A B C D E F G H I J K L M N O P Q R S T U V W X Z _

A

a1 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator

a2 - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator

abbrevExpectedResults1 - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests

abbrevExpectedResults2 - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests

abbrevExpectedResults3 - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests

abbrevTest1 - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests

abbrevTest2 - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests

abbrevTest3 - Variable in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTBTests

aborted() - Method in class org.apache.ctakes.postagger.test.CpeTests.StatusCallbackListenerImpl

Called when the CPM is stopped abruptly due to errors.

aborted() - Method in class org.apache.ctakes.regression.test.RegressionPipelineTest.StatusCallbackListenerImpl

Called when the CPM is stopped abruptly due to errors.

AbstractBaseDictionary - Class in org.apache.ctakes.dictionary.lookup

AbstractBaseDictionary() - Constructor for class org.apache.ctakes.dictionary.lookup.AbstractBaseDictionary

AbstractBaseMetaDataHit - Class in org.apache.ctakes.dictionary.lookup

Base impl for a MetaDataHit implementation.

AbstractBaseMetaDataHit() - Constructor for class org.apache.ctakes.dictionary.lookup.AbstractBaseMetaDataHit

AbstractClassifier - Class in org.apache.ctakes.coreference.util

AbstractClassifier(UimaContext, String, int) - Constructor for class org.apache.ctakes.coreference.util.AbstractClassifier

add(K) - Method in class org.apache.ctakes.utils.struct.CounterMap

add(K, Integer) - Method in class org.apache.ctakes.utils.struct.CounterMap

add(K) - Method in class org.apache.ctakes.utils.struct.CounterTreeMap

add(K, Integer) - Method in class org.apache.ctakes.utils.struct.CounterTreeMap

addAnnotation(Annotation) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData

Adds a single annotation to the syntactic cue annotation list.

addAnnotation(int, XcasAnnotation) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Inserts a new annotation with the specified internal id to this XcasFile.

addAnnotation(int, XcasAnnotation, String) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Inserts a new annotation, along with its position in the file, to this XcasFile object.

addAnnotation(int, XcasAnnotation, int, int) - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

Inserts a new annotation, along with its position in the file, to this XcasFile object.

addAnnotations(List) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData

Adds a list of annotations to the syntactic cue annotation list.

addCacheEntry(String) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Adds an entry to the dictionary lookup cache.

addChild(SimpleTree) - Method in class org.apache.ctakes.utils.tree.SimpleTree

addCollectionFilter(CollectionFilter) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Adds a Collection filter to the engine.

addField(String, String) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTableRow

addInstance(Instance<String>) - Method in class org.apache.ctakes.temporal.utils.SMOTEplus

addMetaData(Object, Object) - Method in class org.apache.ctakes.necontexts.ContextHit

addMetaData(Object, Object) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData

Adds a meta data entry for the document.

addPostLookupFilter(PostLookupFilter) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Adds a Post-lookup filter to the engine.

addPreLookupFilter(PreLookupFilter) - Method in class org.apache.ctakes.dictionary.lookup.DictionaryEngine

Adds a Pre-lookup filter to the engine.

addRow(StringTableRow) - Method in class org.apache.ctakes.dictionary.lookup.strtable.StringTable

addSegment(SegmentMetaData) - Method in class org.apache.ctakes.preprocessor.DocumentMetaData

Adds a segment.

addSpan(int, int) - Method in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation

Create a new span and add it to the list (not publicly available)

addStringAttribute(String, String) - Method in class org.apache.ctakes.dictionary.lookup.ae.LookupAnnotationToJCasAdapter

Adds an attribute that may be used for filtering.

addStringAttribute(String, String) - Method in interface org.apache.ctakes.dictionary.lookup.vo.LookupAnnotation

Adds an attribute that may be used for filtering.

addStringAttribute(String, String) - Method in class org.apache.ctakes.dictionary.lookup.vo.LookupAnnotationToTokAdapter

addToIndexes(JCas, ArrayList<ConllDependencyNode>) - Static method in class org.apache.ctakes.dependency.parser.util.DependencyUtility

ADJP - Class in org.apache.ctakes.typesystem.type.syntax

An adjective phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADJP Updated by JCasGen Tue Apr 09 12:44:03 EDT 2013 XML source: trunk/ctakes-pad-term-spotter-res/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml

ADJP() - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP

Never called.

ADJP(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP

Internal - constructor used by generator

ADJP(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP

ADJP(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP

ADJP_Type - Class in org.apache.ctakes.typesystem.type.syntax

An adjective phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADJP Updated by JCasGen Tue Apr 09 12:44:03 EDT 2013

ADJP_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADJP_Type

initialize variables to correspond with Cas Type and Features

adjustOffsetToBestMatch(int) - Method in class org.apache.ctakes.assertion.medfacts.i2b2.api.CharacterOffsetToLineTokenConverterCtakesImpl

ADVP - Class in org.apache.ctakes.typesystem.type.syntax

An adverb phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADVP Updated by JCasGen Tue Apr 09 12:44:03 EDT 2013 XML source: trunk/ctakes-pad-term-spotter-res/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml

ADVP() - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP

Never called.

ADVP(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP

Internal - constructor used by generator

ADVP(JCas) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP

ADVP(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP

ADVP_Type - Class in org.apache.ctakes.typesystem.type.syntax

An adverb phrase Equivalent to cTAKES: edu.mayo.bmi.uima.chunker.type.ADVP Updated by JCasGen Tue Apr 09 12:44:03 EDT 2013

ADVP_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.syntax.ADVP_Type

initialize variables to correspond with Cas Type and Features

AEROSOL - Static variable in class org.apache.ctakes.drugner.elements.FormElement

Affects - Class in org.apache.ctakes.typesystem.type.relation

A UMLS relation between clinical elements.

Affects() - Constructor for class org.apache.ctakes.typesystem.type.relation.Affects

Never called.

Affects(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Affects

Internal - constructor used by generator

Affects(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.Affects

Affects_Type - Class in org.apache.ctakes.typesystem.type.relation

A UMLS relation between clinical elements.

Affects_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.Affects_Type

initialize variables to correspond with Cas Type and Features

AffectsTextRelation - Class in org.apache.ctakes.typesystem.type.relation

Updated by JCasGen Tue Apr 09 12:44:02 EDT 2013 XML source: trunk/ctakes-pad-term-spotter-res/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml

AffectsTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation

Never called.

AffectsTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation

Internal - constructor used by generator

AffectsTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation

AffectsTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation

Updated by JCasGen Tue Apr 09 12:44:02 EDT 2013

AffectsTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AffectsTextRelation_Type

initialize variables to correspond with Cas Type and Features

al - Variable in class org.apache.ctakes.drugner.cc.ConsumeNamedEntityRecordModel

alias - Variable in class org.apache.ctakes.coreference.util.PairAttributeCalculator

alignId2GoldId - Variable in class org.apache.ctakes.coreference.util.GoldStandardLabeler

ALL_SCOPE - Static variable in class org.apache.ctakes.necontexts.ContextAnnotator

The ALL_SCOPE scope provides the context annotation that are found in all three of the other scopes (LEFT, MIDDLE, and RIGHT).

allDigits(String) - Static method in class org.apache.ctakes.core.nlp.tokenizer.ContractionsPTB

allFieldsValues() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

Returns a string representation of all the attributes and references.

ALLFILELOC - Variable in class org.apache.ctakes.relationextractor.data.Splitter

allFileNames - Variable in class org.apache.ctakes.relationextractor.data.Splitter

allowClassifierModelOnClasspath(UimaContext) - Static method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator

Workaround for https://code.google.com/p/cleartk/issues/detail?id=346 Not intended for external use

allowSmallerSystemArguments - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options

alog(double) - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath

alternateAlgorithm - Variable in class org.apache.ctakes.padtermspotter.cc.PADOffSetsRecord

analyzeContext(List<? extends Annotation>, int) - Method in interface org.apache.ctakes.necontexts.ContextAnalyzer

This method is called by the ContextAnnotator.

analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.necontexts.ContextAnalyzerAdapter

analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.necontexts.negation.NegationContextAnalyzer

This method analyzes a list of tokens looking for a negation pattern as specified by the class NegationFSM.

analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.necontexts.status.StatusContextAnalyzer

Analyze a list of tokens looking for a status pattern as specified by the class StatusIndicatorFSM.

analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.padtermspotter.impl.DxContextAnalyzerImpl

analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.padtermspotter.impl.NegativeContextAnalyzerImpl

analyzeContext(List<? extends Annotation>, int) - Method in class org.apache.ctakes.smokingstatus.context.negation.NegationContextAnalyzer

This method analyzes a list of tokens looking for a negation pattern as specified by the class NegationFSM.

anaph_feats - Static variable in class org.apache.ctakes.coreference.util.FeatureVector

AnaphoricityAttributeCalculator - Class in org.apache.ctakes.coreference.util

AnaphoricityAttributeCalculator(JCas, Markable) - Constructor for class org.apache.ctakes.coreference.util.AnaphoricityAttributeCalculator

AnatomicalSite - Class in org.apache.ctakes.typesystem.type.refsem

A body part or area, corresponding to the UMLS semantic group of Anatomy.

AnatomicalSite() - Constructor for class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite

Never called.

AnatomicalSite(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite

Internal - constructor used by generator

AnatomicalSite(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite

AnatomicalSite_Type - Class in org.apache.ctakes.typesystem.type.refsem

A body part or area, corresponding to the UMLS semantic group of Anatomy.

AnatomicalSite_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.AnatomicalSite_Type

initialize variables to correspond with Cas Type and Features

AnatomicalSiteMention - Class in org.apache.ctakes.typesystem.type.textsem

A text string that refers to a (AnatomicalSite) Entity.

AnatomicalSiteMention() - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention

Never called.

AnatomicalSiteMention(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention

Internal - constructor used by generator

AnatomicalSiteMention(JCas) - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention

AnatomicalSiteMention(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention

AnatomicalSiteMention_Type - Class in org.apache.ctakes.typesystem.type.textsem

A text string that refers to a (AnatomicalSite) Entity.

AnatomicalSiteMention_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention_Type

initialize variables to correspond with Cas Type and Features

AND_RELATION - Static variable in class org.apache.ctakes.dictionary.lookup.filter.PostLookupFilterGroupImpl

ANN_PART_ONE_TYPES_TO_IGNORE - Static variable in class org.apache.ctakes.padtermspotter.ae.PADHitAnnotator

List of type ids to be ignored from being considered as hits.

ANN_PART_TWO_TYPES_TO_IGNORE - Static variable in class org.apache.ctakes.padtermspotter.ae.PADHitAnnotator

List of type ids to be ignored from being considered as hits.

annotateRange(JCas, String, int, int) - Method in class org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster

A utility method that annotates a given range.

annotateRange(JCas, String, Segment, int) - Method in class org.apache.ctakes.core.ae.SentenceDetector

Detect sentences within a section of the text and add annotations to the CAS.

annotateRange(JCas, int, int) - Method in class org.apache.ctakes.core.ae.TokenizerAnnotator

A utility method that tokenizes a range of text.

annotateRange(JCas, int, int) - Method in class org.apache.ctakes.core.ae.TokenizerAnnotatorPTB

Tokenizes a range of text, adding the tokens to the CAS Tokenizes one sentence at a time.

annotateRange(JCas, String, int, int) - Method in class org.apache.ctakes.lvg.ae.LvgAnnotator

A utility method that annotates a given range.

annotateRange(JCas, String, int, int) - Method in class org.apache.ctakes.lvg.ae.LvgBaseTokenAnnotator

A utility method that annotates a given range.

annotateRange(JCas, String, int, int) - Method in class org.apache.ctakes.smokingstatus.ae.SentenceAdjuster

A utility method that annotates a given range.

Annotation - Class in org.apache.ctakes.preprocessor

Annotation() - Constructor for class org.apache.ctakes.preprocessor.Annotation

ANNOTATION_PART_ONE_FILTEROUT_NEGATED - Static variable in class org.apache.ctakes.padtermspotter.ae.PADHitAnnotator

Flag to specify whether to filter out negated hits identified for ANNOTATION_PART_ONE_OF_PAIR

ANNOTATION_PART_ONE_OF_PAIR - Static variable in class org.apache.ctakes.padtermspotter.ae.PADHitAnnotator

Part 1 of the pair (of annotations) that makes up a hit

ANNOTATION_PART_TWO_FILTEROUT_NEGATED - Static variable in class org.apache.ctakes.padtermspotter.ae.PADHitAnnotator

Flag to specify whether to filter out negated hits identified for ANNOTATION_PART_TWO_OF_PAIR

ANNOTATION_PART_TWO_OF_PAIR - Static variable in class org.apache.ctakes.padtermspotter.ae.PADHitAnnotator

Part 2 of the pair (of annotations) that makes up a hit

AnnotationCounter - Class in org.apache.ctakes.coreference.util

AnnotationCounter() - Constructor for class org.apache.ctakes.coreference.util.AnnotationCounter

annotationNode(JCas, Annotation) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils

annotationNode(JCas, int, int) - Static method in class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils

annotations - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasFile

annotationsClone() - Method in class org.apache.ctakes.utils.xcas_comparison.XcasFile

AnnotationSelector - Class in org.apache.ctakes.coreference.util

AnnotationSelector() - Constructor for class org.apache.ctakes.coreference.util.AnnotationSelector

annotationSlots - Variable in class org.apache.ctakes.core.knowtator.KnowtatorAnnotation

The annotation-valued annotation attributes (i.e.

AnnotationTreeUtils - Class in org.apache.ctakes.constituency.parser.util

AnnotationTreeUtils() - Constructor for class org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils

annotationTypes - Variable in class org.apache.ctakes.assertion.eval.AssertionEvaluation

AnnotOffsetComparator - Class in org.apache.ctakes.coreference.util

AnnotOffsetComparator() - Constructor for class org.apache.ctakes.coreference.util.AnnotOffsetComparator

APOSTROPHE - Static variable in class org.apache.ctakes.core.nlp.tokenizer.TokenizerHelper

apply(Feature) - Method in class org.apache.ctakes.temporal.ae.feature.selection.Chi2FeatureSelection

apply(Feature) - Method in class org.apache.ctakes.temporal.ae.feature.selection.FeatureSelection

applyFilter(Collection<MetaDataHit>) - Method in interface org.apache.ctakes.dictionary.lookup.filter.CollectionFilter

Prunes the Collection of MetaDataHit objects that meet the filter implementation's match criteria.

applyFilter(Collection<MetaDataHit>) - Method in class org.apache.ctakes.dictionary.lookup.filter.TruncateCollectionFilterImpl

Implementation

ApproximateMath - Class in org.apache.ctakes.utils.wiki

ApproximateMath() - Constructor for class org.apache.ctakes.utils.wiki.ApproximateMath

ApproximateSimilarity - Class in org.apache.ctakes.utils.wiki

ApproximateSimilarity() - Constructor for class org.apache.ctakes.utils.wiki.ApproximateSimilarity

arg1begin - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments

arg1end - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments

arg2begin - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments

arg2end - Variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments

ArgumentInfo - Class in org.apache.ctakes.assertion.cr

Information about a relation argument.

ArgumentInfo(String, String) - Constructor for class org.apache.ctakes.assertion.cr.ArgumentInfo

ArgumentInfo - Class in org.apache.ctakes.relationextractor.knowtator

Information about a relation argument.

ArgumentInfo(String, String) - Constructor for class org.apache.ctakes.relationextractor.knowtator.ArgumentInfo

ArgumentOrderFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features

Features that indicate the order of the arguments (e.g.

ArgumentOrderFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.ArgumentOrderFeatureExtractor

ASNEEDED - Static variable in class org.apache.ctakes.drugner.elements.FrequencyUnitElement

AspectualTextRelation - Class in org.apache.ctakes.typesystem.type.relation

A UMLS relation between clinical elements.

AspectualTextRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation

Never called.

AspectualTextRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation

Internal - constructor used by generator

AspectualTextRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation

AspectualTextRelation_Type - Class in org.apache.ctakes.typesystem.type.relation

A UMLS relation between clinical elements.

AspectualTextRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AspectualTextRelation_Type

initialize variables to correspond with Cas Type and Features

asqrt(int) - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath

asqrt(double) - Static method in class org.apache.ctakes.utils.wiki.ApproximateMath

Assertion - Class in org.apache.ctakes.assertion.medfacts.types

Updated by JCasGen Tue Apr 09 12:44:13 EDT 2013 XML source: trunk/ctakes-assertion-res/src/main/resources/org/apache/ctakes/assertion/types/TypeSystem.xml

Assertion() - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion

Never called.

Assertion(int, TOP_Type) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion

Internal - constructor used by generator

Assertion(JCas) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion

Assertion(JCas, int, int) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion

Assertion_Type - Class in org.apache.ctakes.assertion.medfacts.types

Updated by JCasGen Tue Apr 09 12:44:13 EDT 2013

Assertion_Type(JCas, Type) - Constructor for class org.apache.ctakes.assertion.medfacts.types.Assertion_Type

initialize variables to correspond with Cas Type and Features

AssertionAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts

AssertionAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine

AssertionCleartkAnalysisEngine - Class in org.apache.ctakes.assertion.medfacts.cleartk

AssertionCleartkAnalysisEngine() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine

AssertionComponents - Class in org.apache.ctakes.assertion.medfacts.cleartk

Copyright (c) 2010, Regents of the University of Colorado
All rights reserved.

AssertionComponents() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.AssertionComponents

AssertionCuePhraseAnnotation - Class in org.apache.ctakes.typesystem.type.temporary.assertion

A cue phrase indicating potential negation, uncertainty, or conditional Updated by JCasGen Tue Apr 09 12:44:04 EDT 2013 XML source: trunk/ctakes-pad-term-spotter-res/src/main/resources/org/apache/ctakes/padtermspotter/types/TypeSystem.xml

AssertionCuePhraseAnnotation() - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation

Never called.

AssertionCuePhraseAnnotation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation

Internal - constructor used by generator

AssertionCuePhraseAnnotation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation

AssertionCuePhraseAnnotation(JCas, int, int) - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation

AssertionCuePhraseAnnotation_Type - Class in org.apache.ctakes.typesystem.type.temporary.assertion

A cue phrase indicating potential negation, uncertainty, or conditional Updated by JCasGen Tue Apr 09 12:44:04 EDT 2013

AssertionCuePhraseAnnotation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation_Type

initialize variables to correspond with Cas Type and Features

AssertionCuePhraseConsumerImpl - Class in org.apache.ctakes.dictionary.lookup.ae

Implementation that takes Rxnorm dictionary lookup hits and stores only the ones that are also present in the Orange Book.

AssertionCuePhraseConsumerImpl(UimaContext, Properties, int) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl

AssertionCuePhraseConsumerImpl(UimaContext, Properties) - Constructor for class org.apache.ctakes.dictionary.lookup.ae.AssertionCuePhraseConsumerImpl

assertionDecoderConfiguration - Variable in class org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine

AssertionEvaluation - Class in org.apache.ctakes.assertion.eval

AssertionEvaluation(File, File, ArrayList<String>, Class<? extends AssertionCleartkAnalysisEngine>, Class<? extends DataWriterFactory<String>>, String...) - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation

AssertionEvaluation.HashableAnnotation - Class in org.apache.ctakes.assertion.eval

AssertionEvaluation.HashableAnnotation(int, int) - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation

AssertionEvaluation.HashableAnnotation(Annotation) - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.HashableAnnotation

AssertionEvaluation.OnlyGoldAssertions - Class in org.apache.ctakes.assertion.eval

Class that copies the manual Modifier annotations to the default CAS.

AssertionEvaluation.OnlyGoldAssertions() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.OnlyGoldAssertions

AssertionEvaluation.Options - Class in org.apache.ctakes.assertion.eval

AssertionEvaluation.Options() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.Options

AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer - Class in org.apache.ctakes.assertion.eval

Class that copies the manual Modifier annotations to the default CAS.

AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer

AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier - Class in org.apache.ctakes.assertion.eval

Class that copies the manual Modifier annotations to the default CAS.

AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier

AssertionEvaluation.ReferenceSupportingAnnotationsSystemToGoldCopier - Class in org.apache.ctakes.assertion.eval

Class that copies the manual Modifier annotations to the default CAS.

AssertionEvaluation.ReferenceSupportingAnnotationsSystemToGoldCopier() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReferenceSupportingAnnotationsSystemToGoldCopier

AssertionEvaluation.ReplaceCTakesEntityMentionsAndModifiersWithGold - Class in org.apache.ctakes.assertion.eval

Annotator that removes cTAKES EntityMentions and Modifiers from the system view, and copies over the manually annotated EntityMentions and Modifiers from the gold view.

AssertionEvaluation.ReplaceCTakesEntityMentionsAndModifiersWithGold() - Constructor for class org.apache.ctakes.assertion.eval.AssertionEvaluation.ReplaceCTakesEntityMentionsAndModifiersWithGold

AssertionSampleFeatureGenerator - Class in org.apache.ctakes.assertion.medfacts.cleartk

AssertionSampleFeatureGenerator() - Constructor for class org.apache.ctakes.assertion.medfacts.cleartk.AssertionSampleFeatureGenerator

assignPatientLevelSmokingStatus() - Static method in class org.apache.ctakes.smokingstatus.patientLevel.PatientLevelSmokingStatus

performs the patient-level smoking status classification based on document-level classification each patient is assigned only one final smoking status RULE: If exists only U assign U Else if exist N and there is no PCS assign N Else if exist S and there is no PC assign S Else if exist P or C (can be both) If exists either P or C assign P or C respectively Else if exist both P and C If(C freq >= P freq) assign C Else assign P

AssociatedCodeElement - Class in org.apache.ctakes.drugner.elements

AssociatedCodeElement() - Constructor for class org.apache.ctakes.drugner.elements.AssociatedCodeElement

AssociatedCodeElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.AssociatedCodeElement

associatedCodePrimary - Variable in class org.apache.ctakes.drugner.DrugMention

associatedCodeSecondary - Variable in class org.apache.ctakes.drugner.DrugMention

terminology unique identifier (e.g.

AssociatedCodeToken - Class in org.apache.ctakes.drugner.fsm.output.elements

AssociatedCodeToken(int, int) - Constructor for class org.apache.ctakes.drugner.fsm.output.elements.AssociatedCodeToken

AssociatedPrimaryCodeElement - Class in org.apache.ctakes.drugner.elements

AssociatedPrimaryCodeElement() - Constructor for class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement

AssociatedPrimaryCodeElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.AssociatedPrimaryCodeElement

AssociatedSecondaryCodeElement - Class in org.apache.ctakes.drugner.elements

AssociatedSecondaryCodeElement() - Constructor for class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement

AssociatedSecondaryCodeElement(String, int, int) - Constructor for class org.apache.ctakes.drugner.elements.AssociatedSecondaryCodeElement

astPatt - Variable in class org.apache.ctakes.assertion.cr.I2B2Challenge2010CollectionReader

ATTR_BODYLATERALITY_DISTAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYLATERALITY_DORSAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYLATERALITY_INFERIOR - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYLATERALITY_LATERAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYLATERALITY_MEDIAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYLATERALITY_PROXIMAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYLATERALITY_SUPERIOR - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYLATERALITY_UNMARKED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYLATERALITY_VENTRAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYSIDE_BILATERAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYSIDE_LEFT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYSIDE_RIGHT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_BODYSIDE_UNMARKED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_HISTORYOF_INDICATOR_ABSENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_HISTORYOF_INDICATOR_PRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ABNORMAL_TRUE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ABNORMAL_VERYTRUE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_DELTAFLAG_CHANGEDOWN - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_DELTAFLAG_CHANGEUP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_DELTAFLAG_NOCHANGE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ESTIMATED_FLAG_FALSE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ESTIMATED_FLAG_TRUE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_1ORMORE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_2ORMORE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_3ORMORE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_4ORMORE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_ANTICOMPLEMENTARYPRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_CYTOTOXICPRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_DETECTED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_INTERMEDIATE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_INTERMEDIATERESISTANCE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_MODERATELYSUSCEPTIBLE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_NEGATIVE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_NO_OR_NA_RANGE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_NORMAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_NOTDETECTED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_POSITIVE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_QUALITYCONTROLFAIL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_REACTIVE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_RESISTANT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_SMALL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_SUSCEPTIBLE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_TRACE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_VERYSUSCEPTIBLE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_LAB_ORDINAL_WEAKLY_REACTIVE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ALLERGY_INDICATOR_ABSENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ALLERGY_INDICATOR_PRESENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_DOSAGE_1 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_DOSAGE_2 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_DOSAGE_3 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_DOSAGE_4 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_DOSAGE_5 - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_DOSAGE_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_DOSAGE_UNDETERMINED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_AEROSOL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_CAPSULE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_CREAM - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_ELIXIR - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_EMULSION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_ENEMA - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_GEL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_IMPLANT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_INHALANT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_INJECTION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_LIQUID - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_LOTION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_LOZENGE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_OINTMENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_PATCH - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_PELLET - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_PILL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_POWDER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_SHAMPOO - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_SOAP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_SOLUTION - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_SPRAY - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_SUPPOSITORY - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_SYRUP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_FORM_TABLET - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_ENTERAL_GASTRIC - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_ENTERAL_ORAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_ENTERAL_RECTAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAARTERIAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_PARENTERAL_INTRACARDIAC - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAMUSCULAR - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAPERIOTONEAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_PARENTERAL_INTRATHECAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_PARENTERAL_INTRAVENOUS - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_PARENTERAL_SUBCUTANEOUS - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_PARENTERAL_TRANSDERMAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_PARENTERAL_TRANSMUCOSAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_TOPICAL - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_ROUTE_UNDETERMINED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_STATUSCHANGE_DECREASE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_STATUSCHANGE_INCREASE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_STATUSCHANGE_NOCHANGE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_STATUSCHANGE_START - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_MEDICATION_STATUSCHANGE_STOP - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_SEVERITY_MODERATE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_SEVERITY_SEVERE - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_SEVERITY_SLIGHT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_SEVERITY_UNMARKED - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_SUBJECT_DONOR_FAMILY_MEMBER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_SUBJECT_DONOR_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_SUBJECT_FAMILY_MEMBER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_SUBJECT_OTHER - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

ATTR_SUBJECT_PATIENT - Static variable in class org.apache.ctakes.typesystem.type.constants.CONST

attrHeadings - Static variable in class org.apache.ctakes.assertion.cr.XMLReader

Attribute - Class in org.apache.ctakes.typesystem.type.refsem

The semantic encapsulation of a modifer.

Attribute() - Constructor for class org.apache.ctakes.typesystem.type.refsem.Attribute

Never called.

Attribute(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Attribute

Internal - constructor used by generator

Attribute(JCas) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Attribute

Attribute_Type - Class in org.apache.ctakes.typesystem.type.refsem

The semantic encapsulation of a modifer.

Attribute_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.refsem.Attribute_Type

initialize variables to correspond with Cas Type and Features

AttributeCalculator - Class in org.apache.ctakes.coreference.util

AttributeCalculator(JCas) - Constructor for class org.apache.ctakes.coreference.util.AttributeCalculator

AttributeRelation - Class in org.apache.ctakes.typesystem.type.relation

A real-world relationship between an Element and an Attribute.

AttributeRelation() - Constructor for class org.apache.ctakes.typesystem.type.relation.AttributeRelation

Never called.

AttributeRelation(int, TOP_Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AttributeRelation

Internal - constructor used by generator

AttributeRelation(JCas) - Constructor for class org.apache.ctakes.typesystem.type.relation.AttributeRelation

AttributeRelation_Type - Class in org.apache.ctakes.typesystem.type.relation

A real-world relationship between an Element and an Attribute.

AttributeRelation_Type(JCas, Type) - Constructor for class org.apache.ctakes.typesystem.type.relation.AttributeRelation_Type

initialize variables to correspond with Cas Type and Features

attributes - Variable in class org.apache.ctakes.utils.xcas_comparison.XcasAnnotation

ATTRIBUTES_TO_IGNORE - Static variable in class org.apache.ctakes.utils.xcas_comparison.Const

AttributeValue - Class in org.apache.ctakes.smokingstatus.type.libsvm

Updated by JCasGen Tue Apr 09 12:43:45 EDT 2013 XML source: trunk/ctakes-smoking-status-res/src/main/resources/org/apache/ctakes/smokingstatus/types/TypeSystem.xml

AttributeValue() - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue

Never called.

AttributeValue(int, TOP_Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue

Internal - constructor used by generator

AttributeValue(JCas) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue

AttributeValue(JCas, int, int) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue

AttributeValue_Type - Class in org.apache.ctakes.smokingstatus.type.libsvm

Updated by JCasGen Tue Apr 09 12:43:45 EDT 2013

AttributeValue_Type(JCas, Type) - Constructor for class org.apache.ctakes.smokingstatus.type.libsvm.AttributeValue_Type

initialize variables to correspond with Cas Type and Features