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/BioCReader.html CHANGED
@@ -2,70 +2,66 @@
2
2
 
3
3
  <html>
4
4
  <head>
5
- <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
5
+ <meta charset="UTF-8">
6
6
 
7
7
  <title>module BioCReader - RDoc Documentation</title>
8
8
 
9
- <link type="text/css" media="screen" href="./rdoc.css" rel="stylesheet">
10
-
11
9
  <script type="text/javascript">
12
10
  var rdoc_rel_prefix = "./";
13
11
  </script>
14
12
 
15
- <script type="text/javascript" charset="utf-8" src="./js/jquery.js"></script>
16
- <script type="text/javascript" charset="utf-8" src="./js/navigation.js"></script>
17
- <script type="text/javascript" charset="utf-8" src="./js/search_index.js"></script>
18
- <script type="text/javascript" charset="utf-8" src="./js/search.js"></script>
19
- <script type="text/javascript" charset="utf-8" src="./js/searcher.js"></script>
20
- <script type="text/javascript" charset="utf-8" src="./js/darkfish.js"></script>
13
+ <script src="./js/jquery.js"></script>
14
+ <script src="./js/darkfish.js"></script>
15
+
16
+ <link href="./css/fonts.css" rel="stylesheet">
17
+ <link href="./css/rdoc.css" rel="stylesheet">
18
+
21
19
 
22
20
 
23
- <body id="top" class="module">
24
- <nav id="metadata">
25
- <nav id="home-section" class="section">
26
- <h3 class="section-header">
27
- <a href="./index.html">Home</a>
21
+ <body id="top" role="document" class="module">
22
+ <nav role="navigation">
23
+ <div id="project-navigation">
24
+ <div id="home-section" role="region" title="Quick navigation" class="nav-section">
25
+ <h2>
26
+ <a href="./index.html" rel="home">Home</a>
27
+ </h2>
28
+
29
+ <div id="table-of-contents-navigation">
30
+ <a href="./table_of_contents.html#pages">Pages</a>
28
31
  <a href="./table_of_contents.html#classes">Classes</a>
29
32
  <a href="./table_of_contents.html#methods">Methods</a>
30
- </h3>
31
- </nav>
32
-
33
+ </div>
34
+ </div>
33
35
 
34
- <nav id="search-section" class="section project-section" class="initially-hidden">
36
+ <div id="search-section" role="search" class="project-section initially-hidden">
35
37
  <form action="#" method="get" accept-charset="utf-8">
36
- <h3 class="section-header">
37
- <input type="text" name="search" placeholder="Search" id="search-field"
38
+ <div id="search-field-wrapper">
39
+ <input id="search-field" role="combobox" aria-label="Search"
40
+ aria-autocomplete="list" aria-controls="search-results"
41
+ type="text" name="search" placeholder="Search" spellcheck="false"
38
42
  title="Type to search, Up and Down to navigate, Enter to load">
39
- </h3>
40
- </form>
43
+ </div>
41
44
 
42
- <ul id="search-results" class="initially-hidden"></ul>
43
- </nav>
45
+ <ul id="search-results" aria-label="Search Results"
46
+ aria-busy="false" aria-expanded="false"
47
+ aria-atomic="false" class="initially-hidden"></ul>
48
+ </form>
49
+ </div>
44
50
 
51
+ </div>
45
52
 
46
53
 
47
54
 
48
- <div id="file-metadata">
49
- <nav id="file-list-section" class="section">
50
- <h3 class="section-header">Defined In</h3>
51
- <ul>
52
- <li>lib/simple_bioc/bioc_reader.rb
53
- </ul>
54
- </nav>
55
-
56
-
57
- </div>
58
-
59
55
  <div id="class-metadata">
60
56
 
61
57
 
62
58
 
63
59
 
64
60
  <!-- Method Quickref -->
65
- <nav id="method-list-section" class="section">
66
- <h3 class="section-header">Methods</h3>
61
+ <div id="method-list-section" class="nav-section">
62
+ <h3>Methods</h3>
67
63
 
68
- <ul class="link-list">
64
+ <ul class="link-list" role="directory">
69
65
 
70
66
  <li ><a href="#method-i-read">#read</a>
71
67
 
@@ -75,6 +71,8 @@
75
71
 
76
72
  <li ><a href="#method-i-read_document">#read_document</a>
77
73
 
74
+ <li ><a href="#method-i-read_from_file_or_string">#read_from_file_or_string</a>
75
+
78
76
  <li ><a href="#method-i-read_infon">#read_infon</a>
79
77
 
80
78
  <li ><a href="#method-i-read_int">#read_int</a>
@@ -94,62 +92,19 @@
94
92
  <li ><a href="#method-i-read_text">#read_text</a>
95
93
 
96
94
  </ul>
97
- </nav>
95
+ </div>
98
96
 
99
97
  </div>
100
-
101
- <div id="project-metadata">
102
- <nav id="fileindex-section" class="section project-section">
103
- <h3 class="section-header">Pages</h3>
104
-
105
- <ul>
106
-
107
- <li class="file"><a href="./README_md.html">README</a>
108
-
109
- </ul>
110
98
  </nav>
111
99
 
112
- <nav id="classindex-section" class="section project-section">
113
- <h3 class="section-header">Class and Module Index</h3>
114
-
115
- <ul class="link-list">
116
-
117
- <li><a href="./BioCReader.html">BioCReader</a>
118
-
119
- <li><a href="./BioCWriter.html">BioCWriter</a>
120
-
121
- <li><a href="./SimpleBioC.html">SimpleBioC</a>
122
-
123
- <li><a href="./SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
124
-
125
- <li><a href="./SimpleBioC/Collection.html">SimpleBioC::Collection</a>
126
-
127
- <li><a href="./SimpleBioC/Document.html">SimpleBioC::Document</a>
128
-
129
- <li><a href="./SimpleBioC/Location.html">SimpleBioC::Location</a>
130
-
131
- <li><a href="./SimpleBioC/Node.html">SimpleBioC::Node</a>
132
-
133
- <li><a href="./SimpleBioC/NodeBase.html">SimpleBioC::NodeBase</a>
134
-
135
- <li><a href="./SimpleBioC/Passage.html">SimpleBioC::Passage</a>
136
-
137
- <li><a href="./SimpleBioC/Relation.html">SimpleBioC::Relation</a>
138
-
139
- <li><a href="./SimpleBioC/Sentence.html">SimpleBioC::Sentence</a>
140
-
141
- </ul>
142
- </nav>
100
+ <main role="main" aria-labelledby="module-BioCReader">
101
+ <h1 id="module-BioCReader" class="module">
102
+ module BioCReader
103
+ </h1>
143
104
 
144
- </div>
145
- </nav>
146
-
147
- <div id="documentation">
148
- <h1 class="module">module BioCReader</h1>
149
-
150
- <div id="description" class="description">
105
+ <section class="description">
151
106
 
152
- </div><!-- description -->
107
+ </section>
153
108
 
154
109
 
155
110
 
@@ -163,10 +118,11 @@
163
118
 
164
119
 
165
120
 
166
- <!-- Methods -->
167
121
 
168
- <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
169
- <h3 class="section-header">Public Instance Methods</h3>
122
+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section">
123
+ <header>
124
+ <h3>Public Instance Methods</h3>
125
+ </header>
170
126
 
171
127
 
172
128
  <div id="method-i-read" class="method-detail ">
@@ -192,27 +148,19 @@
192
148
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read</span>(<span class="ruby-identifier">path</span>, <span class="ruby-identifier">options</span>)
193
149
  <span class="ruby-identifier">collection</span> = <span class="ruby-keyword">nil</span>
194
150
  <span class="ruby-constant">File</span>.<span class="ruby-identifier">open</span>(<span class="ruby-identifier">path</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">file</span><span class="ruby-operator">|</span>
195
- <span class="ruby-identifier">xml_doc</span> = <span class="ruby-constant">Nokogiri</span><span class="ruby-operator">::</span><span class="ruby-constant">XML</span>(<span class="ruby-identifier">file</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">config</span><span class="ruby-operator">|</span>
196
- <span class="ruby-identifier">config</span>.<span class="ruby-identifier">noent</span>.<span class="ruby-identifier">strict</span>.<span class="ruby-identifier">noblanks</span>
197
- <span class="ruby-keyword">end</span>
198
- <span class="ruby-identifier">xml</span> = <span class="ruby-identifier">xml_doc</span>.<span class="ruby-identifier">at_xpath</span>(<span class="ruby-string">&quot;//collection&quot;</span>)
199
- <span class="ruby-keyword">if</span> <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">nil?</span>
200
- <span class="ruby-identifier">fail</span> <span class="ruby-string">&#39;Wrong format&#39;</span>
201
- <span class="ruby-keyword">end</span>
202
- <span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-constant">Collection</span>.<span class="ruby-identifier">new</span>
203
- <span class="ruby-identifier">read_collection</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>, <span class="ruby-identifier">options</span>)
151
+ <span class="ruby-identifier">collection</span> = <span class="ruby-identifier">read_from_file_or_string</span>(<span class="ruby-identifier">file</span>, <span class="ruby-identifier">options</span>)
204
152
  <span class="ruby-keyword">end</span>
205
153
 
206
154
  <span class="ruby-identifier">collection</span>
207
155
  <span class="ruby-keyword">end</span></pre>
208
- </div><!-- read-source -->
156
+ </div>
209
157
 
210
158
  </div>
211
159
 
212
160
 
213
161
 
214
162
 
215
- </div><!-- read-method -->
163
+ </div>
216
164
 
217
165
 
218
166
  <div id="method-i-read_annotation" class="method-detail ">
@@ -234,7 +182,7 @@
234
182
 
235
183
 
236
184
  <div class="method-source-code" id="read_annotation-source">
237
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 86</span>
185
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 94</span>
238
186
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_annotation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">annotation</span>, <span class="ruby-identifier">options</span> = {})
239
187
  <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">id</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">&quot;id&quot;</span>]
240
188
  <span class="ruby-identifier">annotation</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">&quot;text&quot;</span>)
@@ -242,14 +190,14 @@
242
190
  <span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">annotation</span>, <span class="ruby-string">&quot;location&quot;</span>)
243
191
  <span class="ruby-keyword">true</span>
244
192
  <span class="ruby-keyword">end</span></pre>
245
- </div><!-- read_annotation-source -->
193
+ </div>
246
194
 
247
195
  </div>
248
196
 
249
197
 
250
198
 
251
199
 
252
- </div><!-- read_annotation-method -->
200
+ </div>
253
201
 
254
202
 
255
203
  <div id="method-i-read_collection" class="method-detail ">
@@ -271,7 +219,7 @@
271
219
 
272
220
 
273
221
  <div class="method-source-code" id="read_collection-source">
274
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 47</span>
222
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 55</span>
275
223
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_collection</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>, <span class="ruby-identifier">options</span> = {})
276
224
  <span class="ruby-identifier">collection</span>.<span class="ruby-identifier">source</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">&quot;source&quot;</span>)
277
225
  <span class="ruby-identifier">collection</span>.<span class="ruby-identifier">date</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">&quot;date&quot;</span>)
@@ -279,14 +227,14 @@
279
227
  <span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>)
280
228
  <span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>, <span class="ruby-string">&quot;document&quot;</span>, <span class="ruby-identifier">options</span>)
281
229
  <span class="ruby-keyword">end</span></pre>
282
- </div><!-- read_collection-source -->
230
+ </div>
283
231
 
284
232
  </div>
285
233
 
286
234
 
287
235
 
288
236
 
289
- </div><!-- read_collection-method -->
237
+ </div>
290
238
 
291
239
 
292
240
  <div id="method-i-read_document" class="method-detail ">
@@ -308,7 +256,7 @@
308
256
 
309
257
 
310
258
  <div class="method-source-code" id="read_document-source">
311
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 55</span>
259
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 63</span>
312
260
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_document</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">document</span>, <span class="ruby-identifier">options</span> = {})
313
261
  <span class="ruby-identifier">document</span>.<span class="ruby-identifier">id</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">&quot;id&quot;</span>)
314
262
  <span class="ruby-keyword">if</span> <span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">kind_of?</span>(<span class="ruby-constant">Array</span>) <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-operator">!</span><span class="ruby-identifier">options</span>[<span class="ruby-value">:documents</span>].<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">document</span>.<span class="ruby-identifier">id</span>)
@@ -320,14 +268,59 @@
320
268
  <span class="ruby-identifier">document</span>.<span class="ruby-identifier">adjust_ref</span>
321
269
  <span class="ruby-keyword">true</span>
322
270
  <span class="ruby-keyword">end</span></pre>
323
- </div><!-- read_document-source -->
271
+ </div>
324
272
 
325
273
  </div>
326
274
 
327
275
 
328
276
 
329
277
 
330
- </div><!-- read_document-method -->
278
+ </div>
279
+
280
+
281
+ <div id="method-i-read_from_file_or_string" class="method-detail ">
282
+
283
+ <div class="method-heading">
284
+ <span class="method-name">read_from_file_or_string</span><span
285
+ class="method-args">(file_or_string, options)</span>
286
+
287
+ <span class="method-click-advice">click to toggle source</span>
288
+
289
+ </div>
290
+
291
+
292
+ <div class="method-description">
293
+
294
+
295
+
296
+
297
+
298
+
299
+ <div class="method-source-code" id="read_from_file_or_string-source">
300
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 16</span>
301
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_from_file_or_string</span>(<span class="ruby-identifier">file_or_string</span>, <span class="ruby-identifier">options</span>)
302
+ <span class="ruby-identifier">collection</span> = <span class="ruby-keyword">nil</span>
303
+
304
+ <span class="ruby-identifier">xml_doc</span> = <span class="ruby-constant">Nokogiri</span><span class="ruby-operator">::</span><span class="ruby-constant">XML</span>(<span class="ruby-identifier">file_or_string</span>) <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">config</span><span class="ruby-operator">|</span>
305
+ <span class="ruby-identifier">config</span>.<span class="ruby-identifier">noent</span>.<span class="ruby-identifier">strict</span>.<span class="ruby-identifier">noblanks</span>
306
+ <span class="ruby-keyword">end</span>
307
+ <span class="ruby-identifier">xml</span> = <span class="ruby-identifier">xml_doc</span>.<span class="ruby-identifier">at_xpath</span>(<span class="ruby-string">&quot;//collection&quot;</span>)
308
+ <span class="ruby-keyword">if</span> <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">nil?</span>
309
+ <span class="ruby-identifier">fail</span> <span class="ruby-string">&#39;Wrong format&#39;</span>
310
+ <span class="ruby-keyword">end</span>
311
+ <span class="ruby-identifier">collection</span> = <span class="ruby-constant">SimpleBioC</span><span class="ruby-operator">::</span><span class="ruby-constant">Collection</span>.<span class="ruby-identifier">new</span>
312
+ <span class="ruby-identifier">read_collection</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">collection</span>, <span class="ruby-identifier">options</span>)
313
+
314
+ <span class="ruby-identifier">collection</span>
315
+ <span class="ruby-keyword">end</span></pre>
316
+ </div>
317
+
318
+ </div>
319
+
320
+
321
+
322
+
323
+ </div>
331
324
 
332
325
 
333
326
  <div id="method-i-read_infon" class="method-detail ">
@@ -349,18 +342,18 @@
349
342
 
350
343
 
351
344
  <div class="method-source-code" id="read_infon-source">
352
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 34</span>
345
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 42</span>
353
346
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">obj</span>)
354
347
  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">xpath</span>(<span class="ruby-string">&quot;infon&quot;</span>).<span class="ruby-identifier">each</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">i</span><span class="ruby-operator">|</span> <span class="ruby-identifier">obj</span>.<span class="ruby-identifier">infons</span>[<span class="ruby-identifier">i</span>[<span class="ruby-string">&quot;key&quot;</span>]] = <span class="ruby-identifier">i</span>.<span class="ruby-identifier">content</span>}
355
348
  <span class="ruby-keyword">end</span></pre>
356
- </div><!-- read_infon-source -->
349
+ </div>
357
350
 
358
351
  </div>
359
352
 
360
353
 
361
354
 
362
355
 
363
- </div><!-- read_infon-method -->
356
+ </div>
364
357
 
365
358
 
366
359
  <div id="method-i-read_int" class="method-detail ">
@@ -382,19 +375,19 @@
382
375
 
383
376
 
384
377
  <div class="method-source-code" id="read_int-source">
385
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 29</span>
378
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 37</span>
386
379
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_int</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">name</span>)
387
380
  <span class="ruby-identifier">val</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">name</span>)
388
381
  <span class="ruby-identifier">val</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">val</span>.<span class="ruby-identifier">to_i</span>
389
382
  <span class="ruby-keyword">end</span></pre>
390
- </div><!-- read_int-source -->
383
+ </div>
391
384
 
392
385
  </div>
393
386
 
394
387
 
395
388
 
396
389
 
397
- </div><!-- read_int-method -->
390
+ </div>
398
391
 
399
392
 
400
393
  <div id="method-i-read_location" class="method-detail ">
@@ -416,20 +409,20 @@
416
409
 
417
410
 
418
411
  <div class="method-source-code" id="read_location-source">
419
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 101</span>
412
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 109</span>
420
413
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_location</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">location</span>, <span class="ruby-identifier">options</span> = {})
421
414
  <span class="ruby-identifier">location</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">&quot;offset&quot;</span>]
422
415
  <span class="ruby-identifier">location</span>.<span class="ruby-identifier">length</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">&quot;length&quot;</span>]
423
416
  <span class="ruby-keyword">true</span>
424
417
  <span class="ruby-keyword">end</span></pre>
425
- </div><!-- read_location-source -->
418
+ </div>
426
419
 
427
420
  </div>
428
421
 
429
422
 
430
423
 
431
424
 
432
- </div><!-- read_location-method -->
425
+ </div>
433
426
 
434
427
 
435
428
  <div id="method-i-read_node" class="method-detail ">
@@ -451,20 +444,20 @@
451
444
 
452
445
 
453
446
  <div class="method-source-code" id="read_node-source">
454
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 107</span>
447
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 115</span>
455
448
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_node</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">node</span>, <span class="ruby-identifier">options</span> = {})
456
449
  <span class="ruby-identifier">node</span>.<span class="ruby-identifier">refid</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">&quot;refid&quot;</span>]
457
450
  <span class="ruby-identifier">node</span>.<span class="ruby-identifier">role</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">&quot;role&quot;</span>]
458
451
  <span class="ruby-keyword">true</span>
459
452
  <span class="ruby-keyword">end</span></pre>
460
- </div><!-- read_node-source -->
453
+ </div>
461
454
 
462
455
  </div>
463
456
 
464
457
 
465
458
 
466
459
 
467
- </div><!-- read_node-method -->
460
+ </div>
468
461
 
469
462
 
470
463
  <div id="method-i-read_passage" class="method-detail ">
@@ -486,7 +479,7 @@
486
479
 
487
480
 
488
481
  <div class="method-source-code" id="read_passage-source">
489
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 67</span>
482
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 75</span>
490
483
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_passage</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>, <span class="ruby-identifier">options</span> = {})
491
484
  <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">&quot;text&quot;</span>)
492
485
  <span class="ruby-identifier">passage</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">read_int</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">&quot;offset&quot;</span>)
@@ -496,14 +489,14 @@
496
489
  <span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">passage</span>, <span class="ruby-string">&quot;relation&quot;</span>)
497
490
  <span class="ruby-keyword">true</span>
498
491
  <span class="ruby-keyword">end</span></pre>
499
- </div><!-- read_passage-source -->
492
+ </div>
500
493
 
501
494
  </div>
502
495
 
503
496
 
504
497
 
505
498
 
506
- </div><!-- read_passage-method -->
499
+ </div>
507
500
 
508
501
 
509
502
  <div id="method-i-read_recursive" class="method-detail ">
@@ -525,7 +518,7 @@
525
518
 
526
519
 
527
520
  <div class="method-source-code" id="read_recursive-source">
528
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 38</span>
521
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 46</span>
529
522
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">obj</span>, <span class="ruby-identifier">name</span>, <span class="ruby-identifier">options</span> = {})
530
523
  <span class="ruby-identifier">target_class</span> = <span class="ruby-constant">SimpleBioC</span>.<span class="ruby-identifier">const_get</span>(<span class="ruby-identifier">name</span>.<span class="ruby-identifier">capitalize</span>)
531
524
  <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">xpath</span>(<span class="ruby-identifier">name</span>).<span class="ruby-identifier">each</span> <span class="ruby-keyword">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">node</span><span class="ruby-operator">|</span>
@@ -534,14 +527,14 @@
534
527
  <span class="ruby-identifier">obj</span>.<span class="ruby-identifier">instance_variable_get</span>(<span class="ruby-value">:&quot;@#{name}s&quot;</span>) <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">instance</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">ret</span>
535
528
  <span class="ruby-keyword">end</span>
536
529
  <span class="ruby-keyword">end</span></pre>
537
- </div><!-- read_recursive-source -->
530
+ </div>
538
531
 
539
532
  </div>
540
533
 
541
534
 
542
535
 
543
536
 
544
- </div><!-- read_recursive-method -->
537
+ </div>
545
538
 
546
539
 
547
540
  <div id="method-i-read_relation" class="method-detail ">
@@ -563,21 +556,21 @@
563
556
 
564
557
 
565
558
  <div class="method-source-code" id="read_relation-source">
566
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 94</span>
559
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 102</span>
567
560
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_relation</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">relation</span>, <span class="ruby-identifier">options</span> = {})
568
561
  <span class="ruby-identifier">relation</span>.<span class="ruby-identifier">id</span> = <span class="ruby-identifier">xml</span>[<span class="ruby-string">&quot;id&quot;</span>]
569
562
  <span class="ruby-identifier">read_infon</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">relation</span>)
570
563
  <span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">relation</span>, <span class="ruby-string">&quot;node&quot;</span>)
571
564
  <span class="ruby-keyword">true</span>
572
565
  <span class="ruby-keyword">end</span></pre>
573
- </div><!-- read_relation-source -->
566
+ </div>
574
567
 
575
568
  </div>
576
569
 
577
570
 
578
571
 
579
572
 
580
- </div><!-- read_relation-method -->
573
+ </div>
581
574
 
582
575
 
583
576
  <div id="method-i-read_sentence" class="method-detail ">
@@ -599,7 +592,7 @@
599
592
 
600
593
 
601
594
  <div class="method-source-code" id="read_sentence-source">
602
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 77</span>
595
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 85</span>
603
596
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_sentence</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>, <span class="ruby-identifier">options</span> = {})
604
597
  <span class="ruby-identifier">sentence</span>.<span class="ruby-identifier">text</span> = <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">&quot;text&quot;</span>)
605
598
  <span class="ruby-identifier">sentence</span>.<span class="ruby-identifier">offset</span> = <span class="ruby-identifier">read_int</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-string">&quot;offset&quot;</span>)
@@ -608,14 +601,14 @@
608
601
  <span class="ruby-identifier">read_recursive</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">sentence</span>, <span class="ruby-string">&quot;relation&quot;</span>)
609
602
  <span class="ruby-keyword">true</span>
610
603
  <span class="ruby-keyword">end</span></pre>
611
- </div><!-- read_sentence-source -->
604
+ </div>
612
605
 
613
606
  </div>
614
607
 
615
608
 
616
609
 
617
610
 
618
- </div><!-- read_sentence-method -->
611
+ </div>
619
612
 
620
613
 
621
614
  <div id="method-i-read_text" class="method-detail ">
@@ -637,31 +630,30 @@
637
630
 
638
631
 
639
632
  <div class="method-source-code" id="read_text-source">
640
- <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 24</span>
633
+ <pre><span class="ruby-comment"># File lib/simple_bioc/bioc_reader.rb, line 32</span>
641
634
  <span class="ruby-keyword">def</span> <span class="ruby-identifier">read_text</span>(<span class="ruby-identifier">xml</span>, <span class="ruby-identifier">name</span>)
642
635
  <span class="ruby-identifier">node</span> = <span class="ruby-identifier">xml</span>.<span class="ruby-identifier">at_xpath</span>(<span class="ruby-identifier">name</span>)
643
636
  <span class="ruby-identifier">node</span> <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">node</span>.<span class="ruby-identifier">content</span>
644
637
  <span class="ruby-keyword">end</span></pre>
645
- </div><!-- read_text-source -->
638
+ </div>
646
639
 
647
640
  </div>
648
641
 
649
642
 
650
643
 
651
644
 
652
- </div><!-- read_text-method -->
645
+ </div>
653
646
 
654
647
 
655
- </section><!-- public-instance-method-details -->
648
+ </section>
656
649
 
657
- </section><!-- 5Buntitled-5D -->
658
-
659
- </div><!-- documentation -->
650
+ </section>
651
+ </main>
660
652
 
661
653
 
662
- <footer id="validator-badges">
663
- <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
664
- <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.
665
- <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
654
+ <footer id="validator-badges" role="contentinfo">
655
+ <p><a href="http://validator.w3.org/check/referer">Validate</a>
656
+ <p>Generated by <a href="http://docs.seattlerb.org/rdoc/">RDoc</a> 4.2.0.
657
+ <p>Based on <a href="http://deveiate.org/projects/Darkfish-RDoc/">Darkfish</a> by <a href="http://deveiate.org">Michael Granger</a>.
666
658
  </footer>
667
659