Index (Apache cTAKES Relation Extractor 4.0.0 API)

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

A

AddPotentialRelations() - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.AddPotentialRelations
addVectors(List<Double>, List<Double>) - Method in class org.apache.ctakes.relationextractor.ae.features.EmbeddingFeatureExtractor: Add two vectors.
ALLFILELOC - Variable in class org.apache.ctakes.relationextractor.data.Splitter
ANAFORA_ANNOTATIONS_DIR - Static variable in class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline
AnatomicalSiteListExtractorPipeline - Class in org.apache.ctakes.relationextractor.metastasis: Pipeline for detecting very simple lists of anatomical sites.
AnatomicalSiteListExtractorPipeline() - Constructor for class org.apache.ctakes.relationextractor.metastasis.AnatomicalSiteListExtractorPipeline
AnatomicalSiteListExtractorPipeline.ListAndConjunctionAe - Class in org.apache.ctakes.relationextractor.metastasis: Implements a finate state machine for detecting extremely simple lists and conjunctions of anatomical sites.
AnatomicalSiteListExtractorPipeline.ListAndConjunctionAe.State - Enum in org.apache.ctakes.relationextractor.metastasis
ANNOTATOR_CLASSES - Static variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
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.relationextractor.knowtator: Information about a relation argument.
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

B

Baseline1DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotated degree_of relation in sentences containing a single entity mention of a valid degree_of type and a single modifier.
Baseline1DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline1DegreeOfRelationExtractorAnnotator
Baseline1EntityMentionPairRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotate location_of relation between two entities in sentences containing exactly two entities (where the entities are of the correct types).
Baseline1EntityMentionPairRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline1EntityMentionPairRelationExtractorAnnotator
Baseline2DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotated degree_of relation between two entities in sentences with multiple modifiers (arg2) and a single legitimate degree_of arg1 (i.e.
Baseline2DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline2DegreeOfRelationExtractorAnnotator
Baseline2EntityMentionPairRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotate location_of relation between two entities in sentences with multiple anatomical sites and a single legitimate location_of arg2.
Baseline2EntityMentionPairRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline2EntityMentionPairRelationExtractorAnnotator
Baseline3DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: This baseline links each modifier with the closest entity of a type that's suitable for degree_of, as long as there is no intervening modifier.
Baseline3DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
Baseline3EntityMentionPairRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: This baseline links each anatomical site with the closest entity of a type that's suitable for location_of, as long as there is no intervening anatomical site.
Baseline3EntityMentionPairRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
Baseline4DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotate degree_of relation between two entities whenever they are enclosed within the same noun phrse.
Baseline4DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline4DegreeOfRelationExtractorAnnotator
Baseline4EntityMentionPairRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae.baselines: Annotate location_of relation between two entities whenever they are enclosed within the same noun phrse.
Baseline4EntityMentionPairRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Baseline4EntityMentionPairRelationExtractorAnnotator
BEST_PARAMETERS - Static variable in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
BEST_PARAMETERS - Static variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation

C

Callback() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.Utils.Callback
CategoricalDistribution - Class in org.apache.ctakes.relationextractor.data: Class for generating samples from a three dimensional Categorical distribution.
category - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
category_frequency - Static variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
CausesBringsAboutRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae: Identifies causes/brings_about relation.
CausesBringsAboutRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1DegreeOfRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1EntityMentionPairRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2DegreeOfRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2EntityMentionPairRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline4EntityMentionPairRelationExtractorAnnotator
classify(List<Feature>) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Predict an outcome given a set of features.
classifyBothDirections - Variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
clearCategoryFrequency() - Static method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
coin - Variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
collectionProcessComplete() - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
collectionProcessComplete() - Method in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
compareTo(RelationExtractorEvaluation.HashableArguments) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
computeCosineSimilarity(List<Double>, List<Double>) - Method in class org.apache.ctakes.relationextractor.ae.features.EmbeddingFeatureExtractor: Compute cosine similarity between two vectors.
configurationParameters - Variable in class org.apache.ctakes.relationextractor.eval.ParameterSettings
Constants - Class in org.apache.ctakes.relationextractor.data: Various global settings.
Constants() - Constructor for class org.apache.ctakes.relationextractor.data.Constants
CopyDocumentTextToGoldView() - Constructor for class org.apache.ctakes.relationextractor.eval.SHARPXMI.CopyDocumentTextToGoldView
createDirectories() - Method in class org.apache.ctakes.relationextractor.data.Splitter
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.ManifestationOfRelationExtractorAnnotator
createRelation(JCas, IdentifiedAnnotation, IdentifiedAnnotation, String) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Create a UIMA relation type based on arguments and the relation label.

D

dataWriterClass - Variable in class org.apache.ctakes.relationextractor.eval.ParameterSettings
DegreeOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae: Identifies Degree_Of relations between EventMentions and Modifiers.
DegreeOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
DependencyParseUtils - Class in org.apache.ctakes.relationextractor.ae.features
DependencyParseUtils() - Constructor for class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils
DependencyPathFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
DependencyPathFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.DependencyPathFeaturesExtractor
DependencyTreeFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
DependencyTreeFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.DependencyTreeFeaturesExtractor
DEVLOC - Variable in class org.apache.ctakes.relationextractor.data.Splitter
displayContext - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorConsumer
displayEntities - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorConsumer
DocumentIDAnnotator() - Constructor for class org.apache.ctakes.relationextractor.eval.SHARPXMI.DocumentIDAnnotator
dumpDependencyRelations(JCas, Annotation) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils

E

EmbeddingFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Word embedding based features.
EmbeddingFeatureExtractor(Map<String, List<Double>>) - Constructor for class org.apache.ctakes.relationextractor.ae.features.EmbeddingFeatureExtractor
embeddingPath - Static variable in class org.apache.ctakes.relationextractor.data.analysis.Utils
end - Variable in class org.apache.ctakes.relationextractor.knowtator.Span
entityMentionCount - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
entityMentionPairCount - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
entityMentionPairTypes - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
EntitySpanFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Features that indicate whether both arguments are contained within an NP.
EntitySpanFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.EntitySpanFeatureExtractor
equals(Object) - Method in class org.apache.ctakes.relationextractor.eval.ParameterSettings
equals(Object) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
equals(Object) - Method in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
equals(Object) - Method in class org.apache.ctakes.relationextractor.knowtator.Span
evaluate(SHARPXMI.EvaluationOptions, ParameterSettings, List<ParameterSettings>, Function<ParameterSettings, T>) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
Evaluation_ImplBase(File) - Constructor for class org.apache.ctakes.relationextractor.eval.SHARPXMI.Evaluation_ImplBase
EventAndEntityViewer - Class in org.apache.ctakes.relationextractor.data.analysis: Print gold entities and events (potential relation arguments).
EventAndEntityViewer() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.EventAndEntityViewer
EventAndEntityViewer.RelationContextPrinter - Class in org.apache.ctakes.relationextractor.data.analysis: Print gold standard entities and events.
expandEvent - Static variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
expandToNP(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.ae.IdentifiedAnnotationExpander
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.ArgumentOrderFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.DependencyPathFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.DependencyTreeFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.EmbeddingFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.EntitySpanFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.FlatTreeFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PETFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PhraseChunkingExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PrepositionFeatureExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.PunctuationFeatureExtractor
extract(JCas, T1, T2) - Method in interface org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor: Extract features for the pair of named entity mentions.
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor
extract(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.features.TreeFragmentFeatureExtractor
extract(JCas, IdentifiedAnnotation, IDictionary) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetFeatureExtractor
extractForNode(JCas, IdentifiedAnnotation, String) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyTreeFeaturesExtractor

F

findAnnotationHead(JCas, Annotation) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils: Finds the head word within a given annotation span
FlatTreeFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features
FlatTreeFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.FlatTreeFeatureExtractor

G

generateXMI(SHARPXMI.Options) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getAllowSmallerSystemArguments() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getAllTextFiles(File) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getArg1() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair
getArg2() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair
getBatchesDirectory() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.Options
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1EntityMentionPairRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2EntityMentionPairRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline4DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline4EntityMentionPairRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.ManifestationOfRelationExtractorAnnotator
getCandidateRelationArgumentPairs(JCas, Annotation) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Selects the relevant mentions/annotations within a covering annotation for relation identification/extraction.
getClassWeights() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getCollectionReader(File) - Static method in class org.apache.ctakes.relationextractor.data.analysis.Utils: Instantiate an XMI collection reader.
getCollectionReader(List<File>) - Method in class org.apache.ctakes.relationextractor.eval.SHARPXMI.Evaluation_ImplBase
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline1EntityMentionPairRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2DegreeOfRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline2EntityMentionPairRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3DegreeOfRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline3EntityMentionPairRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.baselines.Baseline4EntityMentionPairRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.ManifestationOfRelationExtractorAnnotator
getCoveringClass() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
getCustomizedDictionary(String) - Static method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer: Read comma separate file containing target CUIs.
getDescription(Object...) - Static method in class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
getDescription() - Static method in class org.apache.ctakes.relationextractor.metastasis.MetastasisAnaforaXMLReader
getDevTextFiles(File) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getDictionary() - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: Initialize WordNet dictionary.
getDistance(JCas, RelationExtractorAnnotator.IdentifiedAnnotationPair) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Calculate the distance (in tokens) between two identified annotations.
getEnclosingNP(JCas, IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.ae.IdentifiedAnnotationExpander
getEntityMentions(Document) - Static method in class org.apache.ctakes.relationextractor.knowtator.XMLReader: Get spans of named entity annotations indexed on knowtator mention id
getEntityStats(String) - Static method in class org.apache.ctakes.relationextractor.data.Stats
getEntityTypes(Document) - Static method in class org.apache.ctakes.relationextractor.knowtator.XMLReader: Type of each named entity indexed on mention ids
getEvaluteOn() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluationOptions
getExpandEvents() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getFeatureExtractors() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Defines the list of feature extractors used by the classifier.
getGenerateXMI() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.Options
getGridSearch() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluationOptions
getHeadWord(String) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: A simple way to get the head word of a phrase.
getHyperHypernyms(IDictionary, String, String, boolean) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils
getHypernyms(IDictionary, String, String, boolean) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: Retrieve a set of hypernyms for a word.
getIgnoreImpossibleGoldRelations() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getLastWord(JCas, Annotation) - Static method in class org.apache.ctakes.relationextractor.data.analysis.Utils: Given an annotation, retrieve its last word.
getNext(JCas) - Method in class org.apache.ctakes.relationextractor.eval.XMIReader
getNextState(JCas, AnatomicalSiteListExtractorPipeline.ListAndConjunctionAe.State, BaseToken) - Method in class org.apache.ctakes.relationextractor.metastasis.AnatomicalSiteListExtractorPipeline.ListAndConjunctionAe
getNounPhrases(JCas, Sentence) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Get all noun phrases in a sentence.
getOntologyConceptCodes(IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer: Get the CUIs, RxNorm codes specified for this entity.
getPathBetweenNodes(ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils: Finds the path between two dependency nodes
getPathsToCommonAncestor(ConllDependencyNode, ConllDependencyNode) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils: Returns the paths from each node to the common ancestor between them
getPathToSentenceHead(ConllDependencyNode) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils
getPrintErrors() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getProgress() - Method in class org.apache.ctakes.relationextractor.eval.XMIReader
getRelationCategory(Map<List<Annotation>, BinaryTextRelation>, IdentifiedAnnotation, IdentifiedAnnotation) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator: Looks up the arguments in the specified lookup table and converts the relation into a label for classification
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.CausesBringsAboutRelationExtractorAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.ManifestationOfRelationExtractorAnnotator
getRelationClass() - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
getRelations() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getRelations(Document) - Static method in class org.apache.ctakes.relationextractor.knowtator.XMLReader
getRelationStats(String) - Static method in class org.apache.ctakes.relationextractor.data.Stats
getResult() - Method in class org.apache.ctakes.relationextractor.data.analysis.Utils.Callback
getSemanticType(JCas, BaseToken) - Method in class org.apache.ctakes.relationextractor.metastasis.AnatomicalSiteListExtractorPipeline.ListAndConjunctionAe
getStems(String, String, IDictionary) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: Get a list of possible stems.
getSynonyms(IDictionary, String, String, boolean) - Static method in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils: Retrieve a set of synonyms for a word.
getTestOnCTakes() - Method in interface org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.Options
getTestTextFiles(File) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getTestXmiDir() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluationOptions
getTokenDistance(JCas, IdentifiedAnnotation, IdentifiedAnnotation) - Static method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
getTrainTextFiles(File) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
getTrainXmiDir() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluationOptions
getXMIDirectory() - Method in interface org.apache.ctakes.relationextractor.eval.SHARPXMI.Options
getXMIWritingPreprocessorAggregateBuilder() - Static method in class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.relationextractor.eval.SHARPXMI
GOLD_VIEW_NAME - Static variable in class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline
GoldAnnotationAnalysisPipeline - Class in org.apache.ctakes.relationextractor.data: Pipeline for analyzing gold annotations.
GoldAnnotationAnalysisPipeline() - Constructor for class org.apache.ctakes.relationextractor.data.GoldAnnotationAnalysisPipeline
GoldAnnotationAnalysisPipeline.Options - Class in org.apache.ctakes.relationextractor.data
GoldAnnotationStatsCalculator - Class in org.apache.ctakes.relationextractor.data: Count various stats such as token and relation counts based on the gold standard data.
GoldAnnotationStatsCalculator() - Constructor for class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
GoldRelationViewer - Class in org.apache.ctakes.relationextractor.data.analysis: Print gold standard relations and their context.
GoldRelationViewer() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer
GoldRelationViewer.RelationContextPrinter - Class in org.apache.ctakes.relationextractor.data.analysis: Print gold standard relations and their context.
goldViewName - Static variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator

H

HashableArguments(int, int, int, int) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
HashableArguments(Annotation, Annotation) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
HashableArguments(BinaryTextRelation) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
hashCode() - Method in class org.apache.ctakes.relationextractor.eval.ParameterSettings
hashCode() - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
hashCode() - Method in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
hashCode() - Method in class org.apache.ctakes.relationextractor.knowtator.Span
hasNext() - Method in class org.apache.ctakes.relationextractor.eval.XMIReader

I

id1 - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
id2 - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
IdentifiedAnnotationExpander - Class in org.apache.ctakes.relationextractor.ae
IdentifiedAnnotationExpander() - Constructor for class org.apache.ctakes.relationextractor.ae.IdentifiedAnnotationExpander
IdentifiedAnnotationPair(IdentifiedAnnotation, IdentifiedAnnotation) - Constructor for class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.eval.XMIReader
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline.XMIWriter
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.RelationExtractorPrinter
initialize(UimaContext) - Method in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
inputDirectory - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationAnalysisPipeline.Options
inputDirectory - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer.Options
inputDirectory - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline.Options
inputDirectory - Variable in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.Options
isEnclosed(RelationExtractorAnnotator.IdentifiedAnnotationPair, TreebankNode) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Is this pair of entities enclosed inside a noun phrase?

L

ListAndConjunctionAe() - Constructor for class org.apache.ctakes.relationextractor.metastasis.AnatomicalSiteListExtractorPipeline.ListAndConjunctionAe
LocationOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae: Identifies Location_Of relations between EventMentions and AnatomicalSiteMentions.
LocationOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.LocationOfRelationExtractorAnnotator

M

main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.analysis.EventAndEntityViewer
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.analysis.Utils
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.GoldAnnotationAnalysisPipeline
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.Splitter
main(String[]) - Static method in class org.apache.ctakes.relationextractor.data.Stats
main(String[]) - Static method in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
main(String[]) - Static method in class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics
main(String[]) - Static method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
main(String[]) - Static method in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
main(String[]) - Static method in class org.apache.ctakes.relationextractor.metastasis.AnatomicalSiteListExtractorPipeline
main(String[]) - Static method in class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipelineSingleCas
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorTrain
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer
main(String[]) - Static method in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
ManagesTreatsRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae: Identifies manages/treats relation.
ManagesTreatsRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.ManagesTreatsRelationExtractorAnnotator
ManifestationOfRelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae: Identifies manifestation_of relation.
ManifestationOfRelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.ManifestationOfRelationExtractorAnnotator
MetastasisAnaforaXMLReader - Class in org.apache.ctakes.relationextractor.metastasis
MetastasisAnaforaXMLReader() - Constructor for class org.apache.ctakes.relationextractor.metastasis.MetastasisAnaforaXMLReader
MetastasisXmiGenerationPipeline - Class in org.apache.ctakes.relationextractor.metastasis
MetastasisXmiGenerationPipeline() - Constructor for class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline
MetastasisXmiGenerationPipeline.UriToDocumentTextAnnotatorCtakes - Class in org.apache.ctakes.relationextractor.metastasis
MetastasisXmiGenerationPipeline.XMIWriter - Class in org.apache.ctakes.relationextractor.metastasis
mipacDevXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
mipacqAllXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
mipacqTestXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
mipacqTrainXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
ModifierExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae
ModifierExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
ModifierExtractorEvaluation - Class in org.apache.ctakes.relationextractor.eval
ModifierExtractorEvaluation(File, ParameterSettings) - Constructor for class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
ModifierExtractorEvaluation.OnlyGoldModifiers - Class in org.apache.ctakes.relationextractor.eval: Class that copies the manual Modifier annotations to the default CAS.

N

NamedEntityFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
NamedEntityFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.NamedEntityFeaturesExtractor
NO_RELATION_CATEGORY - Static variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator

O

OnlyGoldModifiers() - Constructor for class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation.OnlyGoldModifiers
Options() - Constructor for class org.apache.ctakes.relationextractor.data.GoldAnnotationAnalysisPipeline.Options
Options() - Constructor for class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics.Options
Options() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer.Options
Options() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline.Options
Options() - Constructor for class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.Options
org.apache.ctakes.relationextractor.ae - package org.apache.ctakes.relationextractor.ae
org.apache.ctakes.relationextractor.ae.baselines - package org.apache.ctakes.relationextractor.ae.baselines
org.apache.ctakes.relationextractor.ae.features - package org.apache.ctakes.relationextractor.ae.features
org.apache.ctakes.relationextractor.data - package org.apache.ctakes.relationextractor.data
org.apache.ctakes.relationextractor.data.analysis - package org.apache.ctakes.relationextractor.data.analysis
org.apache.ctakes.relationextractor.eval - package org.apache.ctakes.relationextractor.eval
org.apache.ctakes.relationextractor.knowtator - package org.apache.ctakes.relationextractor.knowtator
org.apache.ctakes.relationextractor.metastasis - package org.apache.ctakes.relationextractor.metastasis
org.apache.ctakes.relationextractor.pipelines - package org.apache.ctakes.relationextractor.pipelines
OUTCOME1 - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
OUTCOME2 - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
OUTCOME3 - Variable in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
outputDirectory - Variable in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline.Options

P

PARAM_CLASSIFY_BOTH_DIRECTIONS - Static variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
PARAM_FILES - Static variable in class org.apache.ctakes.relationextractor.eval.XMIReader
PARAM_OUTFILE - Static variable in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE - Static variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
PARAM_XMI_DIRECTORY - Static variable in class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline.XMIWriter
ParameterSettings - Class in org.apache.ctakes.relationextractor.eval: Holds a set of parameters for a relation extraction model
ParameterSettings(Class<? extends DataWriter<String>>, Object[], String[]) - Constructor for class org.apache.ctakes.relationextractor.eval.ParameterSettings
ParameterSettings(Class<? extends DataWriter<String>>, String[]) - Constructor for class org.apache.ctakes.relationextractor.eval.ParameterSettings
PartOfSpeechFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
PartOfSpeechFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor
pathToString(LinkedList<ConllDependencyNode>) - Static method in class org.apache.ctakes.relationextractor.ae.features.DependencyParseUtils: This will convert a path into a string lexicalized at the end points with arc labels and POS tags in between
PETFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features
PETFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PETFeatureExtractor
PhraseChunkingExtractor - Class in org.apache.ctakes.relationextractor.ae.features
PhraseChunkingExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PhraseChunkingExtractor
PrepositionFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Features that indicate whether there is a preposition between the two arguments.
PrepositionFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PrepositionFeatureExtractor
PrintRelationStatistics - Class in org.apache.ctakes.relationextractor.eval
PrintRelationStatistics() - Constructor for class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics
PrintRelationStatistics.Options - Class in org.apache.ctakes.relationextractor.eval
probabilityOfKeepingANegativeExample - Variable in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
process(JCas) - Method in class org.apache.ctakes.relationextractor.ae.IdentifiedAnnotationExpander
process(JCas) - Method in class org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator
process(JCas) - Method in class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
process(JCas) - Method in class org.apache.ctakes.relationextractor.data.analysis.EventAndEntityViewer.RelationContextPrinter
process(JCas) - Method in class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer.RelationContextPrinter
process(JCas) - Method in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation.OnlyGoldModifiers
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.AddPotentialRelations
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.RemoveCTakesMentionsAndCopyGoldRelations
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.RemoveSmallerEventMentions
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.ReplaceCTakesMentionsWithGoldMentions
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.SHARPXMI.CopyDocumentTextToGoldView
process(JCas) - Method in class org.apache.ctakes.relationextractor.eval.SHARPXMI.DocumentIDAnnotator
process(JCas) - Method in class org.apache.ctakes.relationextractor.metastasis.AnatomicalSiteListExtractorPipeline.ListAndConjunctionAe
process(JCas) - Method in class org.apache.ctakes.relationextractor.metastasis.MetastasisAnaforaXMLReader
process(JCas) - Method in class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline.UriToDocumentTextAnnotatorCtakes
process(JCas) - Method in class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline.XMIWriter
process(JCas) - Method in class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer.RelationExtractorPrinter
process(JCas) - Method in class org.apache.ctakes.relationextractor.pipelines.RelationExtractorConsumer
process(JCas) - Method in class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.RelationExtractorPrinter
process(JCas) - Method in class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
processLine(String) - Method in class org.apache.ctakes.relationextractor.data.analysis.Utils.Callback
PunctuationFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Features that capture punctuation marks between the two arguments.
PunctuationFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.PunctuationFeatureExtractor

R

readOnlySharpRelations - Static variable in class org.apache.ctakes.relationextractor.data.Stats
RELATION_CLASSES - Static variable in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
RelationAnnotationViewer - Class in org.apache.ctakes.relationextractor.pipelines: View the annotations obtained by running the relation extractor on clinical notes.
RelationAnnotationViewer() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer
RelationAnnotationViewer.Options - Class in org.apache.ctakes.relationextractor.pipelines
RelationAnnotationViewer.RelationExtractorPrinter - Class in org.apache.ctakes.relationextractor.pipelines
relationArgumentDistance - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
RelationContextPrinter() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.EventAndEntityViewer.RelationContextPrinter
RelationContextPrinter() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.GoldRelationViewer.RelationContextPrinter
RelationExtractorAnnotator - Class in org.apache.ctakes.relationextractor.ae
RelationExtractorAnnotator() - Constructor for class org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator
RelationExtractorAnnotator.IdentifiedAnnotationPair - Class in org.apache.ctakes.relationextractor.ae
RelationExtractorConsumer - Class in org.apache.ctakes.relationextractor.pipelines: This is a sample relation annotation consumer.
RelationExtractorConsumer() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorConsumer
RelationExtractorEvaluation - Class in org.apache.ctakes.relationextractor.eval
RelationExtractorEvaluation(File, Class<? extends BinaryTextRelation>, Class<? extends RelationExtractorAnnotator>, ParameterSettings, boolean, boolean, boolean, boolean, boolean, boolean) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation: An evaluation of a relation extractor.
RelationExtractorEvaluation(File, Class<? extends BinaryTextRelation>, Class<? extends RelationExtractorAnnotator>, ParameterSettings) - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
RelationExtractorEvaluation.AddPotentialRelations - Class in org.apache.ctakes.relationextractor.eval
RelationExtractorEvaluation.HashableArguments - Class in org.apache.ctakes.relationextractor.eval: This class is useful for mapping the spans of relation arguments to the relation's category.
RelationExtractorEvaluation.Options - Interface in org.apache.ctakes.relationextractor.eval
RelationExtractorEvaluation.RemoveCTakesMentionsAndCopyGoldRelations - Class in org.apache.ctakes.relationextractor.eval: Annotator that removes cTAKES mentions in the system view and copies relations from the gold view to the system view
RelationExtractorEvaluation.RemoveSmallerEventMentions - Class in org.apache.ctakes.relationextractor.eval
RelationExtractorEvaluation.ReplaceCTakesMentionsWithGoldMentions - Class in org.apache.ctakes.relationextractor.eval: Annotator that removes cTAKES Mentions and Modifiers from the system view, and copies over the manually annotated Mentions and Modifiers from the gold view.
RelationExtractorPipeline - Class in org.apache.ctakes.relationextractor.pipelines: A simple pipeline that runs relation extraction on all files in a directory and saves the resulting annotations as XMI files.
RelationExtractorPipeline() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipeline
RelationExtractorPipeline.Options - Class in org.apache.ctakes.relationextractor.pipelines
RelationExtractorPipelineSingleCas - Class in org.apache.ctakes.relationextractor.pipelines: Run relation extraction AE on a single sentence.
RelationExtractorPipelineSingleCas() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorPipelineSingleCas
RelationExtractorPrinter() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationAnnotationViewer.RelationExtractorPrinter
RelationExtractorPrinter() - Constructor for class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer.RelationExtractorPrinter
RelationExtractorTrain - Class in org.apache.ctakes.relationextractor.pipelines: This class produces production models for the RelationExtractor module.
RelationExtractorTrain() - Constructor for class org.apache.ctakes.relationextractor.pipelines.RelationExtractorTrain
RelationFeaturesExtractor<T1,T2> - Interface in org.apache.ctakes.relationextractor.ae.features: Define an interface for people to implement feature extractors.
RelationInfo - Class in org.apache.ctakes.relationextractor.knowtator: Information about a relation that includes the info about the relation's arguments.
relationTypes - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
RemoveCTakesMentionsAndCopyGoldRelations() - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.RemoveCTakesMentionsAndCopyGoldRelations
RemoveSmallerEventMentions() - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.RemoveSmallerEventMentions
ReplaceCTakesMentionsWithGoldMentions() - Constructor for class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.ReplaceCTakesMentionsWithGoldMentions
reportStats(HashMap<String, Integer>, int) - Static method in class org.apache.ctakes.relationextractor.data.Stats
role - Variable in class org.apache.ctakes.relationextractor.knowtator.ArgumentInfo
role1 - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
role2 - Variable in class org.apache.ctakes.relationextractor.knowtator.RelationInfo

S

sample() - Method in class org.apache.ctakes.relationextractor.data.CategoricalDistribution
SelectiveRelationAnnotationViewer - Class in org.apache.ctakes.relationextractor.pipelines: View relation instances in xmi files.
SelectiveRelationAnnotationViewer() - Constructor for class org.apache.ctakes.relationextractor.pipelines.SelectiveRelationAnnotationViewer
SelectiveRelationAnnotationViewer.Options - Class in org.apache.ctakes.relationextractor.pipelines
SelectiveRelationAnnotationViewer.RelationExtractorPrinter - Class in org.apache.ctakes.relationextractor.pipelines
sentenceCount - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
shareAllXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
shareDevXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
shareTestXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
shareTrainXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpAllXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpDevXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpRelationsAll - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpRelationsHighPriority - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpRelationsLowPriority - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpRelationsSelected - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpTestXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
sharpTrainXmlPath - Static variable in class org.apache.ctakes.relationextractor.data.Constants
SHARPXMI - Class in org.apache.ctakes.relationextractor.eval
SHARPXMI() - Constructor for class org.apache.ctakes.relationextractor.eval.SHARPXMI
SHARPXMI.CopyDocumentTextToGoldView - Class in org.apache.ctakes.relationextractor.eval
SHARPXMI.DocumentIDAnnotator - Class in org.apache.ctakes.relationextractor.eval
SHARPXMI.EvaluateOn - Enum in org.apache.ctakes.relationextractor.eval
SHARPXMI.Evaluation_ImplBase - Class in org.apache.ctakes.relationextractor.eval
SHARPXMI.EvaluationOptions - Interface in org.apache.ctakes.relationextractor.eval
SHARPXMI.Options - Interface in org.apache.ctakes.relationextractor.eval
Span - Class in org.apache.ctakes.relationextractor.knowtator: Represents span of a named entity
Span(int, int) - Constructor for class org.apache.ctakes.relationextractor.knowtator.Span
split() - Method in class org.apache.ctakes.relationextractor.data.Splitter
Splitter - Class in org.apache.ctakes.relationextractor.data: Randomly split a set of files in a directory into three sets: train, dev, and test.
Splitter(double, double) - Constructor for class org.apache.ctakes.relationextractor.data.Splitter: Specify percentages of the split.
Splitter(int, int, int) - Constructor for class org.apache.ctakes.relationextractor.data.Splitter: Specify the size of each set.
start - Variable in class org.apache.ctakes.relationextractor.knowtator.Span
Stats - Class in org.apache.ctakes.relationextractor.data: Calculate relation frequencies in a data set that consists of XML files exported from Knowtator.
Stats() - Constructor for class org.apache.ctakes.relationextractor.data.Stats
stats - Variable in class org.apache.ctakes.relationextractor.eval.ParameterSettings
systemViewName - Static variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator

T

targetRelationType - Static variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
test(CollectionReader, File) - Method in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
test(CollectionReader, File) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
TESTLOC - Variable in class org.apache.ctakes.relationextractor.data.Splitter
tokenCount - Variable in class org.apache.ctakes.relationextractor.data.GoldAnnotationStatsCalculator
TokenFeaturesExtractor - Class in org.apache.ctakes.relationextractor.ae.features
TokenFeaturesExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor
toString() - Method in class org.apache.ctakes.relationextractor.eval.ParameterSettings
toString() - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments
toString() - Method in class org.apache.ctakes.relationextractor.knowtator.RelationInfo
toString() - Method in class org.apache.ctakes.relationextractor.knowtator.Span
toXMIFiles(SHARPXMI.Options, List<File>) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
train(CollectionReader, File) - Method in class org.apache.ctakes.relationextractor.eval.ModifierExtractorEvaluation
train(CollectionReader, File) - Method in class org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation
trainDirectory - Variable in class org.apache.ctakes.relationextractor.eval.PrintRelationStatistics.Options
trainingArguments - Variable in class org.apache.ctakes.relationextractor.eval.ParameterSettings
TRAINLOC - Variable in class org.apache.ctakes.relationextractor.data.Splitter
TreeFeatureConsumer - Class in org.apache.ctakes.relationextractor.pipelines
TreeFeatureConsumer() - Constructor for class org.apache.ctakes.relationextractor.pipelines.TreeFeatureConsumer
TreeFragmentFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features
TreeFragmentFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.TreeFragmentFeatureExtractor

U

UriToDocumentTextAnnotatorCtakes() - Constructor for class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline.UriToDocumentTextAnnotatorCtakes
Utils - Class in org.apache.ctakes.relationextractor.ae.baselines
Utils() - Constructor for class org.apache.ctakes.relationextractor.ae.baselines.Utils
Utils - Class in org.apache.ctakes.relationextractor.data.analysis: Various useful classes and methods.
Utils() - Constructor for class org.apache.ctakes.relationextractor.data.analysis.Utils
Utils.Callback - Class in org.apache.ctakes.relationextractor.data.analysis: Read word embeddings from file.

V

validate(SHARPXMI.EvaluationOptions) - Static method in class org.apache.ctakes.relationextractor.eval.SHARPXMI
validateDegreeOfArgumentTypes(RelationExtractorAnnotator.IdentifiedAnnotationPair) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Are entity types of the arguments valid for degree_of relation? The following are the valid combinations: degree-of(disease/disorder/2, modifier) degree-of(sign/symptom/3, modifier)
validateLocationOfArgumentTypes(RelationExtractorAnnotator.IdentifiedAnnotationPair) - Static method in class org.apache.ctakes.relationextractor.ae.baselines.Utils: Are entity types of the arguments valid for location_of relation? The following combinations are allowed: location-of(anatomical site/6, disorder/2) location-of(anatomical site/6, sign/symptom/3) location-of(anatomical site/6, procedure/5)
value - Variable in class org.apache.ctakes.relationextractor.knowtator.ArgumentInfo
valueOf(String) - Static method in enum org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluateOn: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.apache.ctakes.relationextractor.metastasis.AnatomicalSiteListExtractorPipeline.ListAndConjunctionAe.State: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.apache.ctakes.relationextractor.eval.SHARPXMI.EvaluateOn: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.apache.ctakes.relationextractor.metastasis.AnatomicalSiteListExtractorPipeline.ListAndConjunctionAe.State: Returns an array containing the constants of this enum type, in the order they are declared.

W

WordNetFeatureExtractor - Class in org.apache.ctakes.relationextractor.ae.features: Features that are based on WordNet.
WordNetFeatureExtractor() - Constructor for class org.apache.ctakes.relationextractor.ae.features.WordNetFeatureExtractor
wordNetPath - Static variable in class org.apache.ctakes.relationextractor.ae.features.WordNetUtils
WordNetUtils - Class in org.apache.ctakes.relationextractor.ae.features: This is a wrapper for the MIT WordNet inteface that simplifies basic operations such as retrieving synonyms and hypernyms for a word.
WordNetUtils() - Constructor for class org.apache.ctakes.relationextractor.ae.features.WordNetUtils

X

XMI_OUTPUT_DIR - Static variable in class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline
XMIReader - Class in org.apache.ctakes.relationextractor.eval: UIMA CollectionReader that reads in CASes from XMI files.
XMIReader() - Constructor for class org.apache.ctakes.relationextractor.eval.XMIReader
XMIWriter() - Constructor for class org.apache.ctakes.relationextractor.metastasis.MetastasisXmiGenerationPipeline.XMIWriter
XMLReader - Class in org.apache.ctakes.relationextractor.knowtator
XMLReader() - Constructor for class org.apache.ctakes.relationextractor.knowtator.XMLReader

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