abstractor 1.0.8

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Files changed (346) hide show
  1. checksums.yaml +15 -0
  2. data/MIT-LICENSE +20 -0
  3. data/README.md +14 -0
  4. data/Rakefile +33 -0
  5. data/app/assets/images/abstractor/add.png +0 -0
  6. data/app/assets/images/abstractor/ajax-loader.gif +0 -0
  7. data/app/assets/images/abstractor/bar.gif +0 -0
  8. data/app/assets/images/abstractor/bti_logo.jpg +0 -0
  9. data/app/assets/images/abstractor/bullet_arrow_down.png +0 -0
  10. data/app/assets/images/abstractor/bullet_arrow_up.png +0 -0
  11. data/app/assets/images/abstractor/cog.png +0 -0
  12. data/app/assets/images/abstractor/delete.png +0 -0
  13. data/app/assets/images/abstractor/edit.png +0 -0
  14. data/app/assets/images/abstractor/excel.png +0 -0
  15. data/app/assets/images/abstractor/favicon.ico +0 -0
  16. data/app/assets/images/abstractor/greencheck.gif +0 -0
  17. data/app/assets/images/abstractor/loading.gif +0 -0
  18. data/app/assets/images/abstractor/nu_logo.jpg +0 -0
  19. data/app/assets/images/abstractor/nubic_logo.png +0 -0
  20. data/app/assets/images/abstractor/page.png +0 -0
  21. data/app/assets/images/abstractor/rails.png +0 -0
  22. data/app/assets/images/abstractor/robert_h_lurie.jpg +0 -0
  23. data/app/assets/images/abstractor/show.png +0 -0
  24. data/app/assets/images/abstractor/switch_minus.gif +0 -0
  25. data/app/assets/images/abstractor/switch_plus.gif +0 -0
  26. data/app/assets/javascripts/abstractor/abstractor.js +89 -0
  27. data/app/assets/javascripts/abstractor/application.js +21 -0
  28. data/app/assets/javascripts/abstractor/combobox.js +301 -0
  29. data/app/assets/javascripts/abstractor/jquery/jquery.form.js +1074 -0
  30. data/app/assets/javascripts/abstractor/nested_attributes.js +69 -0
  31. data/app/assets/stylesheets/abstractor/abstractor_abstractions.css +312 -0
  32. data/app/assets/stylesheets/abstractor/application.css +21 -0
  33. data/app/assets/stylesheets/abstractor/jquery.ui.override.css.scss +73 -0
  34. data/app/controllers/abstractor/abstractor_abstraction_groups_controller.rb +5 -0
  35. data/app/controllers/abstractor/abstractor_abstractions_controller.rb +5 -0
  36. data/app/controllers/abstractor/abstractor_suggestions_controller.rb +5 -0
  37. data/app/controllers/abstractor/application_controller.rb +2 -0
  38. data/app/helpers/abstractor/application_helper.rb +4 -0
  39. data/app/models/abstractor/abstractor_abstraction.rb +6 -0
  40. data/app/models/abstractor/abstractor_abstraction_group.rb +6 -0
  41. data/app/models/abstractor/abstractor_abstraction_group_member.rb +6 -0
  42. data/app/models/abstractor/abstractor_abstraction_schema.rb +6 -0
  43. data/app/models/abstractor/abstractor_abstraction_schema_object_value.rb +6 -0
  44. data/app/models/abstractor/abstractor_abstraction_schema_predicate_variant.rb +6 -0
  45. data/app/models/abstractor/abstractor_abstraction_schema_relation.rb +6 -0
  46. data/app/models/abstractor/abstractor_abstraction_source.rb +6 -0
  47. data/app/models/abstractor/abstractor_object_type.rb +6 -0
  48. data/app/models/abstractor/abstractor_object_value.rb +6 -0
  49. data/app/models/abstractor/abstractor_object_value_variant.rb +6 -0
  50. data/app/models/abstractor/abstractor_relation_type.rb +6 -0
  51. data/app/models/abstractor/abstractor_rule_type.rb +6 -0
  52. data/app/models/abstractor/abstractor_subject.rb +6 -0
  53. data/app/models/abstractor/abstractor_subject_group.rb +6 -0
  54. data/app/models/abstractor/abstractor_subject_group_member.rb +6 -0
  55. data/app/models/abstractor/abstractor_subject_relation.rb +6 -0
  56. data/app/models/abstractor/abstractor_suggestion.rb +6 -0
  57. data/app/models/abstractor/abstractor_suggestion_object_value.rb +6 -0
  58. data/app/models/abstractor/abstractor_suggestion_source.rb +6 -0
  59. data/app/models/abstractor/abstractor_suggestion_status.rb +6 -0
  60. data/app/views/abstractor/abstractor_abstraction_groups/_form.html.haml +10 -0
  61. data/app/views/abstractor/abstractor_abstraction_groups/edit.html.haml +1 -0
  62. data/app/views/abstractor/abstractor_abstractions/_fields.html.haml +63 -0
  63. data/app/views/abstractor/abstractor_abstractions/_list.html.haml +45 -0
  64. data/app/views/abstractor/abstractor_abstractions/edit.html.haml +53 -0
  65. data/app/views/abstractor/abstractor_abstractions/show.html.haml +1 -0
  66. data/app/views/abstractor/shared/_error_messages.html.haml +5 -0
  67. data/config/cucumber.yml +8 -0
  68. data/config/routes.rb +7 -0
  69. data/db/migrate/20131227205140_create_abstractor_object_types.rb +10 -0
  70. data/db/migrate/20131227205219_create_abstractor_object_values.rb +10 -0
  71. data/db/migrate/20131227205256_create_abstractor_object_value_variants.rb +11 -0
  72. data/db/migrate/20131227205320_create_abstractor_relation_types.rb +10 -0
  73. data/db/migrate/20131227205354_create_abstractor_rule_types.rb +11 -0
  74. data/db/migrate/20131227205432_create_abstractor_abstraction_schemas.rb +13 -0
  75. data/db/migrate/20131227205456_create_abstractor_abstraction_schema_object_values.rb +10 -0
  76. data/db/migrate/20131227205529_create_abstractor_abstraction_schema_predicate_variants.rb +11 -0
  77. data/db/migrate/20131227205610_create_abstractor_abstraction_schema_relations.rb +11 -0
  78. data/db/migrate/20131227205652_create_abstractor_subjects.rb +12 -0
  79. data/db/migrate/20131227205732_create_abstractor_subject_relations.rb +11 -0
  80. data/db/migrate/20131227205831_create_abstractor_abstraction_sources.rb +11 -0
  81. data/db/migrate/20131227210211_create_abstractor_subject_groups.rb +10 -0
  82. data/db/migrate/20131227210244_create_abstractor_subject_group_members.rb +11 -0
  83. data/db/migrate/20131227210350_create_abstractor_abstraction_groups.rb +12 -0
  84. data/db/migrate/20131227210353_create_abstractor_abstraction_group_members.rb +11 -0
  85. data/db/migrate/20131227211050_create_abstractor_suggestion_statuses.rb +10 -0
  86. data/db/migrate/20131227211303_create_abstractor_abstractions.rb +15 -0
  87. data/db/migrate/20131227213427_create_abstractor_suggestions.rb +14 -0
  88. data/db/migrate/20131228041944_create_abstractor_suggestion_object_values.rb +11 -0
  89. data/db/migrate/20131228041945_create_abstractor_suggestion_sources.rb +16 -0
  90. data/db/seeds.rb +0 -0
  91. data/lib/abstractor.rb +8 -0
  92. data/lib/abstractor/abstractable.rb +190 -0
  93. data/lib/abstractor/core_ext/string.rb +99 -0
  94. data/lib/abstractor/engine.rb +14 -0
  95. data/lib/abstractor/methods/controllers/abstractor_abstraction_groups_controller.rb +37 -0
  96. data/lib/abstractor/methods/controllers/abstractor_abstractions_controller.rb +42 -0
  97. data/lib/abstractor/methods/controllers/abstractor_suggestions_controller.rb +28 -0
  98. data/lib/abstractor/methods/models/abstractor_abstraction.rb +65 -0
  99. data/lib/abstractor/methods/models/abstractor_abstraction_group.rb +37 -0
  100. data/lib/abstractor/methods/models/abstractor_abstraction_group_member.rb +17 -0
  101. data/lib/abstractor/methods/models/abstractor_abstraction_schema.rb +27 -0
  102. data/lib/abstractor/methods/models/abstractor_abstraction_schema_object_value.rb +17 -0
  103. data/lib/abstractor/methods/models/abstractor_abstraction_schema_predicate_variant.rb +16 -0
  104. data/lib/abstractor/methods/models/abstractor_abstraction_schema_relation.rb +18 -0
  105. data/lib/abstractor/methods/models/abstractor_abstraction_source.rb +29 -0
  106. data/lib/abstractor/methods/models/abstractor_object_type.rb +16 -0
  107. data/lib/abstractor/methods/models/abstractor_object_value.rb +24 -0
  108. data/lib/abstractor/methods/models/abstractor_object_value_variant.rb +16 -0
  109. data/lib/abstractor/methods/models/abstractor_relation_type.rb +16 -0
  110. data/lib/abstractor/methods/models/abstractor_rule_type.rb +17 -0
  111. data/lib/abstractor/methods/models/abstractor_subject.rb +258 -0
  112. data/lib/abstractor/methods/models/abstractor_subject_group.rb +19 -0
  113. data/lib/abstractor/methods/models/abstractor_subject_group_member.rb +17 -0
  114. data/lib/abstractor/methods/models/abstractor_subject_relation.rb +18 -0
  115. data/lib/abstractor/methods/models/abstractor_suggestion.rb +88 -0
  116. data/lib/abstractor/methods/models/abstractor_suggestion_object_value.rb +17 -0
  117. data/lib/abstractor/methods/models/abstractor_suggestion_source.rb +17 -0
  118. data/lib/abstractor/methods/models/abstractor_suggestion_status.rb +29 -0
  119. data/lib/abstractor/methods/models/soft_delete.rb +35 -0
  120. data/lib/abstractor/negation_detection.rb +43 -0
  121. data/lib/abstractor/parser.rb +76 -0
  122. data/lib/abstractor/setup.rb +24 -0
  123. data/lib/abstractor/user_interface.rb +40 -0
  124. data/lib/abstractor/utility.rb +8 -0
  125. data/lib/abstractor/version.rb +3 -0
  126. data/lib/generators/abstractor/install/install_generator.rb +118 -0
  127. data/lib/generators/abstractor/install/templates/controllers/abstractor_abstraction_groups_controller.rb +16 -0
  128. data/lib/generators/abstractor/install/templates/controllers/abstractor_abstractions_controller.rb +24 -0
  129. data/lib/generators/abstractor/install/templates/controllers/abstractor_suggestions_controller.rb +12 -0
  130. data/lib/generators/abstractor/install/templates/dictionaries.yml +235 -0
  131. data/lib/generators/abstractor/install/templates/helpers/abstractions_helper.rb +9 -0
  132. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction.rb +9 -0
  133. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_group.rb +9 -0
  134. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_group_member.rb +9 -0
  135. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema.rb +9 -0
  136. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_object_value.rb +9 -0
  137. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_predicate_variant.rb +9 -0
  138. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_relation.rb +9 -0
  139. data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_source.rb +9 -0
  140. data/lib/generators/abstractor/install/templates/models/abstractor_object_type.rb +9 -0
  141. data/lib/generators/abstractor/install/templates/models/abstractor_object_value.rb +9 -0
  142. data/lib/generators/abstractor/install/templates/models/abstractor_object_value_variant.rb +9 -0
  143. data/lib/generators/abstractor/install/templates/models/abstractor_relation_type.rb +9 -0
  144. data/lib/generators/abstractor/install/templates/models/abstractor_rule_type.rb +9 -0
  145. data/lib/generators/abstractor/install/templates/models/abstractor_subject.rb +9 -0
  146. data/lib/generators/abstractor/install/templates/models/abstractor_subject_group.rb +9 -0
  147. data/lib/generators/abstractor/install/templates/models/abstractor_subject_group_member.rb +9 -0
  148. data/lib/generators/abstractor/install/templates/models/abstractor_subject_relation.rb +9 -0
  149. data/lib/generators/abstractor/install/templates/models/abstractor_suggestion.rb +9 -0
  150. data/lib/generators/abstractor/install/templates/models/abstractor_suggestion_object_value.rb +9 -0
  151. data/lib/generators/abstractor/install/templates/models/abstractor_suggestion_source.rb +9 -0
  152. data/lib/generators/abstractor/install/templates/models/abstractor_suggestion_status.rb +9 -0
  153. data/lib/lingscope/build.xml +74 -0
  154. data/lib/lingscope/build/built-jar.properties +4 -0
  155. data/lib/lingscope/build/classes/lingscope/algorithms/AbnerTokenizer.class +0 -0
  156. data/lib/lingscope/build/classes/lingscope/algorithms/AnnotationComparer.class +0 -0
  157. data/lib/lingscope/build/classes/lingscope/algorithms/Annotator.class +0 -0
  158. data/lib/lingscope/build/classes/lingscope/algorithms/BaselineAnnotator.class +0 -0
  159. data/lib/lingscope/build/classes/lingscope/algorithms/BaselineCueAnnotator.class +0 -0
  160. data/lib/lingscope/build/classes/lingscope/algorithms/BaselineScopeAnnotator.class +0 -0
  161. data/lib/lingscope/build/classes/lingscope/algorithms/CrfAnnotator.class +0 -0
  162. data/lib/lingscope/build/classes/lingscope/algorithms/NegexAnnotator.class +0 -0
  163. data/lib/lingscope/build/classes/lingscope/algorithms/NegexCueAnnotator.class +0 -0
  164. data/lib/lingscope/build/classes/lingscope/algorithms/NegexScopeAnnotator.class +0 -0
  165. data/lib/lingscope/build/classes/lingscope/algorithms/PosTagger.class +0 -0
  166. data/lib/lingscope/build/classes/lingscope/algorithms/negex/GenNegEx.class +0 -0
  167. data/lib/lingscope/build/classes/lingscope/algorithms/negex/Sorter.class +0 -0
  168. data/lib/lingscope/build/classes/lingscope/drivers/AnnotatedFilesMerger.class +0 -0
  169. data/lib/lingscope/build/classes/lingscope/drivers/AnnotationComparerDriver.class +0 -0
  170. data/lib/lingscope/build/classes/lingscope/drivers/BaselineDriver.class +0 -0
  171. data/lib/lingscope/build/classes/lingscope/drivers/CrfDriver.class +0 -0
  172. data/lib/lingscope/build/classes/lingscope/drivers/CueAndPosFilesMerger.class +0 -0
  173. data/lib/lingscope/build/classes/lingscope/drivers/ModelTrainer.class +0 -0
  174. data/lib/lingscope/build/classes/lingscope/drivers/NegexDriver.class +0 -0
  175. data/lib/lingscope/build/classes/lingscope/drivers/PosTaggerDriver.class +0 -0
  176. data/lib/lingscope/build/classes/lingscope/drivers/SentencePosTagger.class +0 -0
  177. data/lib/lingscope/build/classes/lingscope/drivers/SentenceTagger.class +0 -0
  178. data/lib/lingscope/build/classes/lingscope/io/AnnotatedSentencesIO.class +0 -0
  179. data/lib/lingscope/build/classes/lingscope/structures/AnnotatedSentence.class +0 -0
  180. data/lib/lingscope/dist/README.TXT +32 -0
  181. data/lib/lingscope/dist/javadoc/allclasses-frame.html +80 -0
  182. data/lib/lingscope/dist/javadoc/allclasses-noframe.html +80 -0
  183. data/lib/lingscope/dist/javadoc/constant-values.html +199 -0
  184. data/lib/lingscope/dist/javadoc/deprecated-list.html +147 -0
  185. data/lib/lingscope/dist/javadoc/help-doc.html +224 -0
  186. data/lib/lingscope/dist/javadoc/index-files/index-1.html +188 -0
  187. data/lib/lingscope/dist/javadoc/index-files/index-10.html +149 -0
  188. data/lib/lingscope/dist/javadoc/index-files/index-11.html +158 -0
  189. data/lib/lingscope/dist/javadoc/index-files/index-12.html +157 -0
  190. data/lib/lingscope/dist/javadoc/index-files/index-13.html +177 -0
  191. data/lib/lingscope/dist/javadoc/index-files/index-14.html +155 -0
  192. data/lib/lingscope/dist/javadoc/index-files/index-15.html +152 -0
  193. data/lib/lingscope/dist/javadoc/index-files/index-16.html +146 -0
  194. data/lib/lingscope/dist/javadoc/index-files/index-2.html +158 -0
  195. data/lib/lingscope/dist/javadoc/index-files/index-3.html +165 -0
  196. data/lib/lingscope/dist/javadoc/index-files/index-4.html +146 -0
  197. data/lib/lingscope/dist/javadoc/index-files/index-5.html +219 -0
  198. data/lib/lingscope/dist/javadoc/index-files/index-6.html +149 -0
  199. data/lib/lingscope/dist/javadoc/index-files/index-7.html +155 -0
  200. data/lib/lingscope/dist/javadoc/index-files/index-8.html +185 -0
  201. data/lib/lingscope/dist/javadoc/index-files/index-9.html +164 -0
  202. data/lib/lingscope/dist/javadoc/index.html +74 -0
  203. data/lib/lingscope/dist/javadoc/lingscope/algorithms/AbnerTokenizer.html +280 -0
  204. data/lib/lingscope/dist/javadoc/lingscope/algorithms/AnnotationComparer.html +526 -0
  205. data/lib/lingscope/dist/javadoc/lingscope/algorithms/Annotator.html +401 -0
  206. data/lib/lingscope/dist/javadoc/lingscope/algorithms/BaselineAnnotator.html +375 -0
  207. data/lib/lingscope/dist/javadoc/lingscope/algorithms/BaselineCueAnnotator.html +309 -0
  208. data/lib/lingscope/dist/javadoc/lingscope/algorithms/BaselineScopeAnnotator.html +340 -0
  209. data/lib/lingscope/dist/javadoc/lingscope/algorithms/CrfAnnotator.html +340 -0
  210. data/lib/lingscope/dist/javadoc/lingscope/algorithms/NegexAnnotator.html +364 -0
  211. data/lib/lingscope/dist/javadoc/lingscope/algorithms/NegexCueAnnotator.html +309 -0
  212. data/lib/lingscope/dist/javadoc/lingscope/algorithms/NegexScopeAnnotator.html +309 -0
  213. data/lib/lingscope/dist/javadoc/lingscope/algorithms/PosTagger.html +268 -0
  214. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/AbnerTokenizer.html +145 -0
  215. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/AnnotationComparer.html +145 -0
  216. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/Annotator.html +299 -0
  217. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/BaselineAnnotator.html +189 -0
  218. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/BaselineCueAnnotator.html +145 -0
  219. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/BaselineScopeAnnotator.html +145 -0
  220. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/CrfAnnotator.html +145 -0
  221. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/NegexAnnotator.html +189 -0
  222. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/NegexCueAnnotator.html +145 -0
  223. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/NegexScopeAnnotator.html +145 -0
  224. data/lib/lingscope/dist/javadoc/lingscope/algorithms/class-use/PosTagger.html +145 -0
  225. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/GenNegEx.html +369 -0
  226. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/Sorter.html +253 -0
  227. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/class-use/GenNegEx.html +181 -0
  228. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/class-use/Sorter.html +145 -0
  229. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-frame.html +35 -0
  230. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-summary.html +165 -0
  231. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-tree.html +154 -0
  232. data/lib/lingscope/dist/javadoc/lingscope/algorithms/negex/package-use.html +174 -0
  233. data/lib/lingscope/dist/javadoc/lingscope/algorithms/package-frame.html +53 -0
  234. data/lib/lingscope/dist/javadoc/lingscope/algorithms/package-summary.html +198 -0
  235. data/lib/lingscope/dist/javadoc/lingscope/algorithms/package-tree.html +160 -0
  236. data/lib/lingscope/dist/javadoc/lingscope/algorithms/package-use.html +202 -0
  237. data/lib/lingscope/dist/javadoc/lingscope/drivers/AnnotatedFilesMerger.html +284 -0
  238. data/lib/lingscope/dist/javadoc/lingscope/drivers/AnnotationComparerDriver.html +258 -0
  239. data/lib/lingscope/dist/javadoc/lingscope/drivers/BaselineDriver.html +260 -0
  240. data/lib/lingscope/dist/javadoc/lingscope/drivers/CrfDriver.html +262 -0
  241. data/lib/lingscope/dist/javadoc/lingscope/drivers/CueAndPosFilesMerger.html +310 -0
  242. data/lib/lingscope/dist/javadoc/lingscope/drivers/ModelTrainer.html +281 -0
  243. data/lib/lingscope/dist/javadoc/lingscope/drivers/NegexDriver.html +262 -0
  244. data/lib/lingscope/dist/javadoc/lingscope/drivers/PosTaggerDriver.html +289 -0
  245. data/lib/lingscope/dist/javadoc/lingscope/drivers/SentencePosTagger.html +313 -0
  246. data/lib/lingscope/dist/javadoc/lingscope/drivers/SentenceTagger.html +512 -0
  247. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/AnnotatedFilesMerger.html +145 -0
  248. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/AnnotationComparerDriver.html +145 -0
  249. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/BaselineDriver.html +145 -0
  250. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/CrfDriver.html +145 -0
  251. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/CueAndPosFilesMerger.html +145 -0
  252. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/ModelTrainer.html +145 -0
  253. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/NegexDriver.html +145 -0
  254. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/PosTaggerDriver.html +145 -0
  255. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/SentencePosTagger.html +145 -0
  256. data/lib/lingscope/dist/javadoc/lingscope/drivers/class-use/SentenceTagger.html +145 -0
  257. data/lib/lingscope/dist/javadoc/lingscope/drivers/package-frame.html +51 -0
  258. data/lib/lingscope/dist/javadoc/lingscope/drivers/package-summary.html +195 -0
  259. data/lib/lingscope/dist/javadoc/lingscope/drivers/package-tree.html +154 -0
  260. data/lib/lingscope/dist/javadoc/lingscope/drivers/package-use.html +145 -0
  261. data/lib/lingscope/dist/javadoc/lingscope/io/AnnotatedSentencesIO.html +285 -0
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  308. data/lib/lingscope/negation_models/crf_scope_words_regex_all_clinical.model +0 -0
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  310. data/lib/lingscope/src/lingscope/algorithms/AnnotationComparer.java +207 -0
  311. data/lib/lingscope/src/lingscope/algorithms/Annotator.java +51 -0
  312. data/lib/lingscope/src/lingscope/algorithms/BaselineAnnotator.java +80 -0
  313. data/lib/lingscope/src/lingscope/algorithms/BaselineCueAnnotator.java +84 -0
  314. data/lib/lingscope/src/lingscope/algorithms/BaselineScopeAnnotator.java +101 -0
  315. data/lib/lingscope/src/lingscope/algorithms/CrfAnnotator.java +45 -0
  316. data/lib/lingscope/src/lingscope/algorithms/NegexAnnotator.java +52 -0
  317. data/lib/lingscope/src/lingscope/algorithms/NegexCueAnnotator.java +26 -0
  318. data/lib/lingscope/src/lingscope/algorithms/NegexScopeAnnotator.java +26 -0
  319. data/lib/lingscope/src/lingscope/algorithms/PosTagger.java +54 -0
  320. data/lib/lingscope/src/lingscope/algorithms/negex/GenNegEx.java +530 -0
  321. data/lib/lingscope/src/lingscope/algorithms/negex/Sorter.java +36 -0
  322. data/lib/lingscope/src/lingscope/drivers/AnnotatedFilesMerger.java +61 -0
  323. data/lib/lingscope/src/lingscope/drivers/AnnotationComparerDriver.java +22 -0
  324. data/lib/lingscope/src/lingscope/drivers/BaselineDriver.java +45 -0
  325. data/lib/lingscope/src/lingscope/drivers/CrfDriver.java +31 -0
  326. data/lib/lingscope/src/lingscope/drivers/CueAndPosFilesMerger.java +86 -0
  327. data/lib/lingscope/src/lingscope/drivers/ModelTrainer.java +39 -0
  328. data/lib/lingscope/src/lingscope/drivers/NegexDriver.java +32 -0
  329. data/lib/lingscope/src/lingscope/drivers/PosTaggerDriver.java +62 -0
  330. data/lib/lingscope/src/lingscope/drivers/SentencePosTagger.java +89 -0
  331. data/lib/lingscope/src/lingscope/drivers/SentenceTagger.java +158 -0
  332. data/lib/lingscope/src/lingscope/io/AnnotatedSentencesIO.java +53 -0
  333. data/lib/lingscope/src/lingscope/structures/AnnotatedSentence.java +105 -0
  334. data/lib/setup/data/ICD-O-3_CSV-metadata/Morphenglish.csv +1 -0
  335. data/lib/setup/data/ICD-O-3_CSV-metadata/Morphenglish.txt +2273 -0
  336. data/lib/setup/data/ICD-O-3_CSV-metadata/Topoenglish.csv +1 -0
  337. data/lib/setup/data/ICD-O-3_CSV-metadata/Topoenglish.txt +1342 -0
  338. data/lib/setup/data/ICD-O-3_CSV-metadata/icd-o3 readme.txt +21 -0
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  340. data/lib/setup/data/diagnosis_categorizations.csv +1 -0
  341. data/lib/setup/data/high_level_primary_cns_diagnosis_categorizations.yml +597 -0
  342. data/lib/setup/data/icdo3_sites_with_laterality.txt +11 -0
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  344. data/lib/tasks/abstractor_tasks.rake +22 -0
  345. data/lib/tasks/cucumber.rake +65 -0
  346. metadata +754 -0
data/lib/lingscope/dist/javadoc/lingscope/drivers/package-tree.html ADDED
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+ <LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/AnnotatedFilesMerger.html" title="class in lingscope.drivers"><B>AnnotatedFilesMerger</B></A><LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/AnnotationComparerDriver.html" title="class in lingscope.drivers"><B>AnnotationComparerDriver</B></A><LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/BaselineDriver.html" title="class in lingscope.drivers"><B>BaselineDriver</B></A><LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/CrfDriver.html" title="class in lingscope.drivers"><B>CrfDriver</B></A><LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/CueAndPosFilesMerger.html" title="class in lingscope.drivers"><B>CueAndPosFilesMerger</B></A><LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/ModelTrainer.html" title="class in lingscope.drivers"><B>ModelTrainer</B></A><LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/NegexDriver.html" title="class in lingscope.drivers"><B>NegexDriver</B></A><LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/PosTaggerDriver.html" title="class in lingscope.drivers"><B>PosTaggerDriver</B></A><LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/SentencePosTagger.html" title="class in lingscope.drivers"><B>SentencePosTagger</B></A><LI TYPE="circle">lingscope.drivers.<A HREF="../../lingscope/drivers/SentenceTagger.html" title="class in lingscope.drivers"><B>SentenceTagger</B></A></UL>
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+ <!-- ======== START OF CLASS DATA ======== -->
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+ <H2>
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+ <FONT SIZE="-1">
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+ lingscope.io</FONT>
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+ <BR>
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+ Class AnnotatedSentencesIO</H2>
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+ <PRE>
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+ java.lang.Object
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+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>lingscope.io.AnnotatedSentencesIO</B>
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+ </PRE>
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+ <HR>
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+ <DL>
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+ <DT><PRE>public class <B>AnnotatedSentencesIO</B><DT>extends java.lang.Object</DL>
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+ </PRE>
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+
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+ <P>
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+ Reads and writes annotated sentences
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+ <P>
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+
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+ <P>
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+ <HR>
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+
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+ <P>
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+
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+ <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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+
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+ <A NAME="constructor_summary"><!-- --></A>
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+ <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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+ <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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+ <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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+ <B>Constructor Summary</B></FONT></TH>
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+ </TR>
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+ <TR BGCOLOR="white" CLASS="TableRowColor">
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+ <TD><CODE><B><A HREF="../../lingscope/io/AnnotatedSentencesIO.html#AnnotatedSentencesIO()">AnnotatedSentencesIO</A></B>()</CODE>
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+
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+ <BR>
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+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
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+ </TR>
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+ </TABLE>
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+ &nbsp;
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+ <!-- ========== METHOD SUMMARY =========== -->
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+
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+ <A NAME="method_summary"><!-- --></A>
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+ <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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+ <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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+ <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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+ <B>Method Summary</B></FONT></TH>
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+ </TR>
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+ <TR BGCOLOR="white" CLASS="TableRowColor">
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+ <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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+ <CODE>static&nbsp;java.util.List&lt;<A HREF="../../lingscope/structures/AnnotatedSentence.html" title="class in lingscope.structures">AnnotatedSentence</A>&gt;</CODE></FONT></TD>
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+ <TD><CODE><B><A HREF="../../lingscope/io/AnnotatedSentencesIO.html#read(java.lang.String)">read</A></B>(java.lang.String&nbsp;fileToRead)</CODE>
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+
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+ <BR>
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+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads and returns the list of <A HREF="../../lingscope/structures/AnnotatedSentence.html" title="class in lingscope.structures"><CODE>AnnotatedSentence</CODE></A> from the given
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+ file</TD>
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+ </TR>
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+ <TR BGCOLOR="white" CLASS="TableRowColor">
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+ <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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+ <CODE>static&nbsp;void</CODE></FONT></TD>
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+ <TD><CODE><B><A HREF="../../lingscope/io/AnnotatedSentencesIO.html#write(java.lang.String, java.util.List)">write</A></B>(java.lang.String&nbsp;fileToWrite,
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+ java.util.List&lt;<A HREF="../../lingscope/structures/AnnotatedSentence.html" title="class in lingscope.structures">AnnotatedSentence</A>&gt;&nbsp;annotatedSentences)</CODE>
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+
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+ <BR>
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+ &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Writes the given list of annotated sentences to the given fileToWrite</TD>
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+ </TR>
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+ </TABLE>
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+ &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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+ <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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+ <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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+ <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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+ </TR>
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+ <TR BGCOLOR="white" CLASS="TableRowColor">
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+ <TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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+ </TR>
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+ </TABLE>
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+ &nbsp;
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+ <P>
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+
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+ <!-- ========= CONSTRUCTOR DETAIL ======== -->
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+
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+ <A NAME="constructor_detail"><!-- --></A>
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+ <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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+ <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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+ <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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+ <B>Constructor Detail</B></FONT></TH>
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+ </TR>
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+ </TABLE>
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+
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+ <A NAME="AnnotatedSentencesIO()"><!-- --></A><H3>
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+ AnnotatedSentencesIO</H3>
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+ <PRE>
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+ public <B>AnnotatedSentencesIO</B>()</PRE>
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+ <DL>
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+ </DL>
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+
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+ <!-- ============ METHOD DETAIL ========== -->
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+
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+ <A NAME="method_detail"><!-- --></A>
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+ <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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+ <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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+ <B>Method Detail</B></FONT></TH>
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+ </TR>
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+ </TABLE>
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+
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+ <A NAME="read(java.lang.String)"><!-- --></A><H3>
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+ read</H3>
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+ <PRE>
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+ public static java.util.List&lt;<A HREF="../../lingscope/structures/AnnotatedSentence.html" title="class in lingscope.structures">AnnotatedSentence</A>&gt; <B>read</B>(java.lang.String&nbsp;fileToRead)</PRE>
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+ <DL>
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+ <DD>Reads and returns the list of <A HREF="../../lingscope/structures/AnnotatedSentence.html" title="class in lingscope.structures"><CODE>AnnotatedSentence</CODE></A> from the given
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+ file
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+ <P>
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+ <DD><DL>
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+ <DT><B>Parameters:</B><DD><CODE>fileToRead</CODE> -
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+ <DT><B>Returns:</B><DD></DL>
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+ </DD>
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+ </DL>
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+ <HR>
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+
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+ <A NAME="write(java.lang.String, java.util.List)"><!-- --></A><H3>
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+ write</H3>
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+ <PRE>
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+ public static void <B>write</B>(java.lang.String&nbsp;fileToWrite,
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+ java.util.List&lt;<A HREF="../../lingscope/structures/AnnotatedSentence.html" title="class in lingscope.structures">AnnotatedSentence</A>&gt;&nbsp;annotatedSentences)</PRE>
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+ <DL>
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+ <DD>Writes the given list of annotated sentences to the given fileToWrite
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+ <P>
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+ <DD><DL>
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+ <DT><B>Parameters:</B><DD><CODE>fileToWrite</CODE> - <DD><CODE>annotatedSentences</CODE> - </DL>
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+ </DD>
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