abstractor 1.0.8
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- checksums.yaml +15 -0
- data/MIT-LICENSE +20 -0
- data/README.md +14 -0
- data/Rakefile +33 -0
- data/app/assets/images/abstractor/add.png +0 -0
- data/app/assets/images/abstractor/ajax-loader.gif +0 -0
- data/app/assets/images/abstractor/bar.gif +0 -0
- data/app/assets/images/abstractor/bti_logo.jpg +0 -0
- data/app/assets/images/abstractor/bullet_arrow_down.png +0 -0
- data/app/assets/images/abstractor/bullet_arrow_up.png +0 -0
- data/app/assets/images/abstractor/cog.png +0 -0
- data/app/assets/images/abstractor/delete.png +0 -0
- data/app/assets/images/abstractor/edit.png +0 -0
- data/app/assets/images/abstractor/excel.png +0 -0
- data/app/assets/images/abstractor/favicon.ico +0 -0
- data/app/assets/images/abstractor/greencheck.gif +0 -0
- data/app/assets/images/abstractor/loading.gif +0 -0
- data/app/assets/images/abstractor/nu_logo.jpg +0 -0
- data/app/assets/images/abstractor/nubic_logo.png +0 -0
- data/app/assets/images/abstractor/page.png +0 -0
- data/app/assets/images/abstractor/rails.png +0 -0
- data/app/assets/images/abstractor/robert_h_lurie.jpg +0 -0
- data/app/assets/images/abstractor/show.png +0 -0
- data/app/assets/images/abstractor/switch_minus.gif +0 -0
- data/app/assets/images/abstractor/switch_plus.gif +0 -0
- data/app/assets/javascripts/abstractor/abstractor.js +89 -0
- data/app/assets/javascripts/abstractor/application.js +21 -0
- data/app/assets/javascripts/abstractor/combobox.js +301 -0
- data/app/assets/javascripts/abstractor/jquery/jquery.form.js +1074 -0
- data/app/assets/javascripts/abstractor/nested_attributes.js +69 -0
- data/app/assets/stylesheets/abstractor/abstractor_abstractions.css +312 -0
- data/app/assets/stylesheets/abstractor/application.css +21 -0
- data/app/assets/stylesheets/abstractor/jquery.ui.override.css.scss +73 -0
- data/app/controllers/abstractor/abstractor_abstraction_groups_controller.rb +5 -0
- data/app/controllers/abstractor/abstractor_abstractions_controller.rb +5 -0
- data/app/controllers/abstractor/abstractor_suggestions_controller.rb +5 -0
- data/app/controllers/abstractor/application_controller.rb +2 -0
- data/app/helpers/abstractor/application_helper.rb +4 -0
- data/app/models/abstractor/abstractor_abstraction.rb +6 -0
- data/app/models/abstractor/abstractor_abstraction_group.rb +6 -0
- data/app/models/abstractor/abstractor_abstraction_group_member.rb +6 -0
- data/app/models/abstractor/abstractor_abstraction_schema.rb +6 -0
- data/app/models/abstractor/abstractor_abstraction_schema_object_value.rb +6 -0
- data/app/models/abstractor/abstractor_abstraction_schema_predicate_variant.rb +6 -0
- data/app/models/abstractor/abstractor_abstraction_schema_relation.rb +6 -0
- data/app/models/abstractor/abstractor_abstraction_source.rb +6 -0
- data/app/models/abstractor/abstractor_object_type.rb +6 -0
- data/app/models/abstractor/abstractor_object_value.rb +6 -0
- data/app/models/abstractor/abstractor_object_value_variant.rb +6 -0
- data/app/models/abstractor/abstractor_relation_type.rb +6 -0
- data/app/models/abstractor/abstractor_rule_type.rb +6 -0
- data/app/models/abstractor/abstractor_subject.rb +6 -0
- data/app/models/abstractor/abstractor_subject_group.rb +6 -0
- data/app/models/abstractor/abstractor_subject_group_member.rb +6 -0
- data/app/models/abstractor/abstractor_subject_relation.rb +6 -0
- data/app/models/abstractor/abstractor_suggestion.rb +6 -0
- data/app/models/abstractor/abstractor_suggestion_object_value.rb +6 -0
- data/app/models/abstractor/abstractor_suggestion_source.rb +6 -0
- data/app/models/abstractor/abstractor_suggestion_status.rb +6 -0
- data/app/views/abstractor/abstractor_abstraction_groups/_form.html.haml +10 -0
- data/app/views/abstractor/abstractor_abstraction_groups/edit.html.haml +1 -0
- data/app/views/abstractor/abstractor_abstractions/_fields.html.haml +63 -0
- data/app/views/abstractor/abstractor_abstractions/_list.html.haml +45 -0
- data/app/views/abstractor/abstractor_abstractions/edit.html.haml +53 -0
- data/app/views/abstractor/abstractor_abstractions/show.html.haml +1 -0
- data/app/views/abstractor/shared/_error_messages.html.haml +5 -0
- data/config/cucumber.yml +8 -0
- data/config/routes.rb +7 -0
- data/db/migrate/20131227205140_create_abstractor_object_types.rb +10 -0
- data/db/migrate/20131227205219_create_abstractor_object_values.rb +10 -0
- data/db/migrate/20131227205256_create_abstractor_object_value_variants.rb +11 -0
- data/db/migrate/20131227205320_create_abstractor_relation_types.rb +10 -0
- data/db/migrate/20131227205354_create_abstractor_rule_types.rb +11 -0
- data/db/migrate/20131227205432_create_abstractor_abstraction_schemas.rb +13 -0
- data/db/migrate/20131227205456_create_abstractor_abstraction_schema_object_values.rb +10 -0
- data/db/migrate/20131227205529_create_abstractor_abstraction_schema_predicate_variants.rb +11 -0
- data/db/migrate/20131227205610_create_abstractor_abstraction_schema_relations.rb +11 -0
- data/db/migrate/20131227205652_create_abstractor_subjects.rb +12 -0
- data/db/migrate/20131227205732_create_abstractor_subject_relations.rb +11 -0
- data/db/migrate/20131227205831_create_abstractor_abstraction_sources.rb +11 -0
- data/db/migrate/20131227210211_create_abstractor_subject_groups.rb +10 -0
- data/db/migrate/20131227210244_create_abstractor_subject_group_members.rb +11 -0
- data/db/migrate/20131227210350_create_abstractor_abstraction_groups.rb +12 -0
- data/db/migrate/20131227210353_create_abstractor_abstraction_group_members.rb +11 -0
- data/db/migrate/20131227211050_create_abstractor_suggestion_statuses.rb +10 -0
- data/db/migrate/20131227211303_create_abstractor_abstractions.rb +15 -0
- data/db/migrate/20131227213427_create_abstractor_suggestions.rb +14 -0
- data/db/migrate/20131228041944_create_abstractor_suggestion_object_values.rb +11 -0
- data/db/migrate/20131228041945_create_abstractor_suggestion_sources.rb +16 -0
- data/db/seeds.rb +0 -0
- data/lib/abstractor.rb +8 -0
- data/lib/abstractor/abstractable.rb +190 -0
- data/lib/abstractor/core_ext/string.rb +99 -0
- data/lib/abstractor/engine.rb +14 -0
- data/lib/abstractor/methods/controllers/abstractor_abstraction_groups_controller.rb +37 -0
- data/lib/abstractor/methods/controllers/abstractor_abstractions_controller.rb +42 -0
- data/lib/abstractor/methods/controllers/abstractor_suggestions_controller.rb +28 -0
- data/lib/abstractor/methods/models/abstractor_abstraction.rb +65 -0
- data/lib/abstractor/methods/models/abstractor_abstraction_group.rb +37 -0
- data/lib/abstractor/methods/models/abstractor_abstraction_group_member.rb +17 -0
- data/lib/abstractor/methods/models/abstractor_abstraction_schema.rb +27 -0
- data/lib/abstractor/methods/models/abstractor_abstraction_schema_object_value.rb +17 -0
- data/lib/abstractor/methods/models/abstractor_abstraction_schema_predicate_variant.rb +16 -0
- data/lib/abstractor/methods/models/abstractor_abstraction_schema_relation.rb +18 -0
- data/lib/abstractor/methods/models/abstractor_abstraction_source.rb +29 -0
- data/lib/abstractor/methods/models/abstractor_object_type.rb +16 -0
- data/lib/abstractor/methods/models/abstractor_object_value.rb +24 -0
- data/lib/abstractor/methods/models/abstractor_object_value_variant.rb +16 -0
- data/lib/abstractor/methods/models/abstractor_relation_type.rb +16 -0
- data/lib/abstractor/methods/models/abstractor_rule_type.rb +17 -0
- data/lib/abstractor/methods/models/abstractor_subject.rb +258 -0
- data/lib/abstractor/methods/models/abstractor_subject_group.rb +19 -0
- data/lib/abstractor/methods/models/abstractor_subject_group_member.rb +17 -0
- data/lib/abstractor/methods/models/abstractor_subject_relation.rb +18 -0
- data/lib/abstractor/methods/models/abstractor_suggestion.rb +88 -0
- data/lib/abstractor/methods/models/abstractor_suggestion_object_value.rb +17 -0
- data/lib/abstractor/methods/models/abstractor_suggestion_source.rb +17 -0
- data/lib/abstractor/methods/models/abstractor_suggestion_status.rb +29 -0
- data/lib/abstractor/methods/models/soft_delete.rb +35 -0
- data/lib/abstractor/negation_detection.rb +43 -0
- data/lib/abstractor/parser.rb +76 -0
- data/lib/abstractor/setup.rb +24 -0
- data/lib/abstractor/user_interface.rb +40 -0
- data/lib/abstractor/utility.rb +8 -0
- data/lib/abstractor/version.rb +3 -0
- data/lib/generators/abstractor/install/install_generator.rb +118 -0
- data/lib/generators/abstractor/install/templates/controllers/abstractor_abstraction_groups_controller.rb +16 -0
- data/lib/generators/abstractor/install/templates/controllers/abstractor_abstractions_controller.rb +24 -0
- data/lib/generators/abstractor/install/templates/controllers/abstractor_suggestions_controller.rb +12 -0
- data/lib/generators/abstractor/install/templates/dictionaries.yml +235 -0
- data/lib/generators/abstractor/install/templates/helpers/abstractions_helper.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_abstraction.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_group.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_group_member.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_object_value.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_predicate_variant.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_schema_relation.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_abstraction_source.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_object_type.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_object_value.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_object_value_variant.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_relation_type.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_rule_type.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_subject.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_subject_group.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_subject_group_member.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_subject_relation.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_suggestion.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_suggestion_object_value.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_suggestion_source.rb +9 -0
- data/lib/generators/abstractor/install/templates/models/abstractor_suggestion_status.rb +9 -0
- data/lib/lingscope/build.xml +74 -0
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- data/lib/lingscope/dist/lib/abner.jar +0 -0
- data/lib/lingscope/dist/lib/commons-lang-2.4.jar +0 -0
- data/lib/lingscope/dist/lib/java_utils.jar +0 -0
- data/lib/lingscope/dist/lib/sptoolkit.jar +0 -0
- data/lib/lingscope/dist/lib/stanford-postagger.jar +0 -0
- data/lib/lingscope/dist/lingscope.jar +0 -0
- data/lib/lingscope/lingscope.zip +0 -0
- data/lib/lingscope/manifest.mf +3 -0
- data/lib/lingscope/nbproject/build-impl.xml +1338 -0
- data/lib/lingscope/nbproject/genfiles.properties +8 -0
- data/lib/lingscope/nbproject/private/config.properties +0 -0
- data/lib/lingscope/nbproject/private/private.properties +10 -0
- data/lib/lingscope/nbproject/private/private.xml +5 -0
- data/lib/lingscope/nbproject/project.properties +85 -0
- data/lib/lingscope/nbproject/project.xml +15 -0
- data/lib/lingscope/negation_models.zip +0 -0
- data/lib/lingscope/negation_models/baseline_cue_all_both.model +49 -0
- data/lib/lingscope/negation_models/baseline_cue_all_clinical.model +19 -0
- data/lib/lingscope/negation_models/crf_cue_all_both.model +0 -0
- data/lib/lingscope/negation_models/crf_cue_all_clinical.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_cue_crf_all_both.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_cue_crf_all_clinical.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_cue_regex_all_both.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_cue_regex_all_clinical.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_words_all_both.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_words_all_clinical.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_words_crf_all_both.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_words_crf_all_clinical.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_words_regex_all_both.model +0 -0
- data/lib/lingscope/negation_models/crf_scope_words_regex_all_clinical.model +0 -0
- data/lib/lingscope/src/lingscope/algorithms/AbnerTokenizer.java +58 -0
- data/lib/lingscope/src/lingscope/algorithms/AnnotationComparer.java +207 -0
- data/lib/lingscope/src/lingscope/algorithms/Annotator.java +51 -0
- data/lib/lingscope/src/lingscope/algorithms/BaselineAnnotator.java +80 -0
- data/lib/lingscope/src/lingscope/algorithms/BaselineCueAnnotator.java +84 -0
- data/lib/lingscope/src/lingscope/algorithms/BaselineScopeAnnotator.java +101 -0
- data/lib/lingscope/src/lingscope/algorithms/CrfAnnotator.java +45 -0
- data/lib/lingscope/src/lingscope/algorithms/NegexAnnotator.java +52 -0
- data/lib/lingscope/src/lingscope/algorithms/NegexCueAnnotator.java +26 -0
- data/lib/lingscope/src/lingscope/algorithms/NegexScopeAnnotator.java +26 -0
- data/lib/lingscope/src/lingscope/algorithms/PosTagger.java +54 -0
- data/lib/lingscope/src/lingscope/algorithms/negex/GenNegEx.java +530 -0
- data/lib/lingscope/src/lingscope/algorithms/negex/Sorter.java +36 -0
- data/lib/lingscope/src/lingscope/drivers/AnnotatedFilesMerger.java +61 -0
- data/lib/lingscope/src/lingscope/drivers/AnnotationComparerDriver.java +22 -0
- data/lib/lingscope/src/lingscope/drivers/BaselineDriver.java +45 -0
- data/lib/lingscope/src/lingscope/drivers/CrfDriver.java +31 -0
- data/lib/lingscope/src/lingscope/drivers/CueAndPosFilesMerger.java +86 -0
- data/lib/lingscope/src/lingscope/drivers/ModelTrainer.java +39 -0
- data/lib/lingscope/src/lingscope/drivers/NegexDriver.java +32 -0
- data/lib/lingscope/src/lingscope/drivers/PosTaggerDriver.java +62 -0
- data/lib/lingscope/src/lingscope/drivers/SentencePosTagger.java +89 -0
- data/lib/lingscope/src/lingscope/drivers/SentenceTagger.java +158 -0
- data/lib/lingscope/src/lingscope/io/AnnotatedSentencesIO.java +53 -0
- data/lib/lingscope/src/lingscope/structures/AnnotatedSentence.java +105 -0
- data/lib/setup/data/ICD-O-3_CSV-metadata/Morphenglish.csv +1 -0
- data/lib/setup/data/ICD-O-3_CSV-metadata/Morphenglish.txt +2273 -0
- data/lib/setup/data/ICD-O-3_CSV-metadata/Topoenglish.csv +1 -0
- data/lib/setup/data/ICD-O-3_CSV-metadata/Topoenglish.txt +1342 -0
- data/lib/setup/data/ICD-O-3_CSV-metadata/icd-o3 readme.txt +21 -0
- data/lib/setup/data/custom_site_synonyms.csv +1 -0
- data/lib/setup/data/diagnosis_categorizations.csv +1 -0
- data/lib/setup/data/high_level_primary_cns_diagnosis_categorizations.yml +597 -0
- data/lib/setup/data/icdo3_sites_with_laterality.txt +11 -0
- data/lib/setup/data/site_site_categories.txt +28 -0
- data/lib/tasks/abstractor_tasks.rake +22 -0
- data/lib/tasks/cucumber.rake +65 -0
- metadata +754 -0
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<?xml version="1.0" encoding="UTF-8"?>
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run: execution of project
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========================
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BUILD OUTPUT DESCRIPTION
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========================
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When you build an Java application project that has a main class, the IDE
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JAR files manifest file (MANIFEST.MF).
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java -jar "lingscope.jar"
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* Only JAR files are copied to the lib folder.
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the projects runtime path.
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* To set a main class in a standard Java project, right-click the project node
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class name in the Main Class field. Alternatively, you can manually type the
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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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<META NAME="date" CONTENT="2014-02-18">
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<LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
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<B>All Classes</B></FONT>
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<BR>
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<TABLE BORDER="0" WIDTH="100%" SUMMARY="">
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<TR>
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<TD NOWRAP><FONT CLASS="FrameItemFont"><A HREF="lingscope/algorithms/AbnerTokenizer.html" title="class in lingscope.algorithms" target="classFrame">AbnerTokenizer</A>
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<BR>
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<A HREF="lingscope/drivers/AnnotatedFilesMerger.html" title="class in lingscope.drivers" target="classFrame">AnnotatedFilesMerger</A>
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<BR>
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<A HREF="lingscope/structures/AnnotatedSentence.html" title="class in lingscope.structures" target="classFrame">AnnotatedSentence</A>
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<BR>
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<A HREF="lingscope/io/AnnotatedSentencesIO.html" title="class in lingscope.io" target="classFrame">AnnotatedSentencesIO</A>
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<BR>
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<A HREF="lingscope/algorithms/AnnotationComparer.html" title="class in lingscope.algorithms" target="classFrame">AnnotationComparer</A>
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<BR>
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<A HREF="lingscope/drivers/AnnotationComparerDriver.html" title="class in lingscope.drivers" target="classFrame">AnnotationComparerDriver</A>
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<BR>
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<A HREF="lingscope/algorithms/Annotator.html" title="class in lingscope.algorithms" target="classFrame">Annotator</A>
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<BR>
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<A HREF="lingscope/algorithms/BaselineAnnotator.html" title="class in lingscope.algorithms" target="classFrame">BaselineAnnotator</A>
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<BR>
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<A HREF="lingscope/algorithms/BaselineCueAnnotator.html" title="class in lingscope.algorithms" target="classFrame">BaselineCueAnnotator</A>
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<BR>
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<A HREF="lingscope/drivers/BaselineDriver.html" title="class in lingscope.drivers" target="classFrame">BaselineDriver</A>
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<BR>
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<A HREF="lingscope/algorithms/BaselineScopeAnnotator.html" title="class in lingscope.algorithms" target="classFrame">BaselineScopeAnnotator</A>
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<BR>
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<A HREF="lingscope/algorithms/CrfAnnotator.html" title="class in lingscope.algorithms" target="classFrame">CrfAnnotator</A>
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<BR>
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<A HREF="lingscope/drivers/CrfDriver.html" title="class in lingscope.drivers" target="classFrame">CrfDriver</A>
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<BR>
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<A HREF="lingscope/drivers/CueAndPosFilesMerger.html" title="class in lingscope.drivers" target="classFrame">CueAndPosFilesMerger</A>
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<BR>
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<A HREF="lingscope/algorithms/negex/GenNegEx.html" title="class in lingscope.algorithms.negex" target="classFrame">GenNegEx</A>
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<BR>
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<A HREF="lingscope/drivers/ModelTrainer.html" title="class in lingscope.drivers" target="classFrame">ModelTrainer</A>
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<BR>
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<A HREF="lingscope/algorithms/NegexAnnotator.html" title="class in lingscope.algorithms" target="classFrame">NegexAnnotator</A>
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<BR>
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<A HREF="lingscope/algorithms/NegexCueAnnotator.html" title="class in lingscope.algorithms" target="classFrame">NegexCueAnnotator</A>
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<BR>
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<A HREF="lingscope/drivers/NegexDriver.html" title="class in lingscope.drivers" target="classFrame">NegexDriver</A>
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<BR>
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<A HREF="lingscope/algorithms/NegexScopeAnnotator.html" title="class in lingscope.algorithms" target="classFrame">NegexScopeAnnotator</A>
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<BR>
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<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>
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<A HREF="lingscope/drivers/SentenceTagger.html" title="class in lingscope.drivers" target="classFrame">SentenceTagger</A>
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<BR>
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<A HREF="lingscope/algorithms/negex/Sorter.html" title="class in lingscope.algorithms.negex" target="classFrame">Sorter</A>
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<BR>
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