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
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  163. data/lib/lingscope/build/classes/lingscope/algorithms/NegexCueAnnotator.class +0 -0
  164. data/lib/lingscope/build/classes/lingscope/algorithms/NegexScopeAnnotator.class +0 -0
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  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
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  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
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  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
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  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
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  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
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  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
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  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
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  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
  262. data/lib/lingscope/dist/javadoc/lingscope/io/class-use/AnnotatedSentencesIO.html +145 -0
  263. data/lib/lingscope/dist/javadoc/lingscope/io/package-frame.html +33 -0
  264. data/lib/lingscope/dist/javadoc/lingscope/io/package-summary.html +158 -0
  265. data/lib/lingscope/dist/javadoc/lingscope/io/package-tree.html +154 -0
  266. data/lib/lingscope/dist/javadoc/lingscope/io/package-use.html +145 -0
  267. data/lib/lingscope/dist/javadoc/lingscope/structures/AnnotatedSentence.html +425 -0
  268. data/lib/lingscope/dist/javadoc/lingscope/structures/class-use/AnnotatedSentence.html +423 -0
  269. data/lib/lingscope/dist/javadoc/lingscope/structures/package-frame.html +33 -0
  270. data/lib/lingscope/dist/javadoc/lingscope/structures/package-summary.html +158 -0
  271. data/lib/lingscope/dist/javadoc/lingscope/structures/package-tree.html +154 -0
  272. data/lib/lingscope/dist/javadoc/lingscope/structures/package-use.html +209 -0
  273. data/lib/lingscope/dist/javadoc/overview-frame.html +51 -0
  274. data/lib/lingscope/dist/javadoc/overview-summary.html +168 -0
  275. data/lib/lingscope/dist/javadoc/overview-tree.html +159 -0
  276. data/lib/lingscope/dist/javadoc/package-list +5 -0
  277. data/lib/lingscope/dist/javadoc/resources/inherit.gif +0 -0
  278. data/lib/lingscope/dist/javadoc/stylesheet.css +29 -0
  279. data/lib/lingscope/dist/lib/abner.jar +0 -0
  280. data/lib/lingscope/dist/lib/commons-lang-2.4.jar +0 -0
  281. data/lib/lingscope/dist/lib/java_utils.jar +0 -0
  282. data/lib/lingscope/dist/lib/sptoolkit.jar +0 -0
  283. data/lib/lingscope/dist/lib/stanford-postagger.jar +0 -0
  284. data/lib/lingscope/dist/lingscope.jar +0 -0
  285. data/lib/lingscope/lingscope.zip +0 -0
  286. data/lib/lingscope/manifest.mf +3 -0
  287. data/lib/lingscope/nbproject/build-impl.xml +1338 -0
  288. data/lib/lingscope/nbproject/genfiles.properties +8 -0
  289. data/lib/lingscope/nbproject/private/config.properties +0 -0
  290. data/lib/lingscope/nbproject/private/private.properties +10 -0
  291. data/lib/lingscope/nbproject/private/private.xml +5 -0
  292. data/lib/lingscope/nbproject/project.properties +85 -0
  293. data/lib/lingscope/nbproject/project.xml +15 -0
  294. data/lib/lingscope/negation_models.zip +0 -0
  295. data/lib/lingscope/negation_models/baseline_cue_all_both.model +49 -0
  296. data/lib/lingscope/negation_models/baseline_cue_all_clinical.model +19 -0
  297. data/lib/lingscope/negation_models/crf_cue_all_both.model +0 -0
  298. data/lib/lingscope/negation_models/crf_cue_all_clinical.model +0 -0
  299. data/lib/lingscope/negation_models/crf_scope_cue_crf_all_both.model +0 -0
  300. data/lib/lingscope/negation_models/crf_scope_cue_crf_all_clinical.model +0 -0
  301. data/lib/lingscope/negation_models/crf_scope_cue_regex_all_both.model +0 -0
  302. data/lib/lingscope/negation_models/crf_scope_cue_regex_all_clinical.model +0 -0
  303. data/lib/lingscope/negation_models/crf_scope_words_all_both.model +0 -0
  304. data/lib/lingscope/negation_models/crf_scope_words_all_clinical.model +0 -0
  305. data/lib/lingscope/negation_models/crf_scope_words_crf_all_both.model +0 -0
  306. data/lib/lingscope/negation_models/crf_scope_words_crf_all_clinical.model +0 -0
  307. data/lib/lingscope/negation_models/crf_scope_words_regex_all_both.model +0 -0
  308. data/lib/lingscope/negation_models/crf_scope_words_regex_all_clinical.model +0 -0
  309. data/lib/lingscope/src/lingscope/algorithms/AbnerTokenizer.java +58 -0
  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
  339. data/lib/setup/data/custom_site_synonyms.csv +1 -0
  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
  343. data/lib/setup/data/site_site_categories.txt +28 -0
  344. data/lib/tasks/abstractor_tasks.rake +22 -0
  345. data/lib/tasks/cucumber.rake +65 -0
  346. metadata +754 -0
@@ -0,0 +1,9 @@
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+ module Abstractor
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+ module AbstractorSubjectGroupMemberCustomMethods
3
+ end
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+
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+ class AbstractorSubjectGroupMember < ActiveRecord::Base
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+ include Abstractor::Methods::Models::AbstractorSubjectGroupMember
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+ include Abstractor::AbstractorSubjectGroupMemberCustomMethods
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+ end
9
+ end
@@ -0,0 +1,9 @@
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+ module Abstractor
2
+ module AbstractorSubjectRelationCustomMethods
3
+ end
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+
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+ class AbstractorSubjectRelation < ActiveRecord::Base
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+ include Abstractor::Methods::Models::AbstractorSubjectRelation
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+ include Abstractor::AbstractorSubjectRelationCustomMethods
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+ end
9
+ end
@@ -0,0 +1,9 @@
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+ module Abstractor
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+ module AbstractorSuggestionCustomMethods
3
+ end
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+
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+ class AbstractorSuggestion < ActiveRecord::Base
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+ include Abstractor::Methods::Models::AbstractorSuggestion
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+ include Abstractor::AbstractorSuggestionCustomMethods
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+ end
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+ end
@@ -0,0 +1,9 @@
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+ module Abstractor
2
+ module AbstractorSuggestionObjectValueCustomMethods
3
+ end
4
+
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+ class SuggestionObjectValue < ActiveRecord::Base
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+ include Abstractor::Methods::Models::AbstractorSuggestionObjectValue
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+ include Abstractor::AbstractorSuggestionObjectValueCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,9 @@
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+ module Abstractor
2
+ module AbstractorSuggestionSourceCustomMethods
3
+ end
4
+
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+ class AbstractorSuggestionSource < ActiveRecord::Base
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+ include Abstractor::Methods::Models::AbstractorSuggestionSource
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+ include Abstractor::AbstractorSuggestionSourceCustomMethods
8
+ end
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+ end
@@ -0,0 +1,9 @@
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+ module Abstractor
2
+ module AbstractorSuggestionStatusCustomMethods
3
+ end
4
+
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+ class AbstractorSuggestionStatus < ActiveRecord::Base
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+ include Abstractor::Methods::Models::AbstractorSuggestionStatus
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+ include Absgtractor::AbstractorSuggestionStatusCustomMethods
8
+ end
9
+ end
@@ -0,0 +1,74 @@
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+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <!-- You may freely edit this file. See commented blocks below for -->
3
+ <!-- some examples of how to customize the build. -->
4
+ <!-- (If you delete it and reopen the project it will be recreated.) -->
5
+ <!-- By default, only the Clean and Build commands use this build script. -->
6
+ <!-- Commands such as Run, Debug, and Test only use this build script if -->
7
+ <!-- the Compile on Save feature is turned off for the project. -->
8
+ <!-- You can turn off the Compile on Save (or Deploy on Save) setting -->
9
+ <!-- in the project's Project Properties dialog box.-->
10
+ <project name="lingscope" default="default" basedir=".">
11
+ <description>Builds, tests, and runs the project lingscope.</description>
12
+ <import file="nbproject/build-impl.xml"/>
13
+ <!--
14
+
15
+ There exist several targets which are by default empty and which can be
16
+ used for execution of your tasks. These targets are usually executed
17
+ before and after some main targets. They are:
18
+
19
+ -pre-init: called before initialization of project properties
20
+ -post-init: called after initialization of project properties
21
+ -pre-compile: called before javac compilation
22
+ -post-compile: called after javac compilation
23
+ -pre-compile-single: called before javac compilation of single file
24
+ -post-compile-single: called after javac compilation of single file
25
+ -pre-compile-test: called before javac compilation of JUnit tests
26
+ -post-compile-test: called after javac compilation of JUnit tests
27
+ -pre-compile-test-single: called before javac compilation of single JUnit test
28
+ -post-compile-test-single: called after javac compilation of single JUunit test
29
+ -pre-jar: called before JAR building
30
+ -post-jar: called after JAR building
31
+ -post-clean: called after cleaning build products
32
+
33
+ (Targets beginning with '-' are not intended to be called on their own.)
34
+
35
+ Example of inserting an obfuscator after compilation could look like this:
36
+
37
+ <target name="-post-compile">
38
+ <obfuscate>
39
+ <fileset dir="${build.classes.dir}"/>
40
+ </obfuscate>
41
+ </target>
42
+
43
+ For list of available properties check the imported
44
+ nbproject/build-impl.xml file.
45
+
46
+
47
+ Another way to customize the build is by overriding existing main targets.
48
+ The targets of interest are:
49
+
50
+ -init-macrodef-javac: defines macro for javac compilation
51
+ -init-macrodef-junit: defines macro for junit execution
52
+ -init-macrodef-debug: defines macro for class debugging
53
+ -init-macrodef-java: defines macro for class execution
54
+ -do-jar-with-manifest: JAR building (if you are using a manifest)
55
+ -do-jar-without-manifest: JAR building (if you are not using a manifest)
56
+ run: execution of project
57
+ -javadoc-build: Javadoc generation
58
+ test-report: JUnit report generation
59
+
60
+ An example of overriding the target for project execution could look like this:
61
+
62
+ <target name="run" depends="lingscope-impl.jar">
63
+ <exec dir="bin" executable="launcher.exe">
64
+ <arg file="${dist.jar}"/>
65
+ </exec>
66
+ </target>
67
+
68
+ Notice that the overridden target depends on the jar target and not only on
69
+ the compile target as the regular run target does. Again, for a list of available
70
+ properties which you can use, check the target you are overriding in the
71
+ nbproject/build-impl.xml file.
72
+
73
+ -->
74
+ </project>
@@ -0,0 +1,4 @@
1
+ #Tue, 18 Feb 2014 19:45:40 -0600
2
+
3
+
4
+ /Users/Mike/source/abstractor/lib/lingscope=
@@ -0,0 +1,32 @@
1
+ ========================
2
+ BUILD OUTPUT DESCRIPTION
3
+ ========================
4
+
5
+ When you build an Java application project that has a main class, the IDE
6
+ automatically copies all of the JAR
7
+ files on the projects classpath to your projects dist/lib folder. The IDE
8
+ also adds each of the JAR files to the Class-Path element in the application
9
+ JAR files manifest file (MANIFEST.MF).
10
+
11
+ To run the project from the command line, go to the dist folder and
12
+ type the following:
13
+
14
+ java -jar "lingscope.jar"
15
+
16
+ To distribute this project, zip up the dist folder (including the lib folder)
17
+ and distribute the ZIP file.
18
+
19
+ Notes:
20
+
21
+ * If two JAR files on the project classpath have the same name, only the first
22
+ JAR file is copied to the lib folder.
23
+ * Only JAR files are copied to the lib folder.
24
+ If the classpath contains other types of files or folders, these files (folders)
25
+ are not copied.
26
+ * If a library on the projects classpath also has a Class-Path element
27
+ specified in the manifest,the content of the Class-Path element has to be on
28
+ the projects runtime path.
29
+ * To set a main class in a standard Java project, right-click the project node
30
+ in the Projects window and choose Properties. Then click Run and enter the
31
+ class name in the Main Class field. Alternatively, you can manually type the
32
+ class name in the manifest Main-Class element.
@@ -0,0 +1,80 @@
1
+ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2
+ <!--NewPage-->
3
+ <HTML>
4
+ <HEAD>
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+ <!-- Generated by javadoc (build 1.6.0_65) on Tue Feb 18 19:45:41 CST 2014 -->
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+ <META http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+ <TITLE>
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+ All Classes
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+ </TITLE>
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+
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+ <META NAME="date" CONTENT="2014-02-18">
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+
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+ <LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
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+
15
+
16
+ </HEAD>
17
+
18
+ <BODY BGCOLOR="white">
19
+ <FONT size="+1" CLASS="FrameHeadingFont">
20
+ <B>All Classes</B></FONT>
21
+ <BR>
22
+
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+ <TABLE BORDER="0" WIDTH="100%" SUMMARY="">
24
+ <TR>
25
+ <TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="lingscope/algorithms/AbnerTokenizer.html" title="class in lingscope.algorithms" target="classFrame">AbnerTokenizer</A>
26
+ <BR>
27
+ <A HREF="lingscope/drivers/AnnotatedFilesMerger.html" title="class in lingscope.drivers" target="classFrame">AnnotatedFilesMerger</A>
28
+ <BR>
29
+ <A HREF="lingscope/structures/AnnotatedSentence.html" title="class in lingscope.structures" target="classFrame">AnnotatedSentence</A>
30
+ <BR>
31
+ <A HREF="lingscope/io/AnnotatedSentencesIO.html" title="class in lingscope.io" target="classFrame">AnnotatedSentencesIO</A>
32
+ <BR>
33
+ <A HREF="lingscope/algorithms/AnnotationComparer.html" title="class in lingscope.algorithms" target="classFrame">AnnotationComparer</A>
34
+ <BR>
35
+ <A HREF="lingscope/drivers/AnnotationComparerDriver.html" title="class in lingscope.drivers" target="classFrame">AnnotationComparerDriver</A>
36
+ <BR>
37
+ <A HREF="lingscope/algorithms/Annotator.html" title="class in lingscope.algorithms" target="classFrame">Annotator</A>
38
+ <BR>
39
+ <A HREF="lingscope/algorithms/BaselineAnnotator.html" title="class in lingscope.algorithms" target="classFrame">BaselineAnnotator</A>
40
+ <BR>
41
+ <A HREF="lingscope/algorithms/BaselineCueAnnotator.html" title="class in lingscope.algorithms" target="classFrame">BaselineCueAnnotator</A>
42
+ <BR>
43
+ <A HREF="lingscope/drivers/BaselineDriver.html" title="class in lingscope.drivers" target="classFrame">BaselineDriver</A>
44
+ <BR>
45
+ <A HREF="lingscope/algorithms/BaselineScopeAnnotator.html" title="class in lingscope.algorithms" target="classFrame">BaselineScopeAnnotator</A>
46
+ <BR>
47
+ <A HREF="lingscope/algorithms/CrfAnnotator.html" title="class in lingscope.algorithms" target="classFrame">CrfAnnotator</A>
48
+ <BR>
49
+ <A HREF="lingscope/drivers/CrfDriver.html" title="class in lingscope.drivers" target="classFrame">CrfDriver</A>
50
+ <BR>
51
+ <A HREF="lingscope/drivers/CueAndPosFilesMerger.html" title="class in lingscope.drivers" target="classFrame">CueAndPosFilesMerger</A>
52
+ <BR>
53
+ <A HREF="lingscope/algorithms/negex/GenNegEx.html" title="class in lingscope.algorithms.negex" target="classFrame">GenNegEx</A>
54
+ <BR>
55
+ <A HREF="lingscope/drivers/ModelTrainer.html" title="class in lingscope.drivers" target="classFrame">ModelTrainer</A>
56
+ <BR>
57
+ <A HREF="lingscope/algorithms/NegexAnnotator.html" title="class in lingscope.algorithms" target="classFrame">NegexAnnotator</A>
58
+ <BR>
59
+ <A HREF="lingscope/algorithms/NegexCueAnnotator.html" title="class in lingscope.algorithms" target="classFrame">NegexCueAnnotator</A>
60
+ <BR>
61
+ <A HREF="lingscope/drivers/NegexDriver.html" title="class in lingscope.drivers" target="classFrame">NegexDriver</A>
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+ <BR>
63
+ <A HREF="lingscope/algorithms/NegexScopeAnnotator.html" title="class in lingscope.algorithms" target="classFrame">NegexScopeAnnotator</A>
64
+ <BR>
65
+ <A HREF="lingscope/algorithms/PosTagger.html" title="class in lingscope.algorithms" target="classFrame">PosTagger</A>
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+ <BR>
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+ <A HREF="lingscope/drivers/PosTaggerDriver.html" title="class in lingscope.drivers" target="classFrame">PosTaggerDriver</A>
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+ <BR>
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+ <A HREF="lingscope/drivers/SentencePosTagger.html" title="class in lingscope.drivers" target="classFrame">SentencePosTagger</A>
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+ <BR>
71
+ <A HREF="lingscope/drivers/SentenceTagger.html" title="class in lingscope.drivers" target="classFrame">SentenceTagger</A>
72
+ <BR>
73
+ <A HREF="lingscope/algorithms/negex/Sorter.html" title="class in lingscope.algorithms.negex" target="classFrame">Sorter</A>
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+ <BR>
75
+ </FONT></TD>
76
+ </TR>
77
+ </TABLE>
78
+
79
+ </BODY>
80
+ </HTML>
@@ -0,0 +1,80 @@
1
+ <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2
+ <!--NewPage-->
3
+ <HTML>
4
+ <HEAD>
5
+ <!-- Generated by javadoc (build 1.6.0_65) on Tue Feb 18 19:45:41 CST 2014 -->
6
+ <META http-equiv="Content-Type" content="text/html; charset=UTF-8">
7
+ <TITLE>
8
+ All Classes
9
+ </TITLE>
10
+
11
+ <META NAME="date" CONTENT="2014-02-18">
12
+
13
+ <LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
14
+
15
+
16
+ </HEAD>
17
+
18
+ <BODY BGCOLOR="white">
19
+ <FONT size="+1" CLASS="FrameHeadingFont">
20
+ <B>All Classes</B></FONT>
21
+ <BR>
22
+
23
+ <TABLE BORDER="0" WIDTH="100%" SUMMARY="">
24
+ <TR>
25
+ <TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="lingscope/algorithms/AbnerTokenizer.html" title="class in lingscope.algorithms">AbnerTokenizer</A>
26
+ <BR>
27
+ <A HREF="lingscope/drivers/AnnotatedFilesMerger.html" title="class in lingscope.drivers">AnnotatedFilesMerger</A>
28
+ <BR>
29
+ <A HREF="lingscope/structures/AnnotatedSentence.html" title="class in lingscope.structures">AnnotatedSentence</A>
30
+ <BR>
31
+ <A HREF="lingscope/io/AnnotatedSentencesIO.html" title="class in lingscope.io">AnnotatedSentencesIO</A>
32
+ <BR>
33
+ <A HREF="lingscope/algorithms/AnnotationComparer.html" title="class in lingscope.algorithms">AnnotationComparer</A>
34
+ <BR>
35
+ <A HREF="lingscope/drivers/AnnotationComparerDriver.html" title="class in lingscope.drivers">AnnotationComparerDriver</A>
36
+ <BR>
37
+ <A HREF="lingscope/algorithms/Annotator.html" title="class in lingscope.algorithms">Annotator</A>
38
+ <BR>
39
+ <A HREF="lingscope/algorithms/BaselineAnnotator.html" title="class in lingscope.algorithms">BaselineAnnotator</A>
40
+ <BR>
41
+ <A HREF="lingscope/algorithms/BaselineCueAnnotator.html" title="class in lingscope.algorithms">BaselineCueAnnotator</A>
42
+ <BR>
43
+ <A HREF="lingscope/drivers/BaselineDriver.html" title="class in lingscope.drivers">BaselineDriver</A>
44
+ <BR>
45
+ <A HREF="lingscope/algorithms/BaselineScopeAnnotator.html" title="class in lingscope.algorithms">BaselineScopeAnnotator</A>
46
+ <BR>
47
+ <A HREF="lingscope/algorithms/CrfAnnotator.html" title="class in lingscope.algorithms">CrfAnnotator</A>
48
+ <BR>
49
+ <A HREF="lingscope/drivers/CrfDriver.html" title="class in lingscope.drivers">CrfDriver</A>
50
+ <BR>
51
+ <A HREF="lingscope/drivers/CueAndPosFilesMerger.html" title="class in lingscope.drivers">CueAndPosFilesMerger</A>
52
+ <BR>
53
+ <A HREF="lingscope/algorithms/negex/GenNegEx.html" title="class in lingscope.algorithms.negex">GenNegEx</A>
54
+ <BR>
55
+ <A HREF="lingscope/drivers/ModelTrainer.html" title="class in lingscope.drivers">ModelTrainer</A>
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+ <BR>
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+ <A HREF="lingscope/algorithms/NegexAnnotator.html" title="class in lingscope.algorithms">NegexAnnotator</A>
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+ <BR>
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+ <A HREF="lingscope/algorithms/NegexCueAnnotator.html" title="class in lingscope.algorithms">NegexCueAnnotator</A>
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+ <BR>
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+ <A HREF="lingscope/drivers/NegexDriver.html" title="class in lingscope.drivers">NegexDriver</A>
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+ <BR>
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+ <A HREF="lingscope/algorithms/NegexScopeAnnotator.html" title="class in lingscope.algorithms">NegexScopeAnnotator</A>
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+ <BR>
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+ <A HREF="lingscope/algorithms/PosTagger.html" title="class in lingscope.algorithms">PosTagger</A>
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+ <BR>
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+ <A HREF="lingscope/drivers/PosTaggerDriver.html" title="class in lingscope.drivers">PosTaggerDriver</A>
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+ <BR>
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+ <A HREF="lingscope/drivers/SentencePosTagger.html" title="class in lingscope.drivers">SentencePosTagger</A>
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+ <BR>
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+ <A HREF="lingscope/drivers/SentenceTagger.html" title="class in lingscope.drivers">SentenceTagger</A>
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+ <BR>
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+ <A HREF="lingscope/algorithms/negex/Sorter.html" title="class in lingscope.algorithms.negex">Sorter</A>
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+ <BR>
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+ </FONT></TD>
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+ </TR>
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+ </TABLE>
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+
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+ </BODY>
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+ </HTML>
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+ Constant Field Values
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+ <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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+ lingscope.drivers.*</FONT></TH>
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+ </TABLE>
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+
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+ <P>
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+
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+ <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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+ <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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+ <TH ALIGN="left" COLSPAN="3">lingscope.drivers.<A HREF="lingscope/drivers/SentenceTagger.html" title="class in lingscope.drivers">SentenceTagger</A></TH>
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+ </TR>
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+ <TR BGCOLOR="white" CLASS="TableRowColor">
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+ <A NAME="lingscope.drivers.SentenceTagger.CUE_INTER"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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+ <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
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+ <TD ALIGN="left"><CODE><A HREF="lingscope/drivers/SentenceTagger.html#CUE_INTER">CUE_INTER</A></CODE></TD>
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+ <TD ALIGN="right"><CODE>"I-C"</CODE></TD>
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+ </TR>
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+ <TR BGCOLOR="white" CLASS="TableRowColor">
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+ <A NAME="lingscope.drivers.SentenceTagger.CUE_START"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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+ <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
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+ <TD ALIGN="left"><CODE><A HREF="lingscope/drivers/SentenceTagger.html#CUE_START">CUE_START</A></CODE></TD>
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+ <TD ALIGN="right"><CODE>"B-C"</CODE></TD>
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+ </TR>
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+ <TR BGCOLOR="white" CLASS="TableRowColor">
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+ <A NAME="lingscope.drivers.SentenceTagger.OTHER"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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+ <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
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+ <TD ALIGN="left"><CODE><A HREF="lingscope/drivers/SentenceTagger.html#OTHER">OTHER</A></CODE></TD>
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+ <TD ALIGN="right"><CODE>"O"</CODE></TD>
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+ </TR>
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+ <TR BGCOLOR="white" CLASS="TableRowColor">
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+ <A NAME="lingscope.drivers.SentenceTagger.SCOPE_INTER"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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+ <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
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+ <TD ALIGN="left"><CODE><A HREF="lingscope/drivers/SentenceTagger.html#SCOPE_INTER">SCOPE_INTER</A></CODE></TD>
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+ <TD ALIGN="right"><CODE>"I-S"</CODE></TD>
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+ </TR>
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+ <TR BGCOLOR="white" CLASS="TableRowColor">
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+ <A NAME="lingscope.drivers.SentenceTagger.SCOPE_START"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
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+ <CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
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+ <TD ALIGN="left"><CODE><A HREF="lingscope/drivers/SentenceTagger.html#SCOPE_START">SCOPE_START</A></CODE></TD>
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+ <TD ALIGN="right"><CODE>"B-S"</CODE></TD>
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+ </TR>
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+ </FONT></TD>
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+ </TR>
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+ </TABLE>
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+
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+ <P>
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