifier">copy_infons</span>(<span class="ruby-identifier">s_d</span>, <span class="ruby-identifier">s_s</span>, <span class="ruby-identifier">warnings</span>)
|
|
692
|
+
<span class="ruby-identifier">copy_text</span>(<span class="ruby-identifier">s_d</span>, <span class="ruby-identifier">s_s</span>)
|
|
693
|
+
<span class="ruby-identifier">copy_relations</span>(<span class="ruby-identifier">doc_d</span>, <span class="ruby-identifier">s_d</span>, <span class="ruby-identifier">s_s</span>, <span class="ruby-identifier">id_map</span>)
|
|
694
|
+
<span class="ruby-identifier">copy_annotations</span>(<span class="ruby-identifier">doc_d</span>, <span class="ruby-identifier">s_d</span>, <span class="ruby-identifier">s_s</span>, <span class="ruby-identifier">id_map</span>)
|
|
695
|
+
<span class="ruby-identifier">adjust_annotation_offset</span>(<span class="ruby-identifier">s_d</span>)
|
|
696
|
+
<span class="ruby-keyword">end</span>
|
|
697
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
|
|
698
|
+
<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">p_s</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span> <span class="ruby-identifier">s</span>.<span class="ruby-identifier">text</span>}.<span class="ruby-identifier">join</span>(<span class="ruby-string">" "</span>) <span class="ruby-keyword">if</span> <span class="ruby-identifier">blank?</span>(<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">text</span>)
|
|
699
|
+
<span class="ruby-identifier">p_s</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
|
|
700
|
+
<span class="ruby-identifier">copy_relations</span>(<span class="ruby-identifier">doc_d</span>, <span class="ruby-identifier">p_d</span>, <span class="ruby-identifier">s</span>, <span class="ruby-identifier">id_map</span>)
|
|
701
|
+
<span class="ruby-identifier">copy_annotations</span>(<span class="ruby-identifier">doc_d</span>, <span class="ruby-identifier">p_d</span>, <span class="ruby-identifier">s</span>, <span class="ruby-identifier">id_map</span>)
|
|
702
|
+
<span class="ruby-keyword">end</span>
|
|
703
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">p_s</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">==</span> <span class="ruby-value">0</span>
|
|
704
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">size</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
705
|
+
<span class="ruby-comment"># dest has sentences, but src has only passages. </span>
|
|
706
|
+
<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">map</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span> <span class="ruby-identifier">s</span>.<span class="ruby-identifier">text</span>}.<span class="ruby-identifier">join</span>(<span class="ruby-string">" "</span>) <span class="ruby-keyword">if</span> <span class="ruby-identifier">blank?</span>(<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">text</span>)
|
|
707
|
+
<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">s</span><span class="ruby-operator">|</span>
|
|
708
|
+
<span class="ruby-identifier">s</span>.<span class="ruby-identifier">annotations</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">a</span><span class="ruby-operator">|</span>
|
|
709
|
+
<span class="ruby-identifier">a</span>.<span class="ruby-identifier">sentence</span> = <span class="ruby-keyword">nil</span>
|
|
710
|
+
<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">annotations</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">a</span>
|
|
711
|
+
<span class="ruby-keyword">end</span>
|
|
712
|
+
<span class="ruby-identifier">s</span>.<span class="ruby-identifier">relations</span>.<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">r</span><span class="ruby-operator">|</span>
|
|
713
|
+
<span class="ruby-identifier">r</span>.<span class="ruby-identifier">sentence</span> = <span class="ruby-keyword">nil</span>
|
|
714
|
+
<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">relations</span> <span class="ruby-operator"><<</span> <span class="ruby-identifier">r</span>
|
|
715
|
+
<span class="ruby-keyword">end</span>
|
|
716
|
+
<span class="ruby-keyword">end</span>
|
|
717
|
+
<span class="ruby-identifier">p_d</span>.<span class="ruby-identifier">sentences</span>.<span class="ruby-identifier">clear</span>
|
|
718
|
+
<span class="ruby-keyword">else</span>
|
|
719
|
+
<span class="ruby-identifier">copy_text</span>(<span class="ruby-identifier">p_d</span>, <span class="ruby-identifier">p_s</span>)
|
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720
|
+
<span class="ruby-keyword">end</span>
|
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721
|
+
<span class="ruby-keyword">end</span>
|
|
722
|
+
<span class="ruby-identifier">copy_annotations</span>(<span class="ruby-identifier">doc_d</span>, <span class="ruby-identifier">p_d</span>, <span class="ruby-identifier">p_s</span>, <span class="ruby-identifier">id_map</span>)
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723
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+
<span class="ruby-identifier">adjust_annotation_offset</span>(<span class="ruby-identifier">p_d</span>)
|
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724
|
+
<span class="ruby-keyword">end</span>
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|
725
|
+
<span class="ruby-identifier">puts</span> <span class="ruby-identifier">warnings</span>
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726
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+
<span class="ruby-keyword">end</span></pre>
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727
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+
</div>
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728
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+
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729
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</div>
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730
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731
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732
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733
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734
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+
</div>
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735
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736
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737
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+
</section>
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738
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+
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739
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+
</section>
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740
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+
</main>
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741
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742
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+
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743
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+
<footer id="validator-badges" role="contentinfo">
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744
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+
<p><a href="http://validator.w3.org/check/referer">Validate</a>
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745
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+
<p>Generated by <a href="http://docs.seattlerb.org/rdoc/">RDoc</a> 4.2.0.
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746
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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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747
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</footer>
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748
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