simple_bioc 0.0.1 → 0.0.2

Sign up to get free protection for your applications and to get access to all the features.
Files changed (67) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +73 -3
  3. data/Rakefile +5 -0
  4. data/html/BioCReader.html +657 -0
  5. data/html/BioCWriter.html +556 -0
  6. data/html/README_md.html +231 -0
  7. data/html/SimpleBioC.html +255 -0
  8. data/html/SimpleBioC/Annotation.html +279 -0
  9. data/html/SimpleBioC/Collection.html +316 -0
  10. data/html/SimpleBioC/Document.html +426 -0
  11. data/html/SimpleBioC/Location.html +288 -0
  12. data/html/SimpleBioC/Node.html +334 -0
  13. data/html/SimpleBioC/NodeBase.html +281 -0
  14. data/html/SimpleBioC/Passage.html +418 -0
  15. data/html/SimpleBioC/Relation.html +301 -0
  16. data/html/SimpleBioC/Sentence.html +399 -0
  17. data/html/created.rid +15 -0
  18. data/html/images/add.png +0 -0
  19. data/html/images/arrow_up.png +0 -0
  20. data/html/images/brick.png +0 -0
  21. data/html/images/brick_link.png +0 -0
  22. data/html/images/bug.png +0 -0
  23. data/html/images/bullet_black.png +0 -0
  24. data/html/images/bullet_toggle_minus.png +0 -0
  25. data/html/images/bullet_toggle_plus.png +0 -0
  26. data/html/images/date.png +0 -0
  27. data/html/images/delete.png +0 -0
  28. data/html/images/find.png +0 -0
  29. data/html/images/loadingAnimation.gif +0 -0
  30. data/html/images/macFFBgHack.png +0 -0
  31. data/html/images/package.png +0 -0
  32. data/html/images/page_green.png +0 -0
  33. data/html/images/page_white_text.png +0 -0
  34. data/html/images/page_white_width.png +0 -0
  35. data/html/images/plugin.png +0 -0
  36. data/html/images/ruby.png +0 -0
  37. data/html/images/tag_blue.png +0 -0
  38. data/html/images/tag_green.png +0 -0
  39. data/html/images/transparent.png +0 -0
  40. data/html/images/wrench.png +0 -0
  41. data/html/images/wrench_orange.png +0 -0
  42. data/html/images/zoom.png +0 -0
  43. data/html/index.html +212 -0
  44. data/html/js/darkfish.js +155 -0
  45. data/html/js/jquery.js +18 -0
  46. data/html/js/navigation.js +142 -0
  47. data/html/js/search.js +94 -0
  48. data/html/js/search_index.js +1 -0
  49. data/html/js/searcher.js +228 -0
  50. data/html/rdoc.css +595 -0
  51. data/html/table_of_contents.html +199 -0
  52. data/lib/simple_bioc.rb +4 -0
  53. data/lib/simple_bioc/annotation.rb +10 -6
  54. data/lib/simple_bioc/bioc_reader.rb +2 -2
  55. data/lib/simple_bioc/collection.rb +13 -11
  56. data/lib/simple_bioc/document.rb +31 -22
  57. data/lib/simple_bioc/location.rb +13 -7
  58. data/lib/simple_bioc/node.rb +14 -8
  59. data/lib/simple_bioc/node_base.rb +13 -10
  60. data/lib/simple_bioc/passage.rb +26 -23
  61. data/lib/simple_bioc/relation.rb +13 -8
  62. data/lib/simple_bioc/sentence.rb +21 -15
  63. data/lib/simple_bioc/version.rb +2 -2
  64. data/samples/print_annotation.rb +18 -0
  65. data/samples/sample1.rb +31 -0
  66. data/simple_bioc.gemspec +1 -1
  67. metadata +52 -2
@@ -0,0 +1,399 @@
1
+ <!DOCTYPE html>
2
+
3
+ <html>
4
+ <head>
5
+ <meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
6
+
7
+ <title>class SimpleBioC::Sentence - RDoc Documentation</title>
8
+
9
+ <link type="text/css" media="screen" href="../rdoc.css" rel="stylesheet">
10
+
11
+ <script type="text/javascript">
12
+ var rdoc_rel_prefix = "../";
13
+ </script>
14
+
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>
21
+
22
+
23
+ <body id="top" class="class">
24
+ <nav id="metadata">
25
+ <nav id="home-section" class="section">
26
+ <h3 class="section-header">
27
+ <a href="../index.html">Home</a>
28
+ <a href="../table_of_contents.html#classes">Classes</a>
29
+ <a href="../table_of_contents.html#methods">Methods</a>
30
+ </h3>
31
+ </nav>
32
+
33
+
34
+ <nav id="search-section" class="section project-section" class="initially-hidden">
35
+ <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
+ title="Type to search, Up and Down to navigate, Enter to load">
39
+ </h3>
40
+ </form>
41
+
42
+ <ul id="search-results" class="initially-hidden"></ul>
43
+ </nav>
44
+
45
+
46
+
47
+
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/sentence.rb
53
+ </ul>
54
+ </nav>
55
+
56
+
57
+ </div>
58
+
59
+ <div id="class-metadata">
60
+
61
+ <nav id="parent-class-section" class="section">
62
+ <h3 class="section-header">Parent</h3>
63
+
64
+ <p class="link">Object
65
+
66
+ </nav>
67
+
68
+
69
+
70
+ <!-- Method Quickref -->
71
+ <nav id="method-list-section" class="section">
72
+ <h3 class="section-header">Methods</h3>
73
+
74
+ <ul class="link-list">
75
+
76
+ <li ><a href="#method-c-new">::new</a>
77
+
78
+ <li ><a href="#method-i-each_relation">#each_relation</a>
79
+
80
+ <li ><a href="#method-i-find_node">#find_node</a>
81
+
82
+ <li ><a href="#method-i-to_c">#to_c</a>
83
+
84
+ </ul>
85
+ </nav>
86
+
87
+ </div>
88
+
89
+ <div id="project-metadata">
90
+ <nav id="fileindex-section" class="section project-section">
91
+ <h3 class="section-header">Pages</h3>
92
+
93
+ <ul>
94
+
95
+ <li class="file"><a href="../README_md.html">README</a>
96
+
97
+ </ul>
98
+ </nav>
99
+
100
+ <nav id="classindex-section" class="section project-section">
101
+ <h3 class="section-header">Class and Module Index</h3>
102
+
103
+ <ul class="link-list">
104
+
105
+ <li><a href="../BioCReader.html">BioCReader</a>
106
+
107
+ <li><a href="../BioCWriter.html">BioCWriter</a>
108
+
109
+ <li><a href="../SimpleBioC.html">SimpleBioC</a>
110
+
111
+ <li><a href="../SimpleBioC/Annotation.html">SimpleBioC::Annotation</a>
112
+
113
+ <li><a href="../SimpleBioC/Collection.html">SimpleBioC::Collection</a>
114
+
115
+ <li><a href="../SimpleBioC/Document.html">SimpleBioC::Document</a>
116
+
117
+ <li><a href="../SimpleBioC/Location.html">SimpleBioC::Location</a>
118
+
119
+ <li><a href="../SimpleBioC/Node.html">SimpleBioC::Node</a>
120
+
121
+ <li><a href="../SimpleBioC/NodeBase.html">SimpleBioC::NodeBase</a>
122
+
123
+ <li><a href="../SimpleBioC/Passage.html">SimpleBioC::Passage</a>
124
+
125
+ <li><a href="../SimpleBioC/Relation.html">SimpleBioC::Relation</a>
126
+
127
+ <li><a href="../SimpleBioC/Sentence.html">SimpleBioC::Sentence</a>
128
+
129
+ </ul>
130
+ </nav>
131
+
132
+ </div>
133
+ </nav>
134
+
135
+ <div id="documentation">
136
+ <h1 class="class">class SimpleBioC::Sentence</h1>
137
+
138
+ <div id="description" class="description">
139
+
140
+ </div><!-- description -->
141
+
142
+
143
+
144
+
145
+ <section id="5Buntitled-5D" class="documentation-section">
146
+
147
+
148
+
149
+
150
+
151
+
152
+
153
+ <!-- Attributes -->
154
+ <section id="attribute-method-details" class="method-section section">
155
+ <h3 class="section-header">Attributes</h3>
156
+
157
+
158
+ <div id="attribute-i-annotations" class="method-detail">
159
+ <div class="method-heading attribute-method-heading">
160
+ <span class="method-name">annotations</span><span
161
+ class="attribute-access-type">[RW]</span>
162
+ </div>
163
+
164
+ <div class="method-description">
165
+
166
+
167
+
168
+ </div>
169
+ </div>
170
+
171
+ <div id="attribute-i-infons" class="method-detail">
172
+ <div class="method-heading attribute-method-heading">
173
+ <span class="method-name">infons</span><span
174
+ class="attribute-access-type">[RW]</span>
175
+ </div>
176
+
177
+ <div class="method-description">
178
+
179
+
180
+
181
+ </div>
182
+ </div>
183
+
184
+ <div id="attribute-i-offset" class="method-detail">
185
+ <div class="method-heading attribute-method-heading">
186
+ <span class="method-name">offset</span><span
187
+ class="attribute-access-type">[RW]</span>
188
+ </div>
189
+
190
+ <div class="method-description">
191
+
192
+
193
+
194
+ </div>
195
+ </div>
196
+
197
+ <div id="attribute-i-passage" class="method-detail">
198
+ <div class="method-heading attribute-method-heading">
199
+ <span class="method-name">passage</span><span
200
+ class="attribute-access-type">[R]</span>
201
+ </div>
202
+
203
+ <div class="method-description">
204
+
205
+
206
+
207
+ </div>
208
+ </div>
209
+
210
+ <div id="attribute-i-relations" class="method-detail">
211
+ <div class="method-heading attribute-method-heading">
212
+ <span class="method-name">relations</span><span
213
+ class="attribute-access-type">[RW]</span>
214
+ </div>
215
+
216
+ <div class="method-description">
217
+
218
+
219
+
220
+ </div>
221
+ </div>
222
+
223
+ <div id="attribute-i-text" class="method-detail">
224
+ <div class="method-heading attribute-method-heading">
225
+ <span class="method-name">text</span><span
226
+ class="attribute-access-type">[RW]</span>
227
+ </div>
228
+
229
+ <div class="method-description">
230
+
231
+
232
+
233
+ </div>
234
+ </div>
235
+
236
+ </section><!-- attribute-method-details -->
237
+
238
+
239
+ <!-- Methods -->
240
+
241
+ <section id="public-class-5Buntitled-5D-method-details" class="method-section section">
242
+ <h3 class="section-header">Public Class Methods</h3>
243
+
244
+
245
+ <div id="method-c-new" class="method-detail ">
246
+
247
+ <div class="method-heading">
248
+ <span class="method-name">new</span><span
249
+ class="method-args">(parent)</span>
250
+
251
+ <span class="method-click-advice">click to toggle source</span>
252
+
253
+ </div>
254
+
255
+
256
+ <div class="method-description">
257
+
258
+
259
+
260
+
261
+
262
+
263
+ <div class="method-source-code" id="new-source">
264
+ <pre><span class="ruby-comment"># File lib/simple_bioc/sentence.rb, line 6</span>
265
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">parent</span>)
266
+ <span class="ruby-ivar">@infons</span> = {}
267
+ <span class="ruby-ivar">@annotations</span> = []
268
+ <span class="ruby-ivar">@relations</span> = []
269
+ <span class="ruby-ivar">@passage</span> = <span class="ruby-identifier">parent</span>
270
+ <span class="ruby-keyword">end</span></pre>
271
+ </div><!-- new-source -->
272
+
273
+ </div>
274
+
275
+
276
+
277
+
278
+ </div><!-- new-method -->
279
+
280
+
281
+ </section><!-- public-class-method-details -->
282
+
283
+ <section id="public-instance-5Buntitled-5D-method-details" class="method-section section">
284
+ <h3 class="section-header">Public Instance Methods</h3>
285
+
286
+
287
+ <div id="method-i-each_relation" class="method-detail ">
288
+
289
+ <div class="method-heading">
290
+ <span class="method-name">each_relation</span><span
291
+ class="method-args">() { |r| ... }</span>
292
+
293
+ <span class="method-click-advice">click to toggle source</span>
294
+
295
+ </div>
296
+
297
+
298
+ <div class="method-description">
299
+
300
+
301
+
302
+
303
+
304
+
305
+ <div class="method-source-code" id="each_relation-source">
306
+ <pre><span class="ruby-comment"># File lib/simple_bioc/sentence.rb, line 18</span>
307
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">each_relation</span>
308
+ <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-keyword">yield</span> <span class="ruby-identifier">r</span>}
309
+ <span class="ruby-keyword">end</span></pre>
310
+ </div><!-- each_relation-source -->
311
+
312
+ </div>
313
+
314
+
315
+
316
+
317
+ </div><!-- each_relation-method -->
318
+
319
+
320
+ <div id="method-i-find_node" class="method-detail ">
321
+
322
+ <div class="method-heading">
323
+ <span class="method-name">find_node</span><span
324
+ class="method-args">(id)</span>
325
+
326
+ <span class="method-click-advice">click to toggle source</span>
327
+
328
+ </div>
329
+
330
+
331
+ <div class="method-description">
332
+
333
+
334
+
335
+
336
+
337
+
338
+ <div class="method-source-code" id="find_node-source">
339
+ <pre><span class="ruby-comment"># File lib/simple_bioc/sentence.rb, line 13</span>
340
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">find_node</span>(<span class="ruby-identifier">id</span>)
341
+ (<span class="ruby-identifier">relations</span><span class="ruby-operator">+</span><span class="ruby-identifier">annotations</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-keyword">return</span> <span class="ruby-identifier">n</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">n</span>.<span class="ruby-identifier">id</span> <span class="ruby-operator">==</span> <span class="ruby-identifier">id</span>}
342
+ <span class="ruby-keyword">nil</span>
343
+ <span class="ruby-keyword">end</span></pre>
344
+ </div><!-- find_node-source -->
345
+
346
+ </div>
347
+
348
+
349
+
350
+
351
+ </div><!-- find_node-method -->
352
+
353
+
354
+ <div id="method-i-to_c" class="method-detail ">
355
+
356
+ <div class="method-heading">
357
+ <span class="method-name">to_c</span><span
358
+ class="method-args">()</span>
359
+
360
+ <span class="method-click-advice">click to toggle source</span>
361
+
362
+ </div>
363
+
364
+
365
+ <div class="method-description">
366
+
367
+
368
+
369
+
370
+
371
+
372
+ <div class="method-source-code" id="to_c-source">
373
+ <pre><span class="ruby-comment"># File lib/simple_bioc/sentence.rb, line 22</span>
374
+ <span class="ruby-keyword">def</span> <span class="ruby-identifier">to_c</span>
375
+ <span class="ruby-node">&quot;Sentence @#{offset}: #{text}&quot;</span>
376
+ <span class="ruby-keyword">end</span></pre>
377
+ </div><!-- to_c-source -->
378
+
379
+ </div>
380
+
381
+
382
+
383
+
384
+ </div><!-- to_c-method -->
385
+
386
+
387
+ </section><!-- public-instance-method-details -->
388
+
389
+ </section><!-- 5Buntitled-5D -->
390
+
391
+ </div><!-- documentation -->
392
+
393
+
394
+ <footer id="validator-badges">
395
+ <p><a href="http://validator.w3.org/check/referer">[Validate]</a>
396
+ <p>Generated by <a href="https://github.com/rdoc/rdoc">RDoc</a> 4.0.0.
397
+ <p>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish Rdoc Generator</a> 3.
398
+ </footer>
399
+
data/html/created.rid ADDED
@@ -0,0 +1,15 @@
1
+ Fri, 06 Dec 2013 22:05:40 -0800
2
+ README.md Fri, 06 Dec 2013 21:17:11 -0800
3
+ lib/simple_bioc.rb Fri, 06 Dec 2013 20:53:53 -0800
4
+ lib/simple_bioc/annotation.rb Fri, 06 Dec 2013 20:52:11 -0800
5
+ lib/simple_bioc/bioc_reader.rb Fri, 06 Dec 2013 20:52:11 -0800
6
+ lib/simple_bioc/bioc_writer.rb Wed, 04 Dec 2013 02:22:25 -0800
7
+ lib/simple_bioc/collection.rb Fri, 06 Dec 2013 20:52:11 -0800
8
+ lib/simple_bioc/document.rb Fri, 06 Dec 2013 21:18:25 -0800
9
+ lib/simple_bioc/location.rb Fri, 06 Dec 2013 20:52:11 -0800
10
+ lib/simple_bioc/node.rb Fri, 06 Dec 2013 20:52:11 -0800
11
+ lib/simple_bioc/node_base.rb Fri, 06 Dec 2013 22:05:33 -0800
12
+ lib/simple_bioc/passage.rb Fri, 06 Dec 2013 20:52:11 -0800
13
+ lib/simple_bioc/relation.rb Fri, 06 Dec 2013 20:52:11 -0800
14
+ lib/simple_bioc/sentence.rb Fri, 06 Dec 2013 20:52:11 -0800
15
+ lib/simple_bioc/version.rb Fri, 06 Dec 2013 20:52:11 -0800
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file
Binary file