Index (ClearTK ML 2.0.0 API)

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

A

accept(File, String) - Method in class org.cleartk.util.cr.RegexFileFilter: Checks to see if the filename matches one of the regular expressions.
accept(File) - Method in class org.cleartk.util.cr.UriCollectionReader.RejectSystemDirectories
accept(File, String) - Method in class org.cleartk.util.cr.UriCollectionReader.RejectSystemDirectories
accept(File) - Method in class org.cleartk.util.cr.UriCollectionReader.RejectSystemFiles
accept(File, String) - Method in class org.cleartk.util.cr.UriCollectionReader.RejectSystemFiles
add(double) - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor.MinMaxRunningStat
add(String) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor.IDFMap
add(double) - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat
add(Feature) - Method in class org.cleartk.ml.Instance: Add a feature to the instance.
add(FeatureVector) - Method in class org.cleartk.ml.util.featurevector.FeatureVector
addAll(Collection<Feature>) - Method in class org.cleartk.ml.Instance: Add a collection of features to the instance.
addChild(TreebankNode) - Method in class org.cleartk.util.treebank.TreebankNode
addEncoder(FeatureEncoder<ENCODED_TYPE>) - Method in class org.cleartk.ml.encoder.features.FeatureEncoderChain
addScores - Variable in class org.cleartk.ml.viterbi.ViterbiClassifier
addToBuffer(String) - Method in class org.cleartk.util.InputStreamHandler
AnnotationUtil - Class in org.cleartk.util: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
AnnotationUtil() - Constructor for class org.cleartk.util.AnnotationUtil
AnnotationWriter<ANNOTATION_TYPE extends Annotation> - Interface in org.cleartk.util.ae.linewriter: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
apply(Feature) - Method in class org.cleartk.ml.feature.function.CapitalTypeFeatureFunction: If the value of the feature is a StringValue and is determined to be one of ALL_UPPERCASE, ALL_LOWERCASE, INITIAL_UPPERCASE, or MIXED_CASE, then a new feature containing one of those four values is returned.
apply(Feature) - Method in class org.cleartk.ml.feature.function.CharacterCategoryPatternFunction
apply(Feature) - Method in class org.cleartk.ml.feature.function.CharacterNgramFeatureFunction
apply(Feature) - Method in class org.cleartk.ml.feature.function.ContainsHyphenFeatureFunction
apply(Function<Feature, List<Feature>>, List<Feature>) - Static method in class org.cleartk.ml.feature.function.FeatureFunctionExtractor
apply(Feature) - Method in class org.cleartk.ml.feature.function.LowerCaseFeatureFunction
apply(Feature) - Method in class org.cleartk.ml.feature.function.NumericTypeFeatureFunction: If the value of the feature is a StringValue and is determined to be one of DIGITS, YEAR_DIGITS, ALPHANUMERIC, SOME_DIGITS, or ROMAN_NUMERAL, then a feature containing one of those five values is returned.
apply(Feature) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
apply(Map<OUTCOME_T, Double>) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.CombineScoreMethod.AverageScores
apply(Map<OUTCOME_T, Double>) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.CombineScoreMethod.MaxScores
apply(String) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats.ComputeFeatureScore
ARCH_PPC - Static variable in class org.cleartk.util.PlatformDetection
ARCH_X86_32 - Static variable in class org.cleartk.util.PlatformDetection
ARCH_X86_64 - Static variable in class org.cleartk.util.PlatformDetection
ArrayFeatureVector - Class in org.cleartk.ml.util.featurevector: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
ArrayFeatureVector() - Constructor for class org.cleartk.ml.util.featurevector.ArrayFeatureVector

B

BagEncoder - Class in org.cleartk.ml.encoder.features: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
BagEncoder(String, NameNumberNormalizer) - Constructor for class org.cleartk.ml.encoder.features.BagEncoder
BagEncoder(String) - Constructor for class org.cleartk.ml.encoder.features.BagEncoder
BagEncoder(NameNumberNormalizer) - Constructor for class org.cleartk.ml.encoder.features.BagEncoder
BagEncoder() - Constructor for class org.cleartk.ml.encoder.features.BagEncoder
BaseConversion - Class in org.cleartk.util: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
BaseConversion() - Constructor for class org.cleartk.util.BaseConversion
BiesoChunking<SUB_CHUNK_TYPE extends Annotation,CHUNK_TYPE extends Annotation> - Class in org.cleartk.ml.chunking: Chunking with Begin-Inside-End-Singleton-Outside labels.
BiesoChunking(Class<? extends SUB_CHUNK_TYPE>, Class<? extends CHUNK_TYPE>) - Constructor for class org.cleartk.ml.chunking.BiesoChunking
BiesoChunking(Class<? extends SUB_CHUNK_TYPE>, Class<? extends CHUNK_TYPE>, String) - Constructor for class org.cleartk.ml.chunking.BiesoChunking
BioChunking<SUB_CHUNK_TYPE extends Annotation,CHUNK_TYPE extends Annotation> - Class in org.cleartk.ml.chunking: Chunking with Begin-Inside-Outside labels
Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
BioChunking(Class<? extends SUB_CHUNK_TYPE>, Class<? extends CHUNK_TYPE>) - Constructor for class org.cleartk.ml.chunking.BioChunking
BioChunking(Class<? extends SUB_CHUNK_TYPE>, Class<? extends CHUNK_TYPE>, String) - Constructor for class org.cleartk.ml.chunking.BioChunking
BlankLineBlockWriter - Class in org.cleartk.util.ae.linewriter.block: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
BlankLineBlockWriter() - Constructor for class org.cleartk.util.ae.linewriter.block.BlankLineBlockWriter
BlockWriter<BLOCK_TYPE extends Annotation> - Interface in org.cleartk.util.ae.linewriter: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
BooleanEncoder - Class in org.cleartk.ml.encoder.features: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
BooleanEncoder() - Constructor for class org.cleartk.ml.encoder.features.BooleanEncoder
BooleanToBooleanOutcomeEncoder - Class in org.cleartk.ml.encoder.outcome: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
BooleanToBooleanOutcomeEncoder() - Constructor for class org.cleartk.ml.encoder.outcome.BooleanToBooleanOutcomeEncoder
BooleanToSignOutcomeEncoder - Class in org.cleartk.ml.encoder.outcome: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
BooleanToSignOutcomeEncoder() - Constructor for class org.cleartk.ml.encoder.outcome.BooleanToSignOutcomeEncoder
BooleanToStringOutcomeEncoder - Class in org.cleartk.ml.encoder.outcome: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
BooleanToStringOutcomeEncoder() - Constructor for class org.cleartk.ml.encoder.outcome.BooleanToStringOutcomeEncoder
BuildJar - Class in org.cleartk.ml.jar: Command line tool for building a model jar file from a directory where a model has been trained, e.g.
BuildJar() - Constructor for class org.cleartk.ml.jar.BuildJar

C

CapitalTypeFeatureFunction - Class in org.cleartk.ml.feature.function: Copyright (c) 2007-2012, Regents of the University of Colorado
All rights reserved.
CapitalTypeFeatureFunction() - Constructor for class org.cleartk.ml.feature.function.CapitalTypeFeatureFunction
CapitalTypeFeatureFunction.CapitalType - Enum in org.cleartk.ml.feature.function
CaseUtil - Class in org.cleartk.ml.feature.util: Copyright (c) 2010, Regents of the University of Colorado
All rights reserved.
CaseUtil() - Constructor for class org.cleartk.ml.feature.util.CaseUtil
CentroidTfidfSimilarityExtractor<OUTCOME_T,FOCUS_T extends Annotation> - Class in org.cleartk.ml.feature.transform.extractor: Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
CentroidTfidfSimilarityExtractor(String) - Constructor for class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
CentroidTfidfSimilarityExtractor(String, FeatureExtractor1<FOCUS_T>) - Constructor for class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
CharacterCategoryPatternFunction<T extends Annotation> - Class in org.cleartk.ml.feature.function: A feature extractor that generates a pattern based on the Unicode categories of each of the characters in the annotation text.
CharacterCategoryPatternFunction() - Constructor for class org.cleartk.ml.feature.function.CharacterCategoryPatternFunction: Create the standard feature extractor, where one category is added to the feature value for each character in the text.
CharacterCategoryPatternFunction(CharacterCategoryPatternFunction.PatternType) - Constructor for class org.cleartk.ml.feature.function.CharacterCategoryPatternFunction: Create a feature extractor with the specified pattern type.
CharacterCategoryPatternFunction.PatternType - Enum in org.cleartk.ml.feature.function: The type of pattern to generate in feature values.
CharacterNgramFeatureFunction - Class in org.cleartk.ml.feature.function: Copyright (c) 2007-2012, Regents of the University of Colorado
All rights reserved.
CharacterNgramFeatureFunction(String, CharacterNgramFeatureFunction.Orientation, int, int, int, boolean) - Constructor for class org.cleartk.ml.feature.function.CharacterNgramFeatureFunction: This feature function serves up character n-grams based on StringValued features.
CharacterNgramFeatureFunction(CharacterNgramFeatureFunction.Orientation, int, int, int, boolean) - Constructor for class org.cleartk.ml.feature.function.CharacterNgramFeatureFunction
CharacterNgramFeatureFunction(String, CharacterNgramFeatureFunction.Orientation, int, int) - Constructor for class org.cleartk.ml.feature.function.CharacterNgramFeatureFunction
CharacterNgramFeatureFunction(CharacterNgramFeatureFunction.Orientation, int, int) - Constructor for class org.cleartk.ml.feature.function.CharacterNgramFeatureFunction
CharacterNgramFeatureFunction.Orientation - Enum in org.cleartk.ml.feature.function
checkTypeParameterIsAssignable(Class<T>, String, T, Class<U>, String, U) - Static method in class org.cleartk.util.ReflectionUtil: Checks that the given type parameters of the given objects are compatible.
checkTypeParametersAreEqual(Class<T>, String, T, Class<U>, String, U, Class<E>) - Static method in class org.cleartk.util.ReflectionUtil: Checks that the given type parameters of the given objects are exactly equal.
chunkClass - Variable in class org.cleartk.ml.chunking.Chunking_ImplBase
Chunking<OUTCOME_TYPE,SUB_CHUNK_TYPE extends Annotation,CHUNK_TYPE extends Annotation> - Interface in org.cleartk.ml.chunking: Interface for classes that assemble individual classifier outcomes on smaller annotations ("sub-chunks") to form larger annotations ("chunks").
Chunking_ImplBase<SUB_CHUNK_TYPE extends Annotation,CHUNK_TYPE extends Annotation> - Class in org.cleartk.ml.chunking: Base class for classes that assemble individual classifier outcomes on smaller annotations ("sub-chunks") to form larger annotations ("chunks").
Chunking_ImplBase(Class<? extends SUB_CHUNK_TYPE>, Class<? extends CHUNK_TYPE>, String) - Constructor for class org.cleartk.ml.chunking.Chunking_ImplBase
classConditionalCounts - Variable in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats
classCounts - Variable in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats
Classifier<OUTCOME_TYPE> - Interface in org.cleartk.ml: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
classifier - Variable in class org.cleartk.ml.CleartkAnnotator
classifier - Variable in class org.cleartk.ml.CleartkSequenceAnnotator
Classifier_ImplBase<ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for Classifier implementations that use FeaturesEncoders and OutcomeEncoders.
Classifier_ImplBase(FeaturesEncoder<ENCODED_FEATURES_TYPE>, OutcomeEncoder<OUTCOME_TYPE, ENCODED_OUTCOME_TYPE>) - Constructor for class org.cleartk.ml.jar.Classifier_ImplBase
classifierBuilder - Variable in class org.cleartk.ml.jar.DirectoryDataWriter
ClassifierBuilder_ImplBase<CLASSIFIER_TYPE extends Classifier<OUTCOME_TYPE>,ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for builders which write to a training data file using FeaturesEncoders and OutcomeEncoders, and build and package Classifiers as jar files.
ClassifierBuilder_ImplBase() - Constructor for class org.cleartk.ml.jar.ClassifierBuilder_ImplBase
ClassifierFactory<OUTCOME_TYPE> - Interface in org.cleartk.ml: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
classifierFactory - Variable in class org.cleartk.ml.multi.CleartkMultiAnnotator
classifierJarPathRoot - Variable in class org.cleartk.ml.multi.CleartkMultiAnnotator
classifiers - Variable in class org.cleartk.ml.multi.CleartkMultiAnnotator
classify(List<Feature>) - Method in class org.cleartk.ml.baseline.SingleOutcomeClassifier
classify(List<Feature>) - Method in interface org.cleartk.ml.Classifier: Classifies a list of features.
classify(List<Instance<OUTCOME_TYPE>>) - Method in class org.cleartk.ml.CleartkSequenceAnnotator
classify(List<List<Feature>>) - Method in interface org.cleartk.ml.SequenceClassifier: Classifies a sequence of feature lists.
classify(List<List<Feature>>) - Method in class org.cleartk.ml.viterbi.ViterbiClassifier
classifyChar(char) - Method in class org.cleartk.ml.feature.function.CharacterCategoryPatternFunction
cleanUPRegex1 - Static variable in class org.cleartk.util.treebank.TreebankFormatParser
cleanUPRegex2 - Static variable in class org.cleartk.util.treebank.TreebankFormatParser
cleanUPRegex3 - Static variable in class org.cleartk.util.treebank.TreebankFormatParser
cleanUPRegex4 - Static variable in class org.cleartk.util.treebank.TreebankFormatParser
clear() - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor.MinMaxRunningStat
clear() - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat
CleartkAnnotator<OUTCOME_TYPE> - Class in org.cleartk.ml: Copyright (c) 2009-2011, Regents of the University of Colorado
All rights reserved.
CleartkAnnotator() - Constructor for class org.cleartk.ml.CleartkAnnotator
CleartkEncoderException - Exception in org.cleartk.ml.encoder: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
CleartkEncoderException(Throwable, String, String, Object...) - Constructor for exception org.cleartk.ml.encoder.CleartkEncoderException
CleartkEncoderException(String, String, Object...) - Constructor for exception org.cleartk.ml.encoder.CleartkEncoderException
CleartkEncoderException(Throwable) - Constructor for exception org.cleartk.ml.encoder.CleartkEncoderException
CleartkExtractor<FOCUS_T extends Annotation,SEARCH_T extends Annotation> - Class in org.cleartk.ml.feature.extractor: A feature extractor that finds other Annotations in the context of a focus annotation and extracts features from these.
CleartkExtractor(Class<SEARCH_T>, FeatureExtractor1<SEARCH_T>, CleartkExtractor.Context...) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor: Create an extractor that finds Annotations of the given type at the specified CleartkExtractor.Contexts and applies the given feature extractor to the annotations.
CleartkExtractor.Bag - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context that aggregates the features of other contexts into a "bag" where position information of each individual feature is no longer maintained.
CleartkExtractor.Bag(CleartkExtractor.Context...) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Bag: Constructs a CleartkExtractor.Context which converts the features extracted by the argument contexts into a bag of features where all features have the same name.
CleartkExtractor.Bounds - Interface in org.cleartk.ml.feature.extractor: A class representing the bounds within which a CleartkExtractor should look for annotations.
CleartkExtractor.Context - Interface in org.cleartk.ml.feature.extractor: A class representing a location that a CleartkExtractor should look for annotations.
CleartkExtractor.Count - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context that aggregates the features of other contexts into a bag of counts where only the count of occurrence of each feature value is maintained.
CleartkExtractor.Count(CleartkExtractor.Context...) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Count: Constructs a CleartkExtractor.Context which converts the features extracted by the argument contexts into a bag of count features.
CleartkExtractor.Covered - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context for extracting all annotations within the focus annotation.
CleartkExtractor.Covered() - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Covered: Constructs a context that will extract features over all annotations within the focus annotation.
CleartkExtractor.FirstCovered - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context for extracting the first annotations within the focus annotation.
CleartkExtractor.FirstCovered(int) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.FirstCovered: Constructs a context that will extract features over the first N annotations within the focus annotation.
CleartkExtractor.FirstCovered(int, int) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.FirstCovered: Constructs a context that will extract features over a slice of the first N annotations within the focus annotation.
CleartkExtractor.Focus - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context for extracting the focus annotation.
CleartkExtractor.Focus() - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Focus: Constructs a context that will extract features over the focus annotation.
CleartkExtractor.Following - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context for extracting annotations appearing after the focus annotation.
CleartkExtractor.Following(int) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Following: Constructs a context that will extract features over the following N annotations.
CleartkExtractor.Following(int, int) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Following: Constructs a context that will extract features over a slice of the following N annotations.
CleartkExtractor.LastCovered - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context for extracting the last annotations within the focus annotation.
CleartkExtractor.LastCovered(int) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.LastCovered: Constructs a context that will extract features over the last N annotations within the focus annotation.
CleartkExtractor.LastCovered(int, int) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.LastCovered: Constructs a context that will extract features over a slice of the last N annotations within the focus annotation.
CleartkExtractor.NestedCountFeature - Class in org.cleartk.ml.feature.extractor
CleartkExtractor.NestedCountFeature(String, Feature, Object) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.NestedCountFeature
CleartkExtractor.Ngram - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context that aggregates the features of other contexts into a single "ngram" feature, where the feature values are concatenated together in order to form a single value.
CleartkExtractor.Ngram(CleartkExtractor.Context...) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Ngram: Constructs a CleartkExtractor.Context which converts the features extracted by the argument contexts into a single ngram feature where all feature values have been concatenated together.
CleartkExtractor.Ngrams - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context that aggregates the features of other contexts into several "ngrams" features, where sub-sequences of the feature values are concatenated together in order to form single values.
CleartkExtractor.Ngrams(int, CleartkExtractor.Context...) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Ngrams: Constructs a CleartkExtractor.Context which converts the features extracted by the argument contexts into ngram features where sub-sequences feature values have been concatenated together.
CleartkExtractor.Preceding - Class in org.cleartk.ml.feature.extractor: A CleartkExtractor.Context for extracting annotations appearing before the focus annotation.
CleartkExtractor.Preceding(int) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Preceding: Constructs a context that will extract features over the preceding N annotations.
CleartkExtractor.Preceding(int, int) - Constructor for class org.cleartk.ml.feature.extractor.CleartkExtractor.Preceding: Constructs a context that will extract features over a slice of the preceding N annotations.
CleartkExtractorException - Exception in org.cleartk.ml.feature.extractor: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
CleartkExtractorException(Throwable, String, String, Object...) - Constructor for exception org.cleartk.ml.feature.extractor.CleartkExtractorException
CleartkExtractorException(String, String, Object...) - Constructor for exception org.cleartk.ml.feature.extractor.CleartkExtractorException
CleartkExtractorException(Throwable) - Constructor for exception org.cleartk.ml.feature.extractor.CleartkExtractorException
CleartkInitializationException - Exception in org.cleartk.util: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
CleartkInitializationException(String, String, Object...) - Constructor for exception org.cleartk.util.CleartkInitializationException
CleartkInitializationException(Throwable, String, String, Object...) - Constructor for exception org.cleartk.util.CleartkInitializationException
CleartkMultiAnnotator<OUTCOME_TYPE> - Class in org.cleartk.ml.multi: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
CleartkMultiAnnotator() - Constructor for class org.cleartk.ml.multi.CleartkMultiAnnotator
CleartkProcessingException - Exception in org.cleartk.ml: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
CleartkProcessingException(Throwable, String, String, Object...) - Constructor for exception org.cleartk.ml.CleartkProcessingException
CleartkProcessingException(String, String, Object...) - Constructor for exception org.cleartk.ml.CleartkProcessingException
CleartkProcessingException(Throwable) - Constructor for exception org.cleartk.ml.CleartkProcessingException
CleartkSequenceAnnotator<OUTCOME_TYPE> - Class in org.cleartk.ml: Copyright (c) 2009-2011, Regents of the University of Colorado
All rights reserved.
CleartkSequenceAnnotator() - Constructor for class org.cleartk.ml.CleartkSequenceAnnotator
close() - Method in class org.cleartk.util.cr.FilesCollectionReader
close() - Method in class org.cleartk.util.cr.linereader.LineReader
collectInstances(AnalysisEngine, JCas) - Static method in class org.cleartk.ml.util.PublicFieldDataWriter.BooleanFactory
collectInstances(AnalysisEngine, JCas) - Static method in class org.cleartk.ml.util.PublicFieldDataWriter.StringFactory
collectInstances(AnalysisEngine, JCas) - Static method in class org.cleartk.ml.util.PublicFieldSequenceDataWriter.BooleanFactory
collectInstances(AnalysisEngine, JCas) - Static method in class org.cleartk.ml.util.PublicFieldSequenceDataWriter.StringFactory
collectionProcessComplete() - Method in class org.cleartk.ml.CleartkAnnotator
collectionProcessComplete() - Method in class org.cleartk.ml.CleartkSequenceAnnotator
collectionProcessComplete() - Method in class org.cleartk.ml.multi.CleartkMultiAnnotator
collectionProcessComplete() - Method in class org.cleartk.util.ae.linewriter.LineWriter
CombinedExtractor1<T extends Annotation> - Class in org.cleartk.ml.feature.extractor: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
CombinedExtractor1(List<FeatureExtractor1<T>>) - Constructor for class org.cleartk.ml.feature.extractor.CombinedExtractor1
CombinedExtractor1(FeatureExtractor1<T>, FeatureExtractor1<T>) - Constructor for class org.cleartk.ml.feature.extractor.CombinedExtractor1
CombinedExtractor1(FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>) - Constructor for class org.cleartk.ml.feature.extractor.CombinedExtractor1
CombinedExtractor1(FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>) - Constructor for class org.cleartk.ml.feature.extractor.CombinedExtractor1
CombinedExtractor1(FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>) - Constructor for class org.cleartk.ml.feature.extractor.CombinedExtractor1
CombinedExtractor1(FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>) - Constructor for class org.cleartk.ml.feature.extractor.CombinedExtractor1
CombinedExtractor1(FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>) - Constructor for class org.cleartk.ml.feature.extractor.CombinedExtractor1
CombinedExtractor1(FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>) - Constructor for class org.cleartk.ml.feature.extractor.CombinedExtractor1
CombinedExtractor1(FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>, FeatureExtractor1<T>) - Constructor for class org.cleartk.ml.feature.extractor.CombinedExtractor1
completed - Variable in class org.cleartk.util.cr.FilesCollectionReader
CompressedStringBiMap - Class in org.cleartk.util.collection: Copyright (c) 2007-2011, Regents of the University of Colorado
All rights reserved.
CompressedStringBiMap() - Constructor for class org.cleartk.util.collection.CompressedStringBiMap
computeCentroid(Iterable<Instance<OUTCOME_T>>, TfidfExtractor.IDFMap) - Method in class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
CONTAINEDBY - Static variable in class org.cleartk.ml.feature.extractor.RelativePositionExtractor
contains(Annotation) - Method in interface org.cleartk.ml.feature.extractor.CleartkExtractor.Bounds: Determines whether or not an annotation lies within the given bounds.
CONTAINS - Static variable in class org.cleartk.ml.feature.extractor.RelativePositionExtractor
contains(Annotation, Annotation) - Static method in class org.cleartk.util.AnnotationUtil
CONTAINS_HYPHEN - Static variable in class org.cleartk.ml.feature.function.ContainsHyphenFeatureFunction: string value contains a hyphen
containsDigits(String) - Static method in class org.cleartk.ml.feature.util.NumericTypeUtil
containsHyphen(String) - Static method in class org.cleartk.ml.feature.util.HyphenUtil
ContainsHyphenFeatureFunction - Class in org.cleartk.ml.feature.function: Copyright (c) 2007-2012, Regents of the University of Colorado
All rights reserved.
ContainsHyphenFeatureFunction() - Constructor for class org.cleartk.ml.feature.function.ContainsHyphenFeatureFunction
convertBase(int, int) - Static method in class org.cleartk.util.BaseConversion
CosineSimilarity - Class in org.cleartk.ml.feature.transform.extractor: Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
CosineSimilarity() - Constructor for class org.cleartk.ml.feature.transform.extractor.CosineSimilarity
countedValue - Variable in class org.cleartk.ml.feature.extractor.CleartkExtractor.NestedCountFeature
countFiles(Iterator<File>) - Method in class org.cleartk.util.cr.FilesCollectionReader
Counts - Class in org.cleartk.ml.feature: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
Counts(String, String, Map<? extends Object, Integer>) - Constructor for class org.cleartk.ml.feature.Counts
Counts(String, Map<? extends Object, Integer>) - Constructor for class org.cleartk.ml.feature.Counts
CoveredTextAnnotationWriter - Class in org.cleartk.util.ae.linewriter.annotation: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
CoveredTextAnnotationWriter() - Constructor for class org.cleartk.util.ae.linewriter.annotation.CoveredTextAnnotationWriter
CoveredTextExtractor<T extends Annotation> - Class in org.cleartk.ml.feature.extractor: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
CoveredTextExtractor() - Constructor for class org.cleartk.ml.feature.extractor.CoveredTextExtractor
createChunks(JCas, List<SUB_CHUNK_TYPE>, List<OUTCOME_TYPE>) - Method in interface org.cleartk.ml.chunking.Chunking
createChunks(JCas, List<SUB_CHUNK_TYPE>, List<String>) - Method in class org.cleartk.ml.chunking.Chunking_ImplBase
createClassifier() - Method in interface org.cleartk.ml.ClassifierFactory
createClassifier() - Method in class org.cleartk.ml.jar.GenericJarClassifierFactory
createClassifier() - Method in interface org.cleartk.ml.SequenceClassifierFactory
createDataWriter() - Method in interface org.cleartk.ml.DataWriterFactory
createDataWriter() - Method in class org.cleartk.ml.jar.DefaultDataWriterFactory
createDataWriter() - Method in class org.cleartk.ml.jar.DefaultSequenceDataWriterFactory
createDataWriter(String, Class<T>) - Method in class org.cleartk.ml.jar.GenericDataWriterFactory
createDataWriter() - Method in interface org.cleartk.ml.SequenceDataWriterFactory
createDataWriter() - Method in class org.cleartk.ml.util.PublicFieldDataWriter.BooleanFactory
createDataWriter() - Method in class org.cleartk.ml.util.PublicFieldDataWriter.StringFactory
createDataWriter() - Method in class org.cleartk.ml.util.PublicFieldSequenceDataWriter.BooleanFactory
createDataWriter() - Method in class org.cleartk.ml.util.PublicFieldSequenceDataWriter.StringFactory
createDataWriter() - Method in class org.cleartk.ml.viterbi.ViterbiDataWriterFactory
createExtractor() - Static method in class org.cleartk.ml.feature.function.CharacterCategoryPatternFunction
createExtractor(CharacterCategoryPatternFunction.PatternType) - Static method in class org.cleartk.ml.feature.function.CharacterCategoryPatternFunction
createFeature(String, Feature) - Static method in class org.cleartk.ml.Feature
createFileIterator() - Method in class org.cleartk.util.cr.FilesCollectionReader
createIdfMap(Iterable<Instance<OUTCOME_T>>) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
createInstance(T, Object...) - Static method in class org.cleartk.ml.util.InstanceFactory
createInstance(T, String) - Static method in class org.cleartk.ml.util.InstanceFactory
createName(String...) - Static method in class org.cleartk.ml.Feature
createName(String, String) - Static method in class org.cleartk.ml.feature.extractor.TypePathExtractor: WARNING: this method is public for TypePathFeature backwards compatibility, but should not be used by anyone else!
createOutcomes(JCas, List<SUB_CHUNK_TYPE>, List<CHUNK_TYPE>) - Method in interface org.cleartk.ml.chunking.Chunking
createOutcomes(JCas, List<SUB_CHUNK_TYPE>, List<CHUNK_TYPE>) - Method in class org.cleartk.ml.chunking.Chunking_ImplBase
currentFile - Variable in class org.cleartk.util.cr.FilesCollectionReader

D

dataWriter - Variable in class org.cleartk.ml.CleartkAnnotator
dataWriter - Variable in class org.cleartk.ml.CleartkSequenceAnnotator
DataWriter<OUTCOME_TYPE> - Interface in org.cleartk.ml: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
DataWriter_ImplBase<CLASSIFIER_BUILDER_TYPE extends EncodingJarClassifierBuilder<? extends Classifier<OUTCOME_TYPE>,ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE>,ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for DataWriter implementations that write training data to a file using FeaturesEncoders and OutcomeEncoders.
DataWriter_ImplBase(File) - Constructor for class org.cleartk.ml.jar.DataWriter_ImplBase
DataWriterFactory<OUTCOME_TYPE> - Interface in org.cleartk.ml: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
dataWriterFactory - Variable in class org.cleartk.ml.multi.CleartkMultiAnnotator
DataWriterFactory_ImplBase<ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for DataWriterFactory implementations that use FeaturesEncoders and OutcomeEncoders.
DataWriterFactory_ImplBase() - Constructor for class org.cleartk.ml.jar.DataWriterFactory_ImplBase
dataWriters - Variable in class org.cleartk.ml.multi.CleartkMultiAnnotator
decode(Boolean) - Method in class org.cleartk.ml.encoder.outcome.BooleanToBooleanOutcomeEncoder
decode(Integer) - Method in class org.cleartk.ml.encoder.outcome.BooleanToSignOutcomeEncoder
decode(String) - Method in class org.cleartk.ml.encoder.outcome.BooleanToStringOutcomeEncoder
decode(Double) - Method in class org.cleartk.ml.encoder.outcome.DoubleToDoubleOutcomeEncoder
decode(ENCODED_OUTCOME_TYPE) - Method in interface org.cleartk.ml.encoder.outcome.OutcomeEncoder
decode(String[]) - Method in class org.cleartk.ml.encoder.outcome.StringArrayToStringArrayEncoder
decode(Integer) - Method in class org.cleartk.ml.encoder.outcome.StringToIntegerOutcomeEncoder
decode(String) - Method in class org.cleartk.ml.encoder.outcome.StringToStringOutcomeEncoder
DEFAULT_NAME - Static variable in class org.cleartk.ml.feature.function.CapitalTypeFeatureFunction
DEFAULT_NAME - Static variable in class org.cleartk.ml.feature.function.ContainsHyphenFeatureFunction
DEFAULT_NAME - Static variable in class org.cleartk.ml.feature.function.LowerCaseFeatureFunction
DEFAULT_NAME - Static variable in class org.cleartk.ml.feature.function.NumericTypeFeatureFunction
DEFAULT_RESOURCE_BUNDLE - Static variable in exception org.cleartk.ml.CleartkProcessingException
DefaultDataWriterFactory<OUTCOME_TYPE> - Class in org.cleartk.ml.jar: A DataWriterFactory that creates a data writer from the class given by DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME and the directory given by DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY.
DefaultDataWriterFactory() - Constructor for class org.cleartk.ml.jar.DefaultDataWriterFactory
DefaultLineHandler - Class in org.cleartk.util.cr.linereader: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
DefaultLineHandler() - Constructor for class org.cleartk.util.cr.linereader.DefaultLineHandler
DefaultOutcomeFeatureExtractor - Class in org.cleartk.ml.viterbi: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
DefaultOutcomeFeatureExtractor() - Constructor for class org.cleartk.ml.viterbi.DefaultOutcomeFeatureExtractor
DefaultSequenceDataWriterFactory<OUTCOME_TYPE> - Class in org.cleartk.ml.jar: A SequenceDataWriterFactory that creates a data writer from the class given by DefaultSequenceDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME and the directory given by DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY.
DefaultSequenceDataWriterFactory() - Constructor for class org.cleartk.ml.jar.DefaultSequenceDataWriterFactory
delegate() - Method in class org.cleartk.util.collection.CompressedStringBiMap
delegatedClassifier - Variable in class org.cleartk.ml.viterbi.ViterbiClassifier
delegatedDataWriter - Variable in class org.cleartk.ml.viterbi.ViterbiDataWriter
delegatedDataWriterFactoryClass - Variable in class org.cleartk.ml.viterbi.ViterbiDataWriterFactory
digitsPattern - Static variable in class org.cleartk.ml.feature.util.NumericTypeUtil
DirectedDistanceExtractor<T extends Annotation,U extends Annotation> - Class in org.cleartk.ml.feature.extractor: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
DirectedDistanceExtractor(String, Class<? extends Annotation>) - Constructor for class org.cleartk.ml.feature.extractor.DirectedDistanceExtractor
DirectoryDataWriter<CLASSIFIER_BUILDER extends JarClassifierBuilder<? extends CLASSIFIER_TYPE>,CLASSIFIER_TYPE> - Class in org.cleartk.ml.jar: Superclass for DataWriter and SequenceDataWriter implementations that saves files to a training directory using a JarClassifierBuilder.
DirectoryDataWriter(File) - Constructor for class org.cleartk.ml.jar.DirectoryDataWriter
DirectoryDataWriterFactory - Class in org.cleartk.ml.jar: Superclass for DataWriterFactory and SequenceDataWriterFactory implementations that use FeaturesEncoders and OutcomeEncoders.
DirectoryDataWriterFactory() - Constructor for class org.cleartk.ml.jar.DirectoryDataWriterFactory
displayText() - Method in class org.cleartk.util.treebank.TreebankNode
distance(Map<String, Double>, Map<String, Double>) - Method in class org.cleartk.ml.feature.transform.extractor.CosineSimilarity
distance(Map<String, Double>) - Method in class org.cleartk.ml.feature.transform.extractor.FixedCosineSimilarity
distance(Map<String, Double>, Map<String, Double>) - Method in class org.cleartk.ml.feature.transform.extractor.FixedCosineSimilarity
distance(Map<String, Double>, Map<String, Double>) - Method in interface org.cleartk.ml.feature.transform.extractor.SimilarityFunction
DistanceExtractor<T extends Annotation,U extends Annotation> - Class in org.cleartk.ml.feature.extractor: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
DistanceExtractor(String, Class<? extends Annotation>) - Constructor for class org.cleartk.ml.feature.extractor.DistanceExtractor
DocumentIdBlockWriter - Class in org.cleartk.util.ae.linewriter.block: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
DocumentIdBlockWriter() - Constructor for class org.cleartk.util.ae.linewriter.block.DocumentIdBlockWriter
DoNothingBlockWriter - Class in org.cleartk.util.ae.linewriter.block: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
DoNothingBlockWriter() - Constructor for class org.cleartk.util.ae.linewriter.block.DoNothingBlockWriter
dotProduct(Map<String, Double>, Map<String, Double>) - Static method in class org.cleartk.ml.feature.transform.extractor.CosineSimilarity
DoubleToDoubleOutcomeEncoder - Class in org.cleartk.ml.encoder.outcome: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
DoubleToDoubleOutcomeEncoder() - Constructor for class org.cleartk.ml.encoder.outcome.DoubleToDoubleOutcomeEncoder

E

editDistance(String, String) - Static method in class org.cleartk.util.similarity.Levenshtein
encode(Feature) - Method in class org.cleartk.ml.encoder.features.BagEncoder
encode(Feature) - Method in class org.cleartk.ml.encoder.features.BooleanEncoder
encode(Feature) - Method in class org.cleartk.ml.encoder.features.FeatureCollectionEncoder
encode(Feature) - Method in interface org.cleartk.ml.encoder.features.FeatureEncoder
encode(Feature) - Method in class org.cleartk.ml.encoder.features.FeatureEncoderChain
encode(Feature) - Method in class org.cleartk.ml.encoder.features.MultiBagEncoder
encode(Feature) - Method in class org.cleartk.ml.encoder.features.NumberEncoder
encode(Feature) - Method in class org.cleartk.ml.encoder.features.StringEncoder
encode(Boolean) - Method in class org.cleartk.ml.encoder.outcome.BooleanToBooleanOutcomeEncoder
encode(Boolean) - Method in class org.cleartk.ml.encoder.outcome.BooleanToSignOutcomeEncoder
encode(Boolean) - Method in class org.cleartk.ml.encoder.outcome.BooleanToStringOutcomeEncoder
encode(Double) - Method in class org.cleartk.ml.encoder.outcome.DoubleToDoubleOutcomeEncoder
encode(OUTCOME_TYPE) - Method in interface org.cleartk.ml.encoder.outcome.OutcomeEncoder
encode(String[]) - Method in class org.cleartk.ml.encoder.outcome.StringArrayToStringArrayEncoder
encode(String) - Method in class org.cleartk.ml.encoder.outcome.StringToIntegerOutcomeEncoder
encode(String) - Method in class org.cleartk.ml.encoder.outcome.StringToStringOutcomeEncoder
encodeAll(Iterable<Feature>) - Method in interface org.cleartk.ml.encoder.features.FeaturesEncoder
encodeAll(Iterable<Feature>) - Method in class org.cleartk.ml.encoder.features.FeatureVectorFeaturesEncoder
encodeAll(Iterable<Feature>) - Method in class org.cleartk.ml.encoder.features.NameNumberFeaturesEncoder
ENCODERS_FILE_NAME - Static variable in class org.cleartk.ml.encoder.features.FeaturesEncoder_ImplBase
encodes(Feature) - Method in class org.cleartk.ml.encoder.features.BagEncoder
encodes(Feature) - Method in class org.cleartk.ml.encoder.features.BooleanEncoder
encodes(Feature) - Method in class org.cleartk.ml.encoder.features.FeatureCollectionEncoder
encodes(Feature) - Method in interface org.cleartk.ml.encoder.features.FeatureEncoder
encodes(Feature) - Method in class org.cleartk.ml.encoder.features.FeatureEncoderChain
encodes(Feature) - Method in class org.cleartk.ml.encoder.features.MultiBagEncoder
encodes(Feature) - Method in class org.cleartk.ml.encoder.features.NumberEncoder
encodes(Feature) - Method in class org.cleartk.ml.encoder.features.StringEncoder
EncodingDirectoryDataWriter<CLASSIFIER_BUILDER_TYPE extends EncodingJarClassifierBuilder<? extends CLASSIFIER_TYPE,ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE>,CLASSIFIER_TYPE,ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for DataWriter and SequenceDataWriter implementations that write training data to a file using a classifier builder with FeaturesEncoders and OutcomeEncoders Note that it does not declare that it implements either of the DataWriter interfaces.
EncodingDirectoryDataWriter(File) - Constructor for class org.cleartk.ml.jar.EncodingDirectoryDataWriter
EncodingDirectoryDataWriterFactory<ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for DataWriterFactory and SequenceDataWriterFactory implementations that use FeaturesEncoders and OutcomeEncoders.
EncodingDirectoryDataWriterFactory() - Constructor for class org.cleartk.ml.jar.EncodingDirectoryDataWriterFactory
EncodingJarClassifier<ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for Classifier and SequenceClassifier implementations that use FeaturesEncoders and OutcomeEncoders.
EncodingJarClassifier(FeaturesEncoder<ENCODED_FEATURES_TYPE>, OutcomeEncoder<OUTCOME_TYPE, ENCODED_OUTCOME_TYPE>) - Constructor for class org.cleartk.ml.jar.EncodingJarClassifier
EncodingJarClassifierBuilder<CLASSIFIER_TYPE,ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for builders which write to a training data file using FeaturesEncoders and OutcomeEncoders, and package classifiers as jar files.
EncodingJarClassifierBuilder() - Constructor for class org.cleartk.ml.jar.EncodingJarClassifierBuilder
equals(Object) - Method in class org.cleartk.ml.Feature
EQUALS - Static variable in class org.cleartk.ml.feature.extractor.RelativePositionExtractor
equals(Object) - Method in class org.cleartk.ml.Instance
equals(Object) - Method in class org.cleartk.ml.util.featurevector.FeatureVector.Entry
equals(Object) - Method in class org.cleartk.ml.util.featurevector.FeatureVector
escape(String) - Static method in class org.cleartk.ml.encoder.FeatureEncoderUtil
escape(String, char[]) - Static method in class org.cleartk.ml.encoder.FeatureEncoderUtil
EuclidianNormalizer - Class in org.cleartk.ml.encoder.features.normalizer: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
EuclidianNormalizer() - Constructor for class org.cleartk.ml.encoder.features.normalizer.EuclidianNormalizer
evaluate(double) - Method in class org.cleartk.ml.sigmoid.Sigmoid
extract(JCas, Annotation, CleartkExtractor.Bounds, Class<SEARCH_T>, FeatureExtractor1<SEARCH_T>) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Bag
extract(JCas, Annotation, CleartkExtractor.Bounds, Class<SEARCH_T>, FeatureExtractor1<SEARCH_T>) - Method in interface org.cleartk.ml.feature.extractor.CleartkExtractor.Context: Extracts features in the given context.
extract(JCas, Annotation, CleartkExtractor.Bounds, Class<SEARCH_T>, FeatureExtractor1<SEARCH_T>) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Count: This method got a bit gnarly in order to support nested Count contexts.
extract(JCas, Annotation, CleartkExtractor.Bounds, Class<SEARCH_T>, FeatureExtractor1<SEARCH_T>) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Covered
extract(JCas, FOCUS_T) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor
extract(JCas, FOCUS_T, FOCUS_T) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor
extract(JCas, Annotation, CleartkExtractor.Bounds, Class<SEARCH_T>, FeatureExtractor1<SEARCH_T>) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Focus
extract(JCas, Annotation, CleartkExtractor.Bounds, Class<SEARCH_T>, FeatureExtractor1<SEARCH_T>) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Ngram
extract(JCas, Annotation, CleartkExtractor.Bounds, Class<SEARCH_T>, FeatureExtractor1<SEARCH_T>) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Ngrams
extract(JCas, T) - Method in class org.cleartk.ml.feature.extractor.CombinedExtractor1: Extract features from the Annotation using the sub-extractors.
extract(JCas, Annotation) - Method in class org.cleartk.ml.feature.extractor.CoveredTextExtractor
extract(JCas, Annotation, Annotation) - Method in class org.cleartk.ml.feature.extractor.DirectedDistanceExtractor
extract(JCas, Annotation, Annotation) - Method in class org.cleartk.ml.feature.extractor.DistanceExtractor
extract(JCas, T) - Method in interface org.cleartk.ml.feature.extractor.FeatureExtractor1: Some feature extractors will require some specific number of annotations that is greater than one.
extract(JCas, T, U) - Method in interface org.cleartk.ml.feature.extractor.FeatureExtractor2
extract(JCas, T) - Method in class org.cleartk.ml.feature.extractor.NamingExtractor1
extract(JCas, T, U) - Method in class org.cleartk.ml.feature.extractor.RelativePositionExtractor
extract(JCas, Annotation) - Method in class org.cleartk.ml.feature.extractor.TypePathExtractor
extract(JCas, Annotation) - Method in class org.cleartk.ml.feature.extractor.WhiteSpaceExtractor
extract(JCas, T) - Method in class org.cleartk.ml.feature.function.FeatureFunctionExtractor
extract(JCas, FOCUS_T) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
extract(JCas, FOCUS_T) - Method in class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
extract(JCas, FOCUS_T) - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor
extract(JCas, FOCUS_T) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
extract(JCas, FOCUS_T) - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor
extractBetween(JCas, FOCUS_T, FOCUS_T) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor
extractFeatures(List<Object>) - Method in class org.cleartk.ml.viterbi.DefaultOutcomeFeatureExtractor
extractFeatures(List<Object>) - Method in interface org.cleartk.ml.viterbi.OutcomeFeatureExtractor
extractWithin(JCas, FOCUS_T, Annotation) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor: Extract features from the annotations around the focus annotation and within the given bounds.

F

Feature - Class in org.cleartk.ml: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
Feature() - Constructor for class org.cleartk.ml.Feature
Feature(Object) - Constructor for class org.cleartk.ml.Feature
Feature(String, Object) - Constructor for class org.cleartk.ml.Feature
FeatureCollection - Class in org.cleartk.ml.feature: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
FeatureCollection(String, Collection<Feature>) - Constructor for class org.cleartk.ml.feature.FeatureCollection
FeatureCollection(Collection<Feature>) - Constructor for class org.cleartk.ml.feature.FeatureCollection
FeatureCollectionEncoder - Class in org.cleartk.ml.encoder.features: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
FeatureCollectionEncoder(String, FeatureEncoder<NameNumber>, NameNumberNormalizer) - Constructor for class org.cleartk.ml.encoder.features.FeatureCollectionEncoder
FeatureCollectionEncoder(FeatureEncoder<NameNumber>, NameNumberNormalizer) - Constructor for class org.cleartk.ml.encoder.features.FeatureCollectionEncoder
FeatureCollectionEncoder(String, FeatureEncoder<NameNumber>) - Constructor for class org.cleartk.ml.encoder.features.FeatureCollectionEncoder
FeatureCollectionEncoder(FeatureEncoder<NameNumber>) - Constructor for class org.cleartk.ml.encoder.features.FeatureCollectionEncoder
FeatureEncoder<T> - Interface in org.cleartk.ml.encoder.features: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
FeatureEncoderChain<ENCODED_TYPE> - Class in org.cleartk.ml.encoder.features: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
FeatureEncoderChain() - Constructor for class org.cleartk.ml.encoder.features.FeatureEncoderChain
featureEncoders - Variable in class org.cleartk.ml.encoder.features.FeatureEncoderChain
FeatureEncoderUtil - Class in org.cleartk.ml.encoder: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
FeatureEncoderUtil() - Constructor for class org.cleartk.ml.encoder.FeatureEncoderUtil
FeatureExtractor1<T extends Annotation> - Interface in org.cleartk.ml.feature.extractor: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
FeatureExtractor2<T extends Annotation,U extends Annotation> - Interface in org.cleartk.ml.feature.extractor: Copyright (c) 2007-2009, Regents of the University of Colorado
All rights reserved.
featureFullName - Variable in class org.cleartk.ml.chunking.Chunking_ImplBase
FeatureFunction - Interface in org.cleartk.ml.feature.function: Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
FeatureFunctionExtractor<T extends Annotation> - Class in org.cleartk.ml.feature.function: Copyright (c) 2007-2012, Regents of the University of Colorado
All rights reserved.
FeatureFunctionExtractor(FeatureExtractor1<T>, FeatureFunction...) - Constructor for class org.cleartk.ml.feature.function.FeatureFunctionExtractor
FeatureFunctionExtractor(FeatureExtractor1<T>, FeatureFunctionExtractor.BaseFeatures, FeatureFunction...) - Constructor for class org.cleartk.ml.feature.function.FeatureFunctionExtractor
FeatureFunctionExtractor.BaseFeatures - Enum in org.cleartk.ml.feature.function: Specify what to do with the base features created by the passed in feature extractor.
features - Variable in class org.cleartk.ml.feature.transform.TransformableFeature
FeatureSelectionExtractor<OUTCOME_T> - Class in org.cleartk.ml.feature.selection: Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
FeatureSelectionExtractor(String) - Constructor for class org.cleartk.ml.feature.selection.FeatureSelectionExtractor
FeaturesEncoder<ENCODED_FEATURES_TYPE> - Interface in org.cleartk.ml.encoder.features: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
featuresEncoder - Variable in class org.cleartk.ml.jar.EncodingDirectoryDataWriterFactory
featuresEncoder - Variable in class org.cleartk.ml.jar.EncodingJarClassifier
featuresEncoder - Variable in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
FeaturesEncoder_ImplBase<ENCODED_FEATURES_TYPE,ENCODED_FEATURE_TYPE> - Class in org.cleartk.ml.encoder.features: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
FeaturesEncoder_ImplBase() - Constructor for class org.cleartk.ml.encoder.features.FeaturesEncoder_ImplBase
featuresToFeatureMap(List<Feature>) - Method in class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
FeatureVector - Class in org.cleartk.ml.util.featurevector: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
FeatureVector() - Constructor for class org.cleartk.ml.util.featurevector.FeatureVector
FeatureVector.Entry - Class in org.cleartk.ml.util.featurevector
FeatureVector.Entry(int, double) - Constructor for class org.cleartk.ml.util.featurevector.FeatureVector.Entry
FeatureVectorFeaturesEncoder - Class in org.cleartk.ml.encoder.features: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
FeatureVectorFeaturesEncoder(int, NameNumberNormalizer) - Constructor for class org.cleartk.ml.encoder.features.FeatureVectorFeaturesEncoder
FeatureVectorFeaturesEncoder(int) - Constructor for class org.cleartk.ml.encoder.features.FeatureVectorFeaturesEncoder
FeatureVectorFeaturesEncoder() - Constructor for class org.cleartk.ml.encoder.features.FeatureVectorFeaturesEncoder
fileNotFound(File) - Static method in exception org.cleartk.util.CleartkInitializationException
files - Variable in class org.cleartk.util.cr.FilesCollectionReader
FilesCollectionReader - Class in org.cleartk.util.cr: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
FilesCollectionReader() - Constructor for class org.cleartk.util.cr.FilesCollectionReader
filesCount - Variable in class org.cleartk.util.cr.FilesCollectionReader
fileToUri - Variable in class org.cleartk.util.cr.UriCollectionReader
finalizeFeatureSet(File) - Method in interface org.cleartk.ml.encoder.features.FeaturesEncoder
finalizeFeatureSet(File) - Method in class org.cleartk.ml.encoder.features.FeaturesEncoder_ImplBase
finalizeFeatureSet(File) - Method in class org.cleartk.ml.encoder.features.FeatureVectorFeaturesEncoder
finalizeFeatureSet(File) - Method in class org.cleartk.ml.encoder.features.NameNumberFeaturesEncoder
finalizeMap() - Method in class org.cleartk.util.collection.GenericStringMapper
finalizeMap() - Method in interface org.cleartk.util.collection.StringMapper
finalizeOutcomeSet(File) - Method in class org.cleartk.ml.encoder.outcome.BooleanToBooleanOutcomeEncoder
finalizeOutcomeSet(File) - Method in class org.cleartk.ml.encoder.outcome.BooleanToSignOutcomeEncoder
finalizeOutcomeSet(File) - Method in class org.cleartk.ml.encoder.outcome.BooleanToStringOutcomeEncoder
finalizeOutcomeSet(File) - Method in class org.cleartk.ml.encoder.outcome.DoubleToDoubleOutcomeEncoder
finalizeOutcomeSet(File) - Method in interface org.cleartk.ml.encoder.outcome.OutcomeEncoder
finalizeOutcomeSet(File) - Method in class org.cleartk.ml.encoder.outcome.StringArrayToStringArrayEncoder
finalizeOutcomeSet(File) - Method in class org.cleartk.ml.encoder.outcome.StringToIntegerOutcomeEncoder
finalizeOutcomeSet(File) - Method in class org.cleartk.ml.encoder.outcome.StringToStringOutcomeEncoder
finish() - Method in class org.cleartk.ml.baseline.OutcomeOnlyDataWriter
finish() - Method in interface org.cleartk.ml.DataWriter
finish() - Method in class org.cleartk.ml.feature.transform.InstanceDataWriter
finish() - Method in class org.cleartk.ml.jar.DirectoryDataWriter: Basic implementation of DataWriter.finish() and SequenceDataWriter.finish() that calls JarClassifierBuilder.saveToTrainingDirectory(File)
finish() - Method in class org.cleartk.ml.jar.EncodingDirectoryDataWriter
finish() - Method in interface org.cleartk.ml.SequenceDataWriter
finish() - Method in class org.cleartk.ml.util.PublicFieldDataWriter
finish() - Method in class org.cleartk.ml.util.PublicFieldSequenceDataWriter
finish() - Method in class org.cleartk.ml.viterbi.ViterbiDataWriter
fit(double[], boolean[]) - Static method in class org.cleartk.ml.sigmoid.LinWengPlatt
FixedCosineSimilarity - Class in org.cleartk.ml.feature.transform.extractor: Like cosine similarity, but accepts a pre-specified vector, to avoid repeated recalculation of the magnitude
Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
FixedCosineSimilarity(Map<String, Double>) - Constructor for class org.cleartk.ml.feature.transform.extractor.FixedCosineSimilarity
fixedMagnitude - Variable in class org.cleartk.ml.feature.transform.extractor.FixedCosineSimilarity
fixedVector - Variable in class org.cleartk.ml.feature.transform.extractor.FixedCosineSimilarity
forcePut(String, String) - Method in class org.cleartk.util.collection.CompressedStringBiMap
fromManifest(Manifest) - Static method in class org.cleartk.ml.jar.JarClassifierBuilder: Loads a classifier builder from a manifest.
fromTrainingDirectory(File) - Static method in class org.cleartk.ml.jar.JarClassifierBuilder: Loads a classifier builder from manifest in the training directory.

G

GenericDataWriterFactory<OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Serves as a common base class for data writer factories such as DefaultDataWriterFactory and DefaultSequenceDataWriterFactory.
GenericDataWriterFactory() - Constructor for class org.cleartk.ml.jar.GenericDataWriterFactory
GenericJarClassifierFactory<CLASSIFIER_TYPE> - Class in org.cleartk.ml.jar: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
GenericJarClassifierFactory() - Constructor for class org.cleartk.ml.jar.GenericJarClassifierFactory
GenericStringMapper - Class in org.cleartk.util.collection: Copyright (c) 2010, Regents of the University of Colorado
All rights reserved.
GenericStringMapper(int) - Constructor for class org.cleartk.util.collection.GenericStringMapper
GenKeyBiMap<K,V> - Interface in org.cleartk.util.collection: Copyright (c) 2007-2011, Regents of the University of Colorado
All rights reserved.
get(int) - Method in class org.cleartk.ml.util.featurevector.ArrayFeatureVector
get(int) - Method in class org.cleartk.ml.util.featurevector.FeatureVector: Return the value at index.
get(int) - Method in class org.cleartk.ml.util.featurevector.SparseFeatureVector
getA() - Method in class org.cleartk.ml.sigmoid.Sigmoid
getAncestor(int) - Method in class org.cleartk.util.treebank.TreebankNode
getAnnotationsExtent(List<? extends Annotation>) - Static method in class org.cleartk.util.AnnotationUtil
getArch() - Method in class org.cleartk.util.PlatformDetection
getB() - Method in class org.cleartk.ml.sigmoid.Sigmoid
getBuffer() - Method in class org.cleartk.util.InputStreamHandler
getCentroidDataURI(String, URI) - Static method in class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
getChildren() - Method in class org.cleartk.util.treebank.TreebankNode
getClassifier(String) - Method in class org.cleartk.ml.multi.CleartkMultiAnnotator: Gets the classifier associated with name.
getClassifierBuilder() - Method in class org.cleartk.ml.jar.DirectoryDataWriter: Get the JarClassifierBuilder associated with this DataWriter.
getClassifierClass() - Method in class org.cleartk.ml.jar.GenericJarClassifierFactory
getClassifierClass() - Method in class org.cleartk.ml.jar.JarClassifierFactory
getClassifierClass() - Method in class org.cleartk.ml.jar.SequenceJarClassifierFactory
getCollectionReader(String) - Static method in class org.cleartk.util.cr.FilesCollectionReader
getCollectionReaderFromDirectory(File) - Static method in class org.cleartk.util.cr.UriCollectionReader
getCollectionReaderFromDirectory(File, Class<? extends IOFileFilter>, Class<? extends IOFileFilter>) - Static method in class org.cleartk.util.cr.UriCollectionReader
getCollectionReaderFromFiles(Collection<File>) - Static method in class org.cleartk.util.cr.UriCollectionReader
getCollectionReaderFromUris(Collection<URI>) - Static method in class org.cleartk.util.cr.UriCollectionReader
getCollectionReaderWithPatterns(String, String, String...) - Static method in class org.cleartk.util.cr.FilesCollectionReader
getCollectionReaderWithSuffixes(String, String, String...) - Static method in class org.cleartk.util.cr.FilesCollectionReader
getCollectionReaderWithView(String, String) - Static method in class org.cleartk.util.cr.FilesCollectionReader
getCount(Object) - Method in class org.cleartk.ml.feature.Counts
getCreateViewAggregateDescription(String) - Static method in class org.cleartk.util.ae.UriToXmiCasAnnotator: Use this aggregate description if UriToDocumentTextAnnotator will be writing to a mapped view.
getDataWriter(String) - Method in class org.cleartk.ml.multi.CleartkMultiAnnotator: Gets the DataWriter associated with name.
getDelegatedModelDirectory(File) - Method in class org.cleartk.ml.viterbi.ViterbiClassifierBuilder
getDescription(Class<? extends Annotation>) - Static method in class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
getDescription(Class<? extends Annotation>, Class<? extends Annotation>) - Static method in class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
getDescription(Class<? extends Annotation>, Class<? extends Annotation>, char, char) - Static method in class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
getDescription() - Static method in class org.cleartk.util.ae.UriToDocumentTextAnnotator
getDescription() - Static method in class org.cleartk.util.ae.UriToXmiCasAnnotator
getDescription(File) - Static method in class org.cleartk.util.ae.XmiWriter
getDescription(String) - Static method in class org.cleartk.util.cr.FilesCollectionReader
getDescription(File) - Static method in class org.cleartk.util.cr.linereader.LineReaderXmiWriter
getDescriptionForView(String) - Static method in class org.cleartk.util.ae.UriToDocumentTextAnnotator: This description will read the contents into the specify view.
getDescriptionFromDirectory(File) - Static method in class org.cleartk.util.cr.UriCollectionReader
getDescriptionFromDirectory(File, Class<? extends IOFileFilter>, Class<? extends IOFileFilter>) - Static method in class org.cleartk.util.cr.UriCollectionReader
getDescriptionFromFiles(Collection<File>) - Static method in class org.cleartk.util.cr.UriCollectionReader
getDescriptionFromUris(Collection<URI>) - Static method in class org.cleartk.util.cr.UriCollectionReader
getDescriptionWithPatterns(String, String, String...) - Static method in class org.cleartk.util.cr.FilesCollectionReader
getDescriptionWithSuffixes(String, String, String...) - Static method in class org.cleartk.util.cr.FilesCollectionReader
getDescriptionWithView(String, String) - Static method in class org.cleartk.util.cr.FilesCollectionReader
getDF(String) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor.IDFMap
getDocumentFrequencyDataURI(String, URI) - Static method in class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
getEncodersFile(File) - Static method in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
getExecutableSuffix() - Method in class org.cleartk.util.PlatformDetection
getExtractors() - Method in class org.cleartk.ml.feature.extractor.CombinedExtractor1
getFeature(JCas) - Method in class org.cleartk.ml.chunking.Chunking_ImplBase
getFeatureName() - Method in class org.cleartk.ml.feature.Counts
getFeatureName() - Method in class org.cleartk.ml.feature.extractor.CoveredTextExtractor
getFeatureName() - Method in interface org.cleartk.ml.feature.extractor.NamedFeatureExtractor1: Gets the name that will be used for all features created by this feature extractor.
getFeatureName() - Method in class org.cleartk.ml.feature.extractor.TypePathExtractor
getFeatureName() - Method in class org.cleartk.ml.feature.extractor.WhiteSpaceExtractor
getFeatureName() - Method in class org.cleartk.ml.feature.function.CharacterCategoryPatternFunction
getFeatures() - Method in class org.cleartk.ml.feature.FeatureCollection
getFeatures() - Method in class org.cleartk.ml.feature.transform.TransformableFeature
getFeatures() - Method in class org.cleartk.ml.Instance: Get the list of features for this instance.
getFeaturesEncoder() - Method in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
getFocusClass() - Method in class org.cleartk.ml.feature.extractor.TypePathExtractor
getIdentifier() - Method in class org.cleartk.ml.feature.Counts
getIdentifier() - Method in class org.cleartk.ml.feature.FeatureCollection
getIDF(String) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor.IDFMap
getIndex() - Method in exception org.cleartk.ml.util.featurevector.InvalidFeatureVectorValueException
getInputStream(Class<?>, String) - Static method in class org.cleartk.util.IoUtil: This method attempts to create an input stream from the given path by: Trying to parse it as a URL Trying to find it on the classpath, relative to the given class Trying to find it as a file on the file system
getInputStreamAsBufferedString(InputStream) - Static method in class org.cleartk.util.InputStreamHandler
getInputStreamAsList(InputStream) - Static method in class org.cleartk.util.InputStreamHandler
getInteger(String) - Method in class org.cleartk.util.collection.GenericStringMapper
getInteger(String) - Method in interface org.cleartk.util.collection.StringMapper
getLeafNode(String) - Static method in class org.cleartk.util.treebank.TreebankFormatParser: Uses the leafNodePattern to identify a string as a terminal.
getModelJarFile(File) - Static method in class org.cleartk.ml.jar.JarClassifierBuilder: Get the classifier jar file, as packaged by JarClassifierBuilder.packageClassifier(File).
getModelJarFile(String) - Static method in class org.cleartk.ml.jar.JarClassifierBuilder
getName() - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Bag
getName() - Method in interface org.cleartk.ml.feature.extractor.CleartkExtractor.Context: Gets the base feature name that will be used in Features generated by this context.
getName() - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Count
getName() - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Covered
getName() - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Focus
getName() - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Ngram
getName() - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Ngrams
getName() - Method in class org.cleartk.ml.Feature
getNext(JCas) - Method in class org.cleartk.util.cr.FilesCollectionReader
getNext(JCas) - Method in class org.cleartk.util.cr.linereader.LineReader
getNext(JCas) - Method in class org.cleartk.util.cr.UriCollectionReader
getNext(JCas) - Method in class org.cleartk.util.cr.XReader
getNextJarEntry(JarInputStream, String) - Static method in class org.cleartk.ml.jar.JarStreams
getNumSamples() - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor.MinMaxRunningStat
getNumSamples() - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat
getOrGenerateInteger(String) - Method in class org.cleartk.util.collection.GenericStringMapper
getOrGenerateInteger(String) - Method in interface org.cleartk.util.collection.StringMapper
getOrGenerateKey(String) - Method in class org.cleartk.util.collection.CompressedStringBiMap
getOrGenerateKey(V) - Method in interface org.cleartk.util.collection.GenKeyBiMap
getOs() - Method in class org.cleartk.util.PlatformDetection
getOutcome() - Method in class org.cleartk.ml.Instance: Get the current label for the instance.
getOutcomeEncoder() - Method in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
getOutcomeSuffix(CHUNK_TYPE, Feature) - Method in class org.cleartk.ml.chunking.Chunking_ImplBase
getOutputDirectory() - Method in class org.cleartk.ml.jar.DirectoryDataWriterFactory
getParameterValue(String, String) - Static method in class org.cleartk.util.ParamUtil
getParent() - Method in class org.cleartk.util.treebank.TreebankNode
getParseBegin() - Method in class org.cleartk.util.treebank.TreebankNode
getParseEnd() - Method in class org.cleartk.util.treebank.TreebankNode
getPath() - Method in class org.cleartk.ml.feature.extractor.TypePathExtractor
getProgress() - Method in class org.cleartk.util.cr.FilesCollectionReader
getProgress() - Method in class org.cleartk.util.cr.linereader.LineReader
getProgress() - Method in class org.cleartk.util.cr.UriCollectionReader
getScoreFunction(MutualInformationFeatureSelectionExtractor.CombineScoreMethod) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats
getSelectedFeatures() - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
getSubChunkToOutcomeMap(JCas, List<SUB_CHUNK_TYPE>, List<CHUNK_TYPE>) - Method in class org.cleartk.ml.chunking.BiesoChunking
getSubChunkToOutcomeMap(JCas, List<SUB_CHUNK_TYPE>, List<CHUNK_TYPE>) - Method in class org.cleartk.ml.chunking.BioChunking
getSubChunkToOutcomeMap(JCas, List<SUB_CHUNK_TYPE>, List<CHUNK_TYPE>) - Method in class org.cleartk.ml.chunking.Chunking_ImplBase: Produce a map from sub-chunk annotations to their outcome prefixes (e.g.
getSubChunkToOutcomeMap(JCas, List<SUB_CHUNK_TYPE>, List<CHUNK_TYPE>) - Method in class org.cleartk.ml.chunking.IoChunking
getSurroundingText(JCas, Annotation, Class<TOKEN_TYPE>, int, boolean) - Static method in class org.cleartk.util.AnnotationUtil: This method provides a way of getting some text before or after an annotation specified by some "window" of "tokens".
getTags() - Method in class org.cleartk.util.treebank.TreebankNode
getTerminal(int) - Method in class org.cleartk.util.treebank.TopTreebankNode
getTerminalCount() - Method in class org.cleartk.util.treebank.TopTreebankNode
getText() - Method in class org.cleartk.util.treebank.TreebankNode
getText() - Method in interface org.cleartk.util.treebank.TreebankObject
getTextBegin() - Method in class org.cleartk.util.treebank.TreebankNode
getTextEnd() - Method in class org.cleartk.util.treebank.TreebankNode
getTopNode() - Method in class org.cleartk.util.treebank.TreebankNode
getTotalCount() - Method in class org.cleartk.ml.feature.Counts
getTotalDocumentCount() - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor.IDFMap
getTrainingDataFile(File) - Method in class org.cleartk.ml.baseline.SingleOutcomeClassifierBuilder
getTrainingDataFile(File) - Method in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
getTreebankParse() - Method in class org.cleartk.util.treebank.TopTreebankNode
getTreebankParse() - Method in class org.cleartk.util.treebank.TreebankNode
getType(String) - Static method in class org.cleartk.util.treebank.TreebankFormatParser: Returns the type of a constituent of some fragment of a treebank parse.
getType() - Method in class org.cleartk.util.treebank.TreebankNode
getTypeArgument(Class<T>, String, T) - Static method in class org.cleartk.util.ReflectionUtil
getTypeArguments(Class<?>) - Method in class org.cleartk.ml.baseline.SingleOutcomeClassifier
getTypeArguments(Class<?>) - Method in class org.cleartk.ml.viterbi.ViterbiClassifier
getTypeArguments(Class<?>) - Method in class org.cleartk.ml.viterbi.ViterbiDataWriter
getTypeArguments(Class<?>, Object) - Static method in class org.cleartk.util.ReflectionUtil: Try to find the instantiation of all of genericTypes type parameters in objs class.
getTypeArguments(Class<?>) - Method in interface org.cleartk.util.ReflectionUtil.TypeArgumentDelegator
getTypePath() - Method in class org.cleartk.ml.feature.TypePathFeature
getURI(JCas) - Static method in class org.cleartk.util.ViewUriUtil: Get the primary Uniform Resource Identifier for this JCas and all its views.
getValue() - Method in class org.cleartk.ml.Feature
getValue() - Method in class org.cleartk.ml.feature.transform.TransformableFeature
getValue() - Method in exception org.cleartk.ml.util.featurevector.InvalidFeatureVectorValueException
getValue() - Method in class org.cleartk.util.treebank.TreebankNode
getValues() - Method in class org.cleartk.ml.feature.Counts
getXmiFile(JCas) - Method in class org.cleartk.util.ae.XmiWriter
getXmiFile(JCas) - Method in class org.cleartk.util.cr.linereader.LineReaderXmiWriter

H

handleLine(JCas, File, File, String) - Method in class org.cleartk.util.cr.linereader.DefaultLineHandler
handleLine(JCas, File, File, String) - Method in interface org.cleartk.util.cr.linereader.LineHandler
handleLine(JCas, File, File, String) - Method in class org.cleartk.util.cr.linereader.SimpleLineHandler
hashCode() - Method in class org.cleartk.ml.Feature
hashCode() - Method in class org.cleartk.ml.Instance
hashCode() - Method in class org.cleartk.ml.util.featurevector.FeatureVector.Entry
hashCode() - Method in class org.cleartk.ml.util.featurevector.FeatureVector
hasNext() - Method in class org.cleartk.ml.feature.transform.InstanceStream.Iterator
hasNext() - Method in class org.cleartk.util.cr.FilesCollectionReader
hasNext() - Method in class org.cleartk.util.cr.linereader.LineReader
hasNext() - Method in class org.cleartk.util.cr.UriCollectionReader
HyphenUtil - Class in org.cleartk.ml.feature.util: Copyright (c) 2010, Regents of the University of Colorado
All rights reserved.
HyphenUtil() - Constructor for class org.cleartk.ml.feature.util.HyphenUtil

I

idfMap - Variable in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
incompatibleTypeParameterAndType(Object, String, Type, Class<?>) - Static method in exception org.cleartk.util.CleartkInitializationException
incompatibleTypeParameters(Object, String, Type, Object, String, Type) - Static method in exception org.cleartk.util.CleartkInitializationException
incTotalDocumentCount() - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor.IDFMap
index - Variable in class org.cleartk.ml.util.featurevector.FeatureVector.Entry
inferPlainText(String) - Static method in class org.cleartk.util.treebank.TreebankFormatParser: A treebank parse does not preserve whitespace information.
init(int, double, double) - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat
initialize(UimaContext) - Method in class org.cleartk.ml.CleartkAnnotator
initialize(UimaContext) - Method in class org.cleartk.ml.CleartkSequenceAnnotator
initialize(UimaContext) - Method in class org.cleartk.ml.jar.DirectoryDataWriterFactory
initialize(UimaContext) - Method in class org.cleartk.ml.jar.EncodingDirectoryDataWriterFactory
initialize(UimaContext) - Method in class org.cleartk.ml.jar.GenericJarClassifierFactory
initialize(UimaContext) - Method in class org.cleartk.ml.multi.CleartkMultiAnnotator
initialize(UimaContext) - Method in class org.cleartk.ml.viterbi.DefaultOutcomeFeatureExtractor
initialize(UimaContext) - Method in interface org.cleartk.ml.viterbi.OutcomeFeatureExtractor
initialize(UimaContext) - Method in class org.cleartk.ml.viterbi.ViterbiClassifier
initialize(UimaContext) - Method in class org.cleartk.ml.viterbi.ViterbiDataWriterFactory
initialize(UimaContext) - Method in class org.cleartk.util.ae.linewriter.annotation.CoveredTextAnnotationWriter
initialize(UimaContext) - Method in interface org.cleartk.util.ae.linewriter.AnnotationWriter
initialize(UimaContext) - Method in class org.cleartk.util.ae.linewriter.block.BlankLineBlockWriter
initialize(UimaContext) - Method in class org.cleartk.util.ae.linewriter.block.DocumentIdBlockWriter
initialize(UimaContext) - Method in class org.cleartk.util.ae.linewriter.block.DoNothingBlockWriter
initialize(UimaContext) - Method in interface org.cleartk.util.ae.linewriter.BlockWriter
initialize(UimaContext) - Method in class org.cleartk.util.ae.linewriter.LineWriter
initialize(UimaContext) - Method in class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
initialize(UimaContext) - Method in class org.cleartk.util.ae.PlainTextWriter
initialize(UimaContext) - Method in class org.cleartk.util.cr.FilesCollectionReader
initialize(UimaContext) - Method in class org.cleartk.util.cr.linereader.DefaultLineHandler
initialize(UimaContext) - Method in interface org.cleartk.util.cr.linereader.LineHandler
initialize(UimaContext) - Method in class org.cleartk.util.cr.linereader.LineReader
initialize(UimaContext) - Method in class org.cleartk.util.cr.linereader.SimpleLineHandler
initialize(UimaContext) - Method in class org.cleartk.util.cr.UriCollectionReader
initialize(UimaContext) - Method in class org.cleartk.util.cr.XReader
initTerminalNodes() - Method in class org.cleartk.util.treebank.TopTreebankNode
innerProduct(FeatureVector) - Method in class org.cleartk.ml.util.featurevector.FeatureVector
innerProduct(FeatureVector) - Method in class org.cleartk.ml.util.featurevector.SparseFeatureVector
InputStreamHandler<T> - Class in org.cleartk.util: Copyright (c) 2011-2012, Technische Universität Darmstadt
All rights reserved.
Instance<OUTCOME_TYPE> - Class in org.cleartk.ml: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
Instance() - Constructor for class org.cleartk.ml.Instance: Create a new ClassifierInstance with an empty set of features and a null label.
Instance(OUTCOME_TYPE) - Constructor for class org.cleartk.ml.Instance
Instance(OUTCOME_TYPE, Collection<Feature>) - Constructor for class org.cleartk.ml.Instance
Instance(Collection<Feature>) - Constructor for class org.cleartk.ml.Instance
InstanceDataWriter<OUTCOME_T> - Class in org.cleartk.ml.feature.transform: Copyright (c) 2011-2012, Regents of the University of Colorado
All rights reserved.
InstanceDataWriter(File) - Constructor for class org.cleartk.ml.feature.transform.InstanceDataWriter
InstanceFactory - Class in org.cleartk.ml.util: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
InstanceFactory() - Constructor for class org.cleartk.ml.util.InstanceFactory
Instances - Class in org.cleartk.ml: Provides static methods for working with Instance objects.
Instances() - Constructor for class org.cleartk.ml.Instances
instances - Variable in class org.cleartk.ml.util.PublicFieldDataWriter
instances - Variable in class org.cleartk.ml.util.PublicFieldSequenceDataWriter
INSTANCES_OUTPUT_FILENAME - Static variable in class org.cleartk.ml.feature.transform.InstanceDataWriter
InstanceStream<OUTCOME_T> - Class in org.cleartk.ml.feature.transform: Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
InstanceStream(URI) - Constructor for class org.cleartk.ml.feature.transform.InstanceStream
InstanceStream.Iterator<OUTCOME_T> - Class in org.cleartk.ml.feature.transform
InstanceStream.Iterator(URI) - Constructor for class org.cleartk.ml.feature.transform.InstanceStream.Iterator
InstanceStream.Terminator<OUTCOME_T> - Class in org.cleartk.ml.feature.transform
InstanceStream.Terminator() - Constructor for class org.cleartk.ml.feature.transform.InstanceStream.Terminator
invalidFeatureVectorValue(Throwable, int, double) - Static method in exception org.cleartk.ml.encoder.CleartkEncoderException
invalidFeatureVectorValue(int, double) - Static method in exception org.cleartk.ml.encoder.CleartkEncoderException
InvalidFeatureVectorValueException - Exception in org.cleartk.ml.util.featurevector: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
InvalidFeatureVectorValueException(int, double) - Constructor for exception org.cleartk.ml.util.featurevector.InvalidFeatureVectorValueException
invalidParameterValueSelectFrom(String, List<?>, Object) - Static method in exception org.cleartk.util.CleartkInitializationException
invalidTypePath(String, Type) - Static method in exception org.cleartk.ml.feature.extractor.CleartkExtractorException
inverse() - Method in class org.cleartk.util.collection.CompressedStringBiMap
IoChunking<SUB_CHUNK_TYPE extends Annotation,CHUNK_TYPE extends Annotation> - Class in org.cleartk.ml.chunking: Chunking with Inside-Outside labels
Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
IoChunking(Class<? extends SUB_CHUNK_TYPE>, Class<? extends CHUNK_TYPE>) - Constructor for class org.cleartk.ml.chunking.IoChunking
IoChunking(Class<? extends SUB_CHUNK_TYPE>, Class<? extends CHUNK_TYPE>, String) - Constructor for class org.cleartk.ml.chunking.IoChunking
IoUtil - Class in org.cleartk.util: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
IoUtil() - Constructor for class org.cleartk.util.IoUtil
isAllPaths() - Method in class org.cleartk.ml.feature.extractor.TypePathExtractor
isAllUppercase(String) - Static method in class org.cleartk.ml.feature.util.CaseUtil
isAllUppercase(String, Locale) - Static method in class org.cleartk.ml.feature.util.CaseUtil
isAllValues() - Method in class org.cleartk.ml.feature.extractor.TypePathExtractor
isAssignableFrom(Type, Type) - Static method in class org.cleartk.util.ReflectionUtil
isCompressFeatures() - Method in class org.cleartk.ml.encoder.features.NameNumberFeaturesEncoder
isDigits(String) - Static method in class org.cleartk.ml.feature.util.NumericTypeUtil
isEndOfChunk(char, String, char, String) - Method in class org.cleartk.ml.chunking.BiesoChunking
isEndOfChunk(char, String, char, String) - Method in class org.cleartk.ml.chunking.BioChunking
isEndOfChunk(char, String, char, String) - Method in class org.cleartk.ml.chunking.Chunking_ImplBase: Determines whether the current outcome represents the end of a chunk.
isEndOfChunk(char, String, char, String) - Method in class org.cleartk.ml.chunking.IoChunking
isInitialUppercase(String) - Static method in class org.cleartk.ml.feature.util.CaseUtil
isInitialUppercase(String, Locale) - Static method in class org.cleartk.ml.feature.util.CaseUtil
isLeaf() - Method in class org.cleartk.util.treebank.TreebankNode
isTrained - Variable in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
isTrained - Variable in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
isTraining() - Method in class org.cleartk.ml.CleartkAnnotator
isTraining() - Method in class org.cleartk.ml.CleartkSequenceAnnotator
isTraining() - Method in class org.cleartk.ml.multi.CleartkMultiAnnotator
isTransformable(Feature) - Method in class org.cleartk.ml.feature.transform.OneToOneTrainableExtractor_ImplBase
isTransformable(Feature) - Method in class org.cleartk.ml.feature.transform.TrainableExtractor_ImplBase
isUniqueValues() - Method in class org.cleartk.ml.feature.extractor.TypePathExtractor
isValidPath(Type, String, JCas) - Static method in class org.cleartk.ml.feature.extractor.TypePathExtractor
isValidType(Type, TypeSystem) - Static method in class org.cleartk.ml.feature.extractor.TypePathExtractor
iterator() - Method in class org.cleartk.ml.feature.transform.InstanceStream
iterator() - Method in class org.cleartk.ml.util.featurevector.ArrayFeatureVector
iterator() - Method in class org.cleartk.ml.util.featurevector.FeatureVector: Gives an iterator over the non-zero features.
iterator() - Method in class org.cleartk.ml.util.featurevector.SparseFeatureVector

J

JarClassifierBuilder<CLASSIFIER_TYPE> - Class in org.cleartk.ml.jar: Superclass for builders which package classifiers as jar files.
JarClassifierBuilder() - Constructor for class org.cleartk.ml.jar.JarClassifierBuilder: Creates a new classifier builder with a default manifest.
JarClassifierFactory<OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Copyright (c) 2007-2011, Regents of the University of Colorado
All rights reserved.
JarClassifierFactory() - Constructor for class org.cleartk.ml.jar.JarClassifierFactory
JarStreams - Class in org.cleartk.ml.jar: Utility class for working with JarInputStream and JarOutputStream objects.
JarStreams() - Constructor for class org.cleartk.ml.jar.JarStreams

L

l2Norm() - Method in class org.cleartk.ml.util.featurevector.FeatureVector
LEAF_NODE_REGEX - Static variable in class org.cleartk.util.treebank.TreebankFormatParser: used to identify tokens in Penn Treebank labeled constituents.
LEFTOF - Static variable in class org.cleartk.ml.feature.extractor.RelativePositionExtractor
Levenshtein - Class in org.cleartk.util.similarity: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
Levenshtein() - Constructor for class org.cleartk.util.similarity.Levenshtein
LineHandler - Interface in org.cleartk.util.cr.linereader: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
LineReader - Class in org.cleartk.util.cr.linereader: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
LineReader() - Constructor for class org.cleartk.util.cr.linereader.LineReader
LineReaderXmiWriter - Class in org.cleartk.util.cr.linereader: This is a simple annotator for writing out XMI files, used by the parsing examples.
LineReaderXmiWriter() - Constructor for class org.cleartk.util.cr.linereader.LineReaderXmiWriter
LineWriter<ANNOTATION_TYPE extends Annotation,BLOCK_TYPE extends Annotation> - Class in org.cleartk.util.ae.linewriter: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
LineWriter() - Constructor for class org.cleartk.util.ae.linewriter.LineWriter
LinWengPlatt - Class in org.cleartk.ml.sigmoid: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
LinWengPlatt() - Constructor for class org.cleartk.ml.sigmoid.LinWengPlatt
LinWengPlatt.ConvergenceFailure - Exception in org.cleartk.ml.sigmoid
LinWengPlatt.ConvergenceFailure(String) - Constructor for exception org.cleartk.ml.sigmoid.LinWengPlatt.ConvergenceFailure
load(URI) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
load(URI) - Method in class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
load(URI) - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor
load(URI) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor.IDFMap
load(URI) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
load(URI) - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor
load(URI) - Method in interface org.cleartk.ml.feature.transform.TrainableExtractor: Loads statistics from location URI
loadClassifier(InputStream) - Method in class org.cleartk.ml.jar.JarClassifierBuilder: Load a classifier packaged by JarClassifierBuilder.packageClassifier(File) from an InputStream.
loadClassifierFromTrainingDirectory(File) - Method in class org.cleartk.ml.jar.JarClassifierBuilder: Load a classifier packaged by JarClassifierBuilder.packageClassifier(File) from the jar file in the training directory.
loadFromDirectory(File) - Static method in class org.cleartk.ml.feature.transform.InstanceStream
loadFromURI(URI) - Static method in class org.cleartk.ml.feature.transform.InstanceStream
LOOKUP_FILE_NAME - Static variable in class org.cleartk.ml.encoder.features.FeatureVectorFeaturesEncoder
LOOKUP_FILE_NAME - Static variable in class org.cleartk.ml.encoder.features.NameNumberFeaturesEncoder
LOOKUP_FILE_NAME - Static variable in class org.cleartk.ml.encoder.outcome.StringToIntegerOutcomeEncoder
LowerCaseFeatureFunction - Class in org.cleartk.ml.feature.function: Copyright (c) 2007-2012, Regents of the University of Colorado
All rights reserved.
LowerCaseFeatureFunction() - Constructor for class org.cleartk.ml.feature.function.LowerCaseFeatureFunction

M

magnitude(Map<String, Double>) - Static method in class org.cleartk.ml.feature.transform.extractor.CosineSimilarity
main(String...) - Static method in class org.cleartk.ml.jar.BuildJar
main(File, String...) - Static method in class org.cleartk.ml.jar.Train: Trains a classifier in the given directory.
main(String...) - Static method in class org.cleartk.ml.jar.Train
manifest - Variable in class org.cleartk.ml.jar.JarClassifierBuilder: The manifest associated with this classifier builder.
max() - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor.MinMaxRunningStat
mean - Variable in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanStddevTuple
mean() - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat
MeanValueClassifierBuilder - Class in org.cleartk.ml.baseline: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
MeanValueClassifierBuilder() - Constructor for class org.cleartk.ml.baseline.MeanValueClassifierBuilder
MeanValueDataWriter - Class in org.cleartk.ml.baseline: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
MeanValueDataWriter(File) - Constructor for class org.cleartk.ml.baseline.MeanValueDataWriter
min() - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor.MinMaxRunningStat
MinMaxNormalizationExtractor<OUTCOME_T,FOCUS_T extends Annotation> - Class in org.cleartk.ml.feature.transform.extractor: Scales features extracted by its subextractor to range 0-1, by scaling by the minimum and maximum values
MinMaxNormalizationExtractor(String) - Constructor for class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor
MinMaxNormalizationExtractor(String, FeatureExtractor1<FOCUS_T>) - Constructor for class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor
MinMaxNormalizationExtractor.MinMaxRunningStat - Class in org.cleartk.ml.feature.transform.extractor
MinMaxNormalizationExtractor.MinMaxRunningStat() - Constructor for class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor.MinMaxRunningStat
moreThanOneName(String, String) - Static method in exception org.cleartk.ml.feature.extractor.CleartkExtractorException
MostFrequentBooleanClassifierBuilder - Class in org.cleartk.ml.baseline: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
MostFrequentBooleanClassifierBuilder() - Constructor for class org.cleartk.ml.baseline.MostFrequentBooleanClassifierBuilder
MostFrequentBooleanDataWriter - Class in org.cleartk.ml.baseline: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
MostFrequentBooleanDataWriter(File) - Constructor for class org.cleartk.ml.baseline.MostFrequentBooleanDataWriter
MostFrequentStringClassifierBuilder - Class in org.cleartk.ml.baseline: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
MostFrequentStringClassifierBuilder() - Constructor for class org.cleartk.ml.baseline.MostFrequentStringClassifierBuilder
MostFrequentStringDataWriter - Class in org.cleartk.ml.baseline
MostFrequentStringDataWriter(File) - Constructor for class org.cleartk.ml.baseline.MostFrequentStringDataWriter
MostFrequentValueClassifierBuilder<OUTCOME_TYPE> - Class in org.cleartk.ml.baseline: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
MostFrequentValueClassifierBuilder() - Constructor for class org.cleartk.ml.baseline.MostFrequentValueClassifierBuilder
movePastWhiteSpaceChars(String, int) - Static method in class org.cleartk.util.treebank.TreebankFormatParser
MultiBagEncoder - Class in org.cleartk.ml.encoder.features: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
MultiBagEncoder(String, NameNumberNormalizer) - Constructor for class org.cleartk.ml.encoder.features.MultiBagEncoder
MultiBagEncoder(String) - Constructor for class org.cleartk.ml.encoder.features.MultiBagEncoder
MultiBagEncoder(NameNumberNormalizer) - Constructor for class org.cleartk.ml.encoder.features.MultiBagEncoder
MultiBagEncoder() - Constructor for class org.cleartk.ml.encoder.features.MultiBagEncoder
multipleExceptions(List<? extends Throwable>) - Static method in exception org.cleartk.ml.CleartkProcessingException
multiply(double) - Method in class org.cleartk.ml.util.featurevector.FeatureVector
mutualInformation(String, OUTCOME_T) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats
MutualInformationFeatureSelectionExtractor<OUTCOME_T,FOCUS_T extends Annotation> - Class in org.cleartk.ml.feature.selection: Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
MutualInformationFeatureSelectionExtractor(String, FeatureExtractor1<FOCUS_T>) - Constructor for class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
MutualInformationFeatureSelectionExtractor(String, FeatureExtractor1<FOCUS_T>, int) - Constructor for class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
MutualInformationFeatureSelectionExtractor(String, FeatureExtractor1<FOCUS_T>, MutualInformationFeatureSelectionExtractor.CombineScoreMethod, double, int) - Constructor for class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
MutualInformationFeatureSelectionExtractor.CombineScoreMethod - Enum in org.cleartk.ml.feature.selection: Specifies how scores for each outcome should be combined/aggregated into a single score
MutualInformationFeatureSelectionExtractor.CombineScoreMethod.AverageScores<OUTCOME_T> - Class in org.cleartk.ml.feature.selection
MutualInformationFeatureSelectionExtractor.CombineScoreMethod.AverageScores() - Constructor for class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.CombineScoreMethod.AverageScores
MutualInformationFeatureSelectionExtractor.CombineScoreMethod.CombineScoreFunction<OUTCOME_T> - Class in org.cleartk.ml.feature.selection
MutualInformationFeatureSelectionExtractor.CombineScoreMethod.CombineScoreFunction() - Constructor for class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.CombineScoreMethod.CombineScoreFunction
MutualInformationFeatureSelectionExtractor.CombineScoreMethod.MaxScores<OUTCOME_T> - Class in org.cleartk.ml.feature.selection
MutualInformationFeatureSelectionExtractor.CombineScoreMethod.MaxScores() - Constructor for class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.CombineScoreMethod.MaxScores
MutualInformationFeatureSelectionExtractor.MutualInformationStats<OUTCOME_T> - Class in org.cleartk.ml.feature.selection: Helper class for aggregating and computing mutual information statistics
MutualInformationFeatureSelectionExtractor.MutualInformationStats(double) - Constructor for class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats
MutualInformationFeatureSelectionExtractor.MutualInformationStats.ComputeFeatureScore<OUTCOME_T> - Class in org.cleartk.ml.feature.selection
MutualInformationFeatureSelectionExtractor.MutualInformationStats.ComputeFeatureScore(MutualInformationFeatureSelectionExtractor.MutualInformationStats<OUTCOME_T>, MutualInformationFeatureSelectionExtractor.CombineScoreMethod) - Constructor for class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats.ComputeFeatureScore

N

name - Variable in class org.cleartk.ml.encoder.features.NameNumber
name - Variable in class org.cleartk.ml.Feature
name - Variable in class org.cleartk.ml.feature.transform.OneToOneTrainableExtractor_ImplBase
name - Variable in class org.cleartk.ml.feature.transform.TrainableExtractor_ImplBase
NamedFeatureExtractor1<T extends Annotation> - Interface in org.cleartk.ml.feature.extractor: A FeatureExtractor1 that provides the name used for the features it creates.
nameFeature(Feature) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
NameNumber - Class in org.cleartk.ml.encoder.features: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
NameNumber(String, Number) - Constructor for class org.cleartk.ml.encoder.features.NameNumber
NameNumberFeaturesEncoder - Class in org.cleartk.ml.encoder.features: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
NameNumberFeaturesEncoder(boolean, boolean) - Constructor for class org.cleartk.ml.encoder.features.NameNumberFeaturesEncoder
NameNumberFeaturesEncoder() - Constructor for class org.cleartk.ml.encoder.features.NameNumberFeaturesEncoder
NameNumberNormalizer - Interface in org.cleartk.ml.encoder.features.normalizer: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
NamingExtractor1<T extends Annotation> - Class in org.cleartk.ml.feature.extractor: Copyright (c) 2007-2009, Regents of the University of Colorado
All rights reserved.
NamingExtractor1(String, FeatureExtractor1<T>) - Constructor for class org.cleartk.ml.feature.extractor.NamingExtractor1: Prepends the name of the features produced by subExtractor with the passed in name.
neitherParameterSet(String, Object, String, Object) - Static method in exception org.cleartk.util.CleartkInitializationException
newClassifier() - Method in class org.cleartk.ml.baseline.SingleOutcomeClassifierBuilder
newClassifier() - Method in class org.cleartk.ml.jar.JarClassifierBuilder: Create a new classifier using the attributes loaded by JarClassifierBuilder.unpackageClassifier(JarInputStream).
newClassifier() - Method in class org.cleartk.ml.viterbi.ViterbiClassifierBuilder
newClassifierBuilder() - Method in class org.cleartk.ml.baseline.MeanValueDataWriter
newClassifierBuilder() - Method in class org.cleartk.ml.baseline.MostFrequentBooleanDataWriter
newClassifierBuilder() - Method in class org.cleartk.ml.baseline.MostFrequentStringDataWriter
newClassifierBuilder() - Method in class org.cleartk.ml.jar.DirectoryDataWriter: Constructs a new JarClassifierBuilder that will be set as the DirectoryDataWriter.classifierBuilder during object construction.
newClassifierBuilder() - Method in class org.cleartk.ml.viterbi.ViterbiDataWriter
next() - Method in class org.cleartk.ml.feature.transform.InstanceStream.Iterator
noAnnotationInWindow(Class<? extends Annotation>, Annotation) - Static method in exception org.cleartk.ml.feature.extractor.CleartkExtractorException
noAnnotationMatchingWindow(Class<? extends Annotation>, Annotation) - Static method in exception org.cleartk.ml.feature.extractor.CleartkExtractorException
noInstanceOutcome(List<?>) - Static method in exception org.cleartk.ml.CleartkProcessingException
noMatchingEncoder(Feature, List<? extends FeatureEncoder<?>>) - Static method in exception org.cleartk.ml.encoder.CleartkEncoderException
NoOpNormalizer - Class in org.cleartk.ml.encoder.features.normalizer: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
NoOpNormalizer() - Constructor for class org.cleartk.ml.encoder.features.normalizer.NoOpNormalizer
normalize(List<NameNumber>) - Method in class org.cleartk.ml.encoder.features.normalizer.EuclidianNormalizer
normalize(List<NameNumber>) - Method in interface org.cleartk.ml.encoder.features.normalizer.NameNumberNormalizer
normalize(List<NameNumber>) - Method in class org.cleartk.ml.encoder.features.normalizer.NoOpNormalizer
notExactlyOneParameterSet(String, Object, String, Object) - Static method in exception org.cleartk.util.CleartkInitializationException
notPrimitive(Feature) - Static method in exception org.cleartk.ml.feature.extractor.CleartkExtractorException
notPrimitiveArray(Feature) - Static method in exception org.cleartk.ml.feature.extractor.CleartkExtractorException
notSingleCharacter(String, Object) - Static method in exception org.cleartk.util.CleartkInitializationException
number - Variable in class org.cleartk.ml.encoder.features.NameNumber
NumberEncoder - Class in org.cleartk.ml.encoder.features: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
NumberEncoder() - Constructor for class org.cleartk.ml.encoder.features.NumberEncoder
NumericTypeFeatureFunction - Class in org.cleartk.ml.feature.function: Copyright (c) 2007-2012, Regents of the University of Colorado
All rights reserved.
NumericTypeFeatureFunction() - Constructor for class org.cleartk.ml.feature.function.NumericTypeFeatureFunction
NumericTypeFeatureFunction.NumericType - Enum in org.cleartk.ml.feature.function
NumericTypeUtil - Class in org.cleartk.ml.feature.util: Copyright (c) 2010, Regents of the University of Colorado
All rights reserved.
NumericTypeUtil() - Constructor for class org.cleartk.ml.feature.util.NumericTypeUtil
numUrisCompleted - Variable in class org.cleartk.util.cr.UriCollectionReader

O

OneToOneTrainableExtractor_ImplBase<OUTCOME_T> - Class in org.cleartk.ml.feature.transform: Copyright (c) 2012, Regents of the University of Colorado
All rights reserved.
OneToOneTrainableExtractor_ImplBase(String) - Constructor for class org.cleartk.ml.feature.transform.OneToOneTrainableExtractor_ImplBase
org.cleartk.ml - package org.cleartk.ml
org.cleartk.ml.baseline - package org.cleartk.ml.baseline
org.cleartk.ml.chunking - package org.cleartk.ml.chunking
org.cleartk.ml.encoder - package org.cleartk.ml.encoder
org.cleartk.ml.encoder.features - package org.cleartk.ml.encoder.features
org.cleartk.ml.encoder.features.normalizer - package org.cleartk.ml.encoder.features.normalizer
org.cleartk.ml.encoder.outcome - package org.cleartk.ml.encoder.outcome
org.cleartk.ml.feature - package org.cleartk.ml.feature
org.cleartk.ml.feature.extractor - package org.cleartk.ml.feature.extractor
org.cleartk.ml.feature.function - package org.cleartk.ml.feature.function
org.cleartk.ml.feature.selection - package org.cleartk.ml.feature.selection
org.cleartk.ml.feature.transform - package org.cleartk.ml.feature.transform
org.cleartk.ml.feature.transform.extractor - package org.cleartk.ml.feature.transform.extractor
org.cleartk.ml.feature.util - package org.cleartk.ml.feature.util
org.cleartk.ml.jar - package org.cleartk.ml.jar
org.cleartk.ml.multi - package org.cleartk.ml.multi
org.cleartk.ml.sigmoid - package org.cleartk.ml.sigmoid
org.cleartk.ml.util - package org.cleartk.ml.util
org.cleartk.ml.util.featurevector - package org.cleartk.ml.util.featurevector
org.cleartk.ml.viterbi - package org.cleartk.ml.viterbi
org.cleartk.util - package org.cleartk.util
org.cleartk.util.ae - package org.cleartk.util.ae
org.cleartk.util.ae.linewriter - package org.cleartk.util.ae.linewriter
org.cleartk.util.ae.linewriter.annotation - package org.cleartk.util.ae.linewriter.annotation
org.cleartk.util.ae.linewriter.block - package org.cleartk.util.ae.linewriter.block
org.cleartk.util.ae.parenthetical - package org.cleartk.util.ae.parenthetical
org.cleartk.util.collection - package org.cleartk.util.collection
org.cleartk.util.cr - package org.cleartk.util.cr
org.cleartk.util.cr.linereader - package org.cleartk.util.cr.linereader
org.cleartk.util.similarity - package org.cleartk.util.similarity
org.cleartk.util.treebank - package org.cleartk.util.treebank
ORIENTATION_LEFT - Static variable in class org.cleartk.ml.feature.extractor.WhiteSpaceExtractor
ORIENTATION_RIGHT - Static variable in class org.cleartk.ml.feature.extractor.WhiteSpaceExtractor
OS_LINUX - Static variable in class org.cleartk.util.PlatformDetection
OS_OSX - Static variable in class org.cleartk.util.PlatformDetection
OS_SOLARIS - Static variable in class org.cleartk.util.PlatformDetection
OS_WINDOWS - Static variable in class org.cleartk.util.PlatformDetection
OutcomeEncoder<OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Interface in org.cleartk.ml.encoder.outcome: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
outcomeEncoder - Variable in class org.cleartk.ml.jar.EncodingDirectoryDataWriterFactory
outcomeEncoder - Variable in class org.cleartk.ml.jar.EncodingJarClassifier
outcomeEncoder - Variable in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
OutcomeFeatureExtractor - Interface in org.cleartk.ml.viterbi: Copyright (c) 2009, Regents of the University of Colorado
All rights reserved.
outcomeFeatureExtractorNames - Variable in class org.cleartk.ml.viterbi.ViterbiDataWriterFactory
outcomeFeatureExtractors - Variable in class org.cleartk.ml.viterbi.ViterbiClassifier
outcomeFeatureExtractors - Variable in class org.cleartk.ml.viterbi.ViterbiDataWriter
OutcomeOnlyDataWriter<CLASSIFIER_BUILDER extends SingleOutcomeClassifierBuilder<OUTCOME_TYPE>,OUTCOME_TYPE> - Class in org.cleartk.ml.baseline: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
OutcomeOnlyDataWriter(File) - Constructor for class org.cleartk.ml.baseline.OutcomeOnlyDataWriter
outputDirectory - Variable in class org.cleartk.ml.jar.DirectoryDataWriter
outputDirectory - Variable in class org.cleartk.ml.jar.DirectoryDataWriterFactory
outputDirectory - Variable in class org.cleartk.ml.viterbi.ViterbiDataWriter
outputDirectory - Variable in class org.cleartk.util.ae.XmiWriter
outputDirectoryRoot - Variable in class org.cleartk.ml.multi.CleartkMultiAnnotator
overlaps(Annotation, Annotation) - Static method in class org.cleartk.util.AnnotationUtil
OVERLAPS_LEFT - Static variable in class org.cleartk.ml.feature.extractor.RelativePositionExtractor
OVERLAPS_RIGHT - Static variable in class org.cleartk.ml.feature.extractor.RelativePositionExtractor

P

packageClassifier(File, JarOutputStream) - Method in class org.cleartk.ml.baseline.SingleOutcomeClassifierBuilder
packageClassifier(File, JarOutputStream) - Method in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
packageClassifier(File) - Method in class org.cleartk.ml.jar.JarClassifierBuilder: Create a classifier jar file from a directory where a classifier model was trained by JarClassifierBuilder.trainClassifier(File, String[]).
packageClassifier(File, JarOutputStream) - Method in class org.cleartk.ml.jar.JarClassifierBuilder: Add elements to a classifier jar.
packageClassifier(File, JarOutputStream) - Method in class org.cleartk.ml.viterbi.ViterbiClassifierBuilder
PARAM_ADD_SCORES - Static variable in class org.cleartk.ml.viterbi.ViterbiClassifier
PARAM_ANNOTATION_WRITER_CLASS_NAME - Static variable in class org.cleartk.util.ae.linewriter.LineWriter
PARAM_BLOCK_ANNOTATION_CLASS_NAME - Static variable in class org.cleartk.util.ae.linewriter.LineWriter
PARAM_BLOCK_WRITER_CLASS_NAME - Static variable in class org.cleartk.util.ae.linewriter.LineWriter
PARAM_CLASSIFIER_FACTORY_CLASS_NAME - Static variable in class org.cleartk.ml.CleartkAnnotator
PARAM_CLASSIFIER_FACTORY_CLASS_NAME - Static variable in class org.cleartk.ml.CleartkSequenceAnnotator
PARAM_CLASSIFIER_FACTORY_CLASS_NAME - Static variable in class org.cleartk.ml.multi.CleartkMultiAnnotator
PARAM_CLASSIFIER_JAR_PATH - Static variable in class org.cleartk.ml.jar.GenericJarClassifierFactory
PARAM_COMMENT_SPECIFIERS - Static variable in class org.cleartk.util.cr.linereader.LineReader
PARAM_DATA_WRITER_CLASS_NAME - Static variable in class org.cleartk.ml.jar.DefaultDataWriterFactory
PARAM_DATA_WRITER_CLASS_NAME - Static variable in class org.cleartk.ml.jar.DefaultSequenceDataWriterFactory
PARAM_DATA_WRITER_FACTORY_CLASS_NAME - Static variable in class org.cleartk.ml.CleartkAnnotator
PARAM_DATA_WRITER_FACTORY_CLASS_NAME - Static variable in class org.cleartk.ml.CleartkSequenceAnnotator
PARAM_DATA_WRITER_FACTORY_CLASS_NAME - Static variable in class org.cleartk.ml.multi.CleartkMultiAnnotator
PARAM_DELEGATED_DATA_WRITER_FACTORY_CLASS - Static variable in class org.cleartk.ml.viterbi.ViterbiDataWriterFactory
PARAM_DELIMITER - Static variable in class org.cleartk.util.cr.linereader.SimpleLineHandler
PARAM_DIRECTORY - Static variable in class org.cleartk.util.cr.UriCollectionReader
PARAM_DIRECTORY_FILTER_CLASS - Static variable in class org.cleartk.util.cr.UriCollectionReader
PARAM_ENCODING - Static variable in class org.cleartk.util.cr.FilesCollectionReader
PARAM_ENCODING - Static variable in class org.cleartk.util.cr.linereader.LineReader
PARAM_FILE_FILTER_CLASS - Static variable in class org.cleartk.util.cr.UriCollectionReader
PARAM_FILE_NAMES - Static variable in class org.cleartk.util.cr.FilesCollectionReader
PARAM_FILE_OR_DIRECTORY_NAME - Static variable in class org.cleartk.util.cr.linereader.LineReader
PARAM_FILE_SUFFIX - Static variable in class org.cleartk.util.ae.linewriter.LineWriter
PARAM_FILES - Static variable in class org.cleartk.util.cr.UriCollectionReader
PARAM_IGNORE_SYSTEM_FILES - Static variable in class org.cleartk.util.cr.FilesCollectionReader
PARAM_IS_TRAINING - Static variable in class org.cleartk.ml.CleartkAnnotator
PARAM_IS_TRAINING - Static variable in class org.cleartk.ml.CleartkSequenceAnnotator
PARAM_IS_TRAINING - Static variable in class org.cleartk.ml.multi.CleartkMultiAnnotator
PARAM_LANGUAGE - Static variable in class org.cleartk.util.cr.FilesCollectionReader
PARAM_LANGUAGE - Static variable in class org.cleartk.util.cr.linereader.LineReader
PARAM_LEAST_RECENT_OUTCOME - Static variable in class org.cleartk.ml.viterbi.DefaultOutcomeFeatureExtractor
PARAM_LEFT_PARENTHESIS - Static variable in class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
PARAM_LINE_HANDLER_CLASS_NAME - Static variable in class org.cleartk.util.cr.linereader.LineReader
PARAM_LOAD_ENCODERS_FROM_FILE_SYSTEM - Static variable in class org.cleartk.ml.jar.EncodingDirectoryDataWriterFactory
PARAM_MOST_RECENT_OUTCOME - Static variable in class org.cleartk.ml.viterbi.DefaultOutcomeFeatureExtractor
PARAM_NAME_FILES_FILE_NAMES - Static variable in class org.cleartk.util.cr.FilesCollectionReader
PARAM_OUTCOME_FEATURE_EXTRACTOR_NAMES - Static variable in class org.cleartk.ml.viterbi.ViterbiDataWriterFactory
PARAM_OUTPUT_ANNOTATION_CLASS_NAME - Static variable in class org.cleartk.util.ae.linewriter.LineWriter
PARAM_OUTPUT_DIRECTORY - Static variable in class org.cleartk.ml.jar.DirectoryDataWriterFactory
PARAM_OUTPUT_DIRECTORY - Static variable in class org.cleartk.util.ae.XmiWriter
PARAM_OUTPUT_DIRECTORY_NAME - Static variable in class org.cleartk.util.ae.linewriter.LineWriter
PARAM_OUTPUT_DIRECTORY_NAME - Static variable in class org.cleartk.util.ae.PlainTextWriter
PARAM_OUTPUT_FILE_NAME - Static variable in class org.cleartk.util.ae.linewriter.LineWriter
PARAM_PARENTHETICAL_TYPE_NAME - Static variable in class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
PARAM_PATTERNS - Static variable in class org.cleartk.util.cr.FilesCollectionReader
PARAM_RIGHT_PARENTHESIS - Static variable in class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
PARAM_ROOT_FILE - Static variable in class org.cleartk.util.cr.FilesCollectionReader
PARAM_SKIP_BLANK_LINES - Static variable in class org.cleartk.util.cr.linereader.LineReader
PARAM_STACK_SIZE - Static variable in class org.cleartk.ml.viterbi.ViterbiClassifier
PARAM_SUFFIXES - Static variable in class org.cleartk.util.cr.FilesCollectionReader
PARAM_SUFFIXES - Static variable in class org.cleartk.util.cr.linereader.LineReader
PARAM_URIS - Static variable in class org.cleartk.util.cr.UriCollectionReader
PARAM_USE4GRAM - Static variable in class org.cleartk.ml.viterbi.DefaultOutcomeFeatureExtractor
PARAM_USE_BIGRAM - Static variable in class org.cleartk.ml.viterbi.DefaultOutcomeFeatureExtractor
PARAM_USE_TRIGRAM - Static variable in class org.cleartk.ml.viterbi.DefaultOutcomeFeatureExtractor
PARAM_VIEW_NAME - Static variable in class org.cleartk.util.cr.FilesCollectionReader
PARAM_VIEW_NAME - Static variable in class org.cleartk.util.cr.linereader.LineReader
PARAM_WINDOW_TYPE_NAME - Static variable in class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
PARAM_XML_SCHEME - Static variable in class org.cleartk.util.ae.UriToXmiCasAnnotator
PARAM_XML_SCHEME - Static variable in class org.cleartk.util.cr.XReader
parameterLessThan(String, Object, Object) - Static method in exception org.cleartk.util.CleartkInitializationException
ParamUtil - Class in org.cleartk.util: Copyright (c) 2010, Regents of the University of Colorado
All rights reserved.
ParamUtil() - Constructor for class org.cleartk.util.ParamUtil
parensMatch(String) - Static method in class org.cleartk.util.treebank.TreebankFormatParser
ParentheticalAnnotator - Class in org.cleartk.util.ae.parenthetical: Copyright (c) 2011, Regents of the University of Colorado
All rights reserved.
ParentheticalAnnotator() - Constructor for class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
parse(String) - Static method in class org.cleartk.util.treebank.TreebankFormatParser: Create TreebankNode objects corresponding to the given TreeBank format parse, e.g.:
parse(String, String, int) - Static method in class org.cleartk.util.treebank.TreebankFormatParser: Create TreebankNode objects corresponding to the given TreeBank format parse, e.g.:
parseDocument(String, int, String) - Static method in class org.cleartk.util.treebank.TreebankFormatParser: This method parses an entire documents worth of treebanked sentences.
parseOutcome(String) - Method in class org.cleartk.ml.baseline.MeanValueClassifierBuilder
parseOutcome(String) - Method in class org.cleartk.ml.baseline.MostFrequentBooleanClassifierBuilder
parseOutcome(String) - Method in class org.cleartk.ml.baseline.MostFrequentStringClassifierBuilder
parseOutcome(String) - Method in class org.cleartk.ml.baseline.SingleOutcomeClassifierBuilder
PlainTextWriter - Class in org.cleartk.util.ae: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
PlainTextWriter() - Constructor for class org.cleartk.util.ae.PlainTextWriter
PlatformDetection - Class in org.cleartk.util: Copyright (c) 2011-2012, Technische Universität Darmstadt
All rights reserved.
PlatformDetection() - Constructor for class org.cleartk.util.PlatformDetection
prepareString(String) - Static method in class org.cleartk.util.treebank.TreebankFormatParser: This method was created simply as a way to clean up the parse string for a sentence in the treebank syntax.
process(JCas) - Method in class org.cleartk.util.ae.linewriter.LineWriter
process(JCas) - Method in class org.cleartk.util.ae.parenthetical.ParentheticalAnnotator
process(JCas) - Method in class org.cleartk.util.ae.PlainTextWriter
process(JCas) - Method in class org.cleartk.util.ae.UriToDocumentTextAnnotator
process(JCas) - Method in class org.cleartk.util.ae.UriToXmiCasAnnotator
process(JCas) - Method in class org.cleartk.util.ae.XmiWriter
PublicFieldDataWriter<T> - Class in org.cleartk.ml.util: A simple DataWriter that stores all instances in a public attribute.
PublicFieldDataWriter() - Constructor for class org.cleartk.ml.util.PublicFieldDataWriter
PublicFieldDataWriter.BooleanFactory - Class in org.cleartk.ml.util: Returns a single static instance of InstanceCollector.
PublicFieldDataWriter.BooleanFactory() - Constructor for class org.cleartk.ml.util.PublicFieldDataWriter.BooleanFactory
PublicFieldDataWriter.StringFactory - Class in org.cleartk.ml.util: Returns a single static instance of InstanceCollector.
PublicFieldDataWriter.StringFactory() - Constructor for class org.cleartk.ml.util.PublicFieldDataWriter.StringFactory
PublicFieldSequenceDataWriter<T> - Class in org.cleartk.ml.util: A simple SequenceDataWriter that stores all instances in a public attribute.
PublicFieldSequenceDataWriter() - Constructor for class org.cleartk.ml.util.PublicFieldSequenceDataWriter
PublicFieldSequenceDataWriter.BooleanFactory - Class in org.cleartk.ml.util: Returns a single static instance of InstanceCollector.
PublicFieldSequenceDataWriter.BooleanFactory() - Constructor for class org.cleartk.ml.util.PublicFieldSequenceDataWriter.BooleanFactory
PublicFieldSequenceDataWriter.StringFactory - Class in org.cleartk.ml.util: Returns a single static instance of InstanceCollector.
PublicFieldSequenceDataWriter.StringFactory() - Constructor for class org.cleartk.ml.util.PublicFieldSequenceDataWriter.StringFactory
put(String, String) - Method in class org.cleartk.util.collection.CompressedStringBiMap
putAll(Map<? extends String, ? extends String>) - Method in class org.cleartk.util.collection.CompressedStringBiMap
putNextJarEntry(JarOutputStream, String, File) - Static method in class org.cleartk.ml.jar.JarStreams

R

read(Reader) - Method in class org.cleartk.util.collection.CompressedStringBiMap
ReflectionUtil - Class in org.cleartk.util: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
ReflectionUtil() - Constructor for class org.cleartk.util.ReflectionUtil
ReflectionUtil.TypeArgumentDelegator - Interface in org.cleartk.util
RegexFileFilter - Class in org.cleartk.util.cr: Filters files using supplied regular expression(s).
RegexFileFilter(String) - Constructor for class org.cleartk.util.cr.RegexFileFilter: Construct a new regular expression filter.
RegexFileFilter(String, IOCase) - Constructor for class org.cleartk.util.cr.RegexFileFilter: Construct a new regular expression filter with the specified flags case sensitivity.
RegexFileFilter(String, int) - Constructor for class org.cleartk.util.cr.RegexFileFilter: Construct a new regular expression filter with the specified flags.
RegexFileFilter(Pattern) - Constructor for class org.cleartk.util.cr.RegexFileFilter: Construct a new regular expression filter for a compiled regular expression
RelativePositionExtractor<T extends Annotation,U extends Annotation> - Class in org.cleartk.ml.feature.extractor: Copyright (c) 2007-2008, Regents of the University of Colorado
All rights reserved.
RelativePositionExtractor() - Constructor for class org.cleartk.ml.feature.extractor.RelativePositionExtractor
remove() - Method in class org.cleartk.ml.feature.transform.InstanceStream.Iterator
RIGHTOF - Static variable in class org.cleartk.ml.feature.extractor.RelativePositionExtractor
rootFile - Variable in class org.cleartk.util.cr.FilesCollectionReader
run() - Method in class org.cleartk.util.InputStreamHandler: read data into buffer

S

save(URI) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats
save(URI) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
save(URI) - Method in class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
save(URI) - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor
save(URI) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor.IDFMap
save(URI) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
save(URI) - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor
save(URI) - Method in interface org.cleartk.ml.feature.transform.TrainableExtractor: Saves statistics from train in location URI
saveToTrainingDirectory(File) - Method in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
saveToTrainingDirectory(File) - Method in class org.cleartk.ml.jar.JarClassifierBuilder: Write all information stored in the classifier builder to the training directory.
saveToTrainingDirectory(File) - Method in class org.cleartk.ml.viterbi.ViterbiClassifierBuilder
score(List<Feature>) - Method in class org.cleartk.ml.baseline.SingleOutcomeClassifier
score(List<Feature>) - Method in interface org.cleartk.ml.Classifier: Classify a list of features, and return the scores for each of the outcomes
score(List<Feature>) - Method in class org.cleartk.ml.jar.Classifier_ImplBase
score(List<List<Feature>>) - Method in class org.cleartk.ml.jar.SequenceClassifier_ImplBase
score(List<List<Feature>>) - Method in interface org.cleartk.ml.SequenceClassifier: Classify a sequence of feature lists, and return the scores for each of the outcomes for each feature list.
score(List<List<Feature>>) - Method in class org.cleartk.ml.viterbi.ViterbiClassifier
select(JCas, Annotation, Class<T>, int) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.FirstCovered
select(JCas, Annotation, Class<T>, int) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Following
select(JCas, Annotation, Class<T>, int) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.LastCovered
select(JCas, Annotation, Class<T>, int) - Method in class org.cleartk.ml.feature.extractor.CleartkExtractor.Preceding
selectFirstMatching(JCas, Class<T>, Annotation) - Static method in class org.cleartk.util.AnnotationUtil
selectMatching(JCas, Class<T>, Annotation) - Static method in class org.cleartk.util.AnnotationUtil
selectTransformableFeatures(Instance<OUTCOME_T>) - Method in class org.cleartk.ml.feature.transform.TrainableExtractor_ImplBase: Recursively look through all features in an instance to find the features this extractor is responsible for extracting
SequenceClassifier_ImplBase<ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for SequenceClassifier implementations that use FeaturesEncoders and OutcomeEncoders.
SequenceClassifier_ImplBase(FeaturesEncoder<ENCODED_FEATURES_TYPE>, OutcomeEncoder<OUTCOME_TYPE, ENCODED_OUTCOME_TYPE>) - Constructor for class org.cleartk.ml.jar.SequenceClassifier_ImplBase
SequenceClassifierBuilder_ImplBase<CLASSIFIER_TYPE extends SequenceClassifier<OUTCOME_TYPE>,ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for builders which write to a training data file using FeaturesEncoders and OutcomeEncoders, and build and package SequenceClassifiers as jar files.
SequenceClassifierBuilder_ImplBase() - Constructor for class org.cleartk.ml.jar.SequenceClassifierBuilder_ImplBase
SequenceDataWriter_ImplBase<CLASSIFIER_BUILDER_TYPE extends EncodingJarClassifierBuilder<? extends SequenceClassifier<OUTCOME_TYPE>,ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE>,ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for SequenceDataWriter implementations that write training data to a file using FeaturesEncoders and OutcomeEncoders.
SequenceDataWriter_ImplBase(File) - Constructor for class org.cleartk.ml.jar.SequenceDataWriter_ImplBase
SequenceDataWriterFactory_ImplBase<ENCODED_FEATURES_TYPE,OUTCOME_TYPE,ENCODED_OUTCOME_TYPE> - Class in org.cleartk.ml.jar: Superclass for SequenceDataWriterFactory implementations that use FeaturesEncoders and OutcomeEncoders.
SequenceDataWriterFactory_ImplBase() - Constructor for class org.cleartk.ml.jar.SequenceDataWriterFactory_ImplBase
SequenceJarClassifierFactory() - Constructor for class org.cleartk.ml.jar.SequenceJarClassifierFactory
set(int, double) - Method in class org.cleartk.ml.util.featurevector.ArrayFeatureVector
set(int, double) - Method in class org.cleartk.ml.util.featurevector.FeatureVector: Set the feature at index to value.
set(int, double) - Method in class org.cleartk.ml.util.featurevector.SparseFeatureVector
setArch(String) - Method in class org.cleartk.util.PlatformDetection
setChildren(List<TreebankNode>) - Method in class org.cleartk.util.treebank.TreebankNode
setClassifierJarPath(String) - Method in class org.cleartk.ml.jar.GenericJarClassifierFactory
setDelegatedDataWriter(DataWriter<OUTCOME_TYPE>) - Method in class org.cleartk.ml.viterbi.ViterbiDataWriter
setEncodersFromFileSystem(EncodingDirectoryDataWriter<?, ?, ENCODED_FEATURES_TYPE, OUTCOME_TYPE, ENCODED_OUTCOME_TYPE>) - Method in class org.cleartk.ml.jar.EncodingDirectoryDataWriterFactory
setFeaturesEncoder(FeaturesEncoder<ENCODED_FEATURES_TYPE>) - Method in class org.cleartk.ml.jar.EncodingDirectoryDataWriter
setFeaturesEncoder(FeaturesEncoder<ENCODED_FEATURES_TYPE>) - Method in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
setLeaf(boolean) - Method in class org.cleartk.util.treebank.TreebankNode
setName(String) - Method in class org.cleartk.ml.Feature
setNormalizer(NameNumberNormalizer) - Method in class org.cleartk.ml.encoder.features.FeatureVectorFeaturesEncoder
setOs(String) - Method in class org.cleartk.util.PlatformDetection
setOutcome(OUTCOME_TYPE) - Method in class org.cleartk.ml.Instance: Set the current label for the instance.
setOutcomeEncoder(OutcomeEncoder<OUTCOME_TYPE, ENCODED_OUTCOME_TYPE>) - Method in class org.cleartk.ml.jar.EncodingDirectoryDataWriter
setOutcomeEncoder(OutcomeEncoder<OUTCOME_TYPE, ENCODED_OUTCOME_TYPE>) - Method in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
setOutcomeFeatureExtractors(OutcomeFeatureExtractor[]) - Method in class org.cleartk.ml.viterbi.ViterbiClassifierBuilder
setOutputDirectory(File) - Method in class org.cleartk.ml.jar.DirectoryDataWriterFactory
setOutputDirectoryName(String) - Method in class org.cleartk.util.ae.PlainTextWriter
setParent(TreebankNode) - Method in class org.cleartk.util.treebank.TreebankNode
setParseBegin(int) - Method in class org.cleartk.util.treebank.TreebankNode
setParseEnd(int) - Method in class org.cleartk.util.treebank.TreebankNode
setTags(String[]) - Method in class org.cleartk.util.treebank.TreebankNode
setText(String) - Method in class org.cleartk.util.treebank.TreebankNode
setTextBegin(int) - Method in class org.cleartk.util.treebank.TreebankNode: the offset of the plain text for this node with respect to the sentence text adjusted by the textOffset passed into the parse method.
setTextEnd(int) - Method in class org.cleartk.util.treebank.TreebankNode
setTopNode(TopTreebankNode) - Method in class org.cleartk.util.treebank.TreebankNode
setTreebankParse(String) - Method in class org.cleartk.util.treebank.TopTreebankNode
setType(String) - Method in class org.cleartk.util.treebank.TreebankNode
setURI(CAS, URI) - Static method in class org.cleartk.util.ViewUriUtil: Set the primary Uniform Resource Identifier for this CAS and all its views.
setURI(JCas, URI) - Static method in class org.cleartk.util.ViewUriUtil: Set the primary Uniform Resource Identifier for this JCas and all its views.
setValue(Object) - Method in class org.cleartk.ml.Feature
setValue(Object) - Method in class org.cleartk.ml.feature.transform.TransformableFeature
setValue(String) - Method in class org.cleartk.util.treebank.TreebankNode
Sigmoid(double, double) - Constructor for class org.cleartk.ml.sigmoid.Sigmoid
similarity(String, String) - Static method in class org.cleartk.util.similarity.Levenshtein
SimpleLineHandler() - Constructor for class org.cleartk.util.cr.linereader.SimpleLineHandler
SingleOutcomeClassifier(OUTCOME_TYPE) - Constructor for class org.cleartk.ml.baseline.SingleOutcomeClassifier
SingleOutcomeClassifierBuilder() - Constructor for class org.cleartk.ml.baseline.SingleOutcomeClassifierBuilder
size(Annotation) - Static method in class org.cleartk.util.AnnotationUtil
smoothingCount - Variable in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats
someDigitsPattern - Static variable in class org.cleartk.ml.feature.util.NumericTypeUtil
sort(List<T>) - Static method in class org.cleartk.util.AnnotationUtil
SparseFeatureVector() - Constructor for class org.cleartk.ml.util.featurevector.SparseFeatureVector
SparseFeatureVector(FeatureVector) - Constructor for class org.cleartk.ml.util.featurevector.SparseFeatureVector
splitSentences(String) - Static method in class org.cleartk.util.treebank.TreebankFormatParser: Generally speaking, we expect one treebanked sentence per line.
stackSize - Variable in class org.cleartk.ml.viterbi.ViterbiClassifier
stddev - Variable in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanStddevTuple
stddev() - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat
stddevPop() - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat
StringArrayToStringArrayEncoder() - Constructor for class org.cleartk.ml.encoder.outcome.StringArrayToStringArrayEncoder
StringEncoder() - Constructor for class org.cleartk.ml.encoder.features.StringEncoder
StringToIntegerOutcomeEncoder() - Constructor for class org.cleartk.ml.encoder.outcome.StringToIntegerOutcomeEncoder
StringToIntegerOutcomeEncoder(int) - Constructor for class org.cleartk.ml.encoder.outcome.StringToIntegerOutcomeEncoder
StringToStringOutcomeEncoder() - Constructor for class org.cleartk.ml.encoder.outcome.StringToStringOutcomeEncoder
stringToUri - Variable in class org.cleartk.util.cr.UriCollectionReader
subChunkClass - Variable in class org.cleartk.ml.chunking.Chunking_ImplBase
subExtractor - Variable in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor

T

TfidfExtractor<OUTCOME_T,FOCUS_T extends Annotation> - Class in org.cleartk.ml.feature.transform.extractor: Transforms count features produced by its subextractor into TF*IDF values
TfidfExtractor(String) - Constructor for class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
TfidfExtractor(String, FeatureExtractor1<FOCUS_T>) - Constructor for class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
TfidfExtractor.IDFMap - Class in org.cleartk.ml.feature.transform.extractor
TfidfExtractor.IDFMap() - Constructor for class org.cleartk.ml.feature.transform.extractor.TfidfExtractor.IDFMap
toArray() - Method in class org.cleartk.ml.util.featurevector.ArrayFeatureVector
toInstances(List<OUTCOME_TYPE>, List<List<Feature>>) - Static method in class org.cleartk.ml.Instances: Create a list of Instances from a list of outcomes and a list of feature-lists.
TopTreebankNode() - Constructor for class org.cleartk.util.treebank.TopTreebankNode
toString() - Method in class org.cleartk.ml.feature.FeatureCollection
toString() - Method in class org.cleartk.ml.Feature
toString() - Method in class org.cleartk.ml.Instance
toString() - Method in class org.cleartk.ml.sigmoid.Sigmoid
toString() - Method in class org.cleartk.util.PlatformDetection
train(Iterable<Instance<OUTCOME_T>>) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor
train(Iterable<Instance<OUTCOME_T>>) - Method in class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
train(Iterable<Instance<OUTCOME_T>>) - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor
train(Iterable<Instance<OUTCOME_T>>) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
train(Iterable<Instance<OUTCOME_T>>) - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor
train(Iterable<Instance<OUTCOME_T>>) - Method in interface org.cleartk.ml.feature.transform.TrainableExtractor: In the prototypical case, train takes a collection of instances and computes statistics over the values such as computing mean, standard deviation, TF*IDF, etc...
Train - Class in org.cleartk.ml.jar: Command line tool for training a classifier from an output directory that has been filled by a DirectoryDataWriter.
Train() - Constructor for class org.cleartk.ml.jar.Train
TrainableExtractor_ImplBase(String) - Constructor for class org.cleartk.ml.feature.transform.TrainableExtractor_ImplBase
trainAndPackage(File, String...) - Static method in class org.cleartk.ml.jar.JarClassifierBuilder: Loads a classifier builder from the training directory and invokes JarClassifierBuilder.trainClassifier(File, String...) and JarClassifierBuilder.packageClassifier(File).
trainClassifier(File, String...) - Method in class org.cleartk.ml.baseline.MeanValueClassifierBuilder
trainClassifier(File, String...) - Method in class org.cleartk.ml.baseline.MostFrequentValueClassifierBuilder
trainClassifier(File, String...) - Method in class org.cleartk.ml.jar.JarClassifierBuilder: Train a classifier from a training directory, as prepared by JarClassifierBuilder.saveToTrainingDirectory(File).
trainClassifier(File, String...) - Method in class org.cleartk.ml.viterbi.ViterbiClassifierBuilder
trainingDataFile - Variable in class org.cleartk.ml.baseline.OutcomeOnlyDataWriter
trainingDataFile - Variable in class org.cleartk.ml.jar.EncodingDirectoryDataWriter
trainingDataWriter - Variable in class org.cleartk.ml.baseline.OutcomeOnlyDataWriter
trainingDataWriter - Variable in class org.cleartk.ml.jar.EncodingDirectoryDataWriter
transform(Instance<OUTCOME_T>) - Method in class org.cleartk.ml.feature.selection.FeatureSelectionExtractor
transform(Instance<OUTCOME_T>) - Method in class org.cleartk.ml.feature.transform.extractor.CentroidTfidfSimilarityExtractor
transform(Feature) - Method in class org.cleartk.ml.feature.transform.extractor.MinMaxNormalizationExtractor
transform(Feature) - Method in class org.cleartk.ml.feature.transform.extractor.TfidfExtractor
transform(Feature) - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor
transform(Instance<OUTCOME_T>) - Method in class org.cleartk.ml.feature.transform.OneToOneTrainableExtractor_ImplBase
transform(Feature) - Method in class org.cleartk.ml.feature.transform.OneToOneTrainableExtractor_ImplBase
transform(Instance<OUTCOME_T>) - Method in interface org.cleartk.ml.feature.transform.TrainableExtractor: Transforms all features handled by this extractor.
TransformableFeature - Class in org.cleartk.ml.feature.transform: Abstract base class for transformable features.
TransformableFeature(String, List<Feature>) - Constructor for class org.cleartk.ml.feature.transform.TransformableFeature
TreebankFormatParser - Class in org.cleartk.util.treebank: This class was written to be a stand alone parser for the Penn Treebank data.
TreebankFormatParser() - Constructor for class org.cleartk.util.treebank.TreebankFormatParser
TreebankNode() - Constructor for class org.cleartk.util.treebank.TreebankNode
TreeFeature(Object) - Constructor for class org.cleartk.ml.TreeFeature
TreeFeature(String, Object) - Constructor for class org.cleartk.ml.TreeFeature
TYPE_REGEX - Static variable in class org.cleartk.util.treebank.TreebankFormatParser: used to identify the type of a consituent in a treebank parse tree.
TypePathExtractor(Class<T>, String, boolean, boolean, boolean) - Constructor for class org.cleartk.ml.feature.extractor.TypePathExtractor: This extractor creates features from attributes of an annotation.
TypePathExtractor(Class<T>, String) - Constructor for class org.cleartk.ml.feature.extractor.TypePathExtractor: calls this(type, typePath, false, false, true, jCas)
TypePathFeature(String, Object, String, String) - Constructor for class org.cleartk.ml.feature.TypePathFeature
TypePathFeature(String, Object, String) - Constructor for class org.cleartk.ml.feature.TypePathFeature

U

uncheckedCast(Object) - Static method in class org.cleartk.util.ReflectionUtil: Perform an unchecked cast based on a type parameter.
UnknownKeyException(String) - Constructor for exception org.cleartk.util.collection.UnknownKeyException
unpackageClassifier(JarInputStream) - Method in class org.cleartk.ml.baseline.SingleOutcomeClassifierBuilder
unpackageClassifier(JarInputStream) - Method in class org.cleartk.ml.jar.EncodingJarClassifierBuilder
unpackageClassifier(JarInputStream) - Method in class org.cleartk.ml.jar.JarClassifierBuilder: Load classifier elements from a classifier jar.
unpackageClassifier(JarInputStream) - Method in class org.cleartk.ml.viterbi.ViterbiClassifierBuilder
unsupportedOperationSetParameter(Throwable, Object, String, String, Object) - Static method in exception org.cleartk.ml.CleartkProcessingException
update(String, OUTCOME_T, int) - Method in class org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.MutualInformationStats
URI - Static variable in class org.cleartk.util.ViewUriUtil: The view where the document Uniform Resource Identifier is placed.
UriCollectionReader() - Constructor for class org.cleartk.util.cr.UriCollectionReader
UriCollectionReader.RejectSystemDirectories - Class in org.cleartk.util.cr
UriCollectionReader.RejectSystemDirectories() - Constructor for class org.cleartk.util.cr.UriCollectionReader.RejectSystemDirectories
UriCollectionReader.RejectSystemFiles - Class in org.cleartk.util.cr
UriCollectionReader.RejectSystemFiles() - Constructor for class org.cleartk.util.cr.UriCollectionReader.RejectSystemFiles
uriCount - Variable in class org.cleartk.util.cr.UriCollectionReader
uriIter - Variable in class org.cleartk.util.cr.UriCollectionReader
UriToDocumentTextAnnotator() - Constructor for class org.cleartk.util.ae.UriToDocumentTextAnnotator
UriToXmiCasAnnotator() - Constructor for class org.cleartk.util.ae.UriToXmiCasAnnotator
UriToXmiCasAnnotator.XmlScheme - Enum in org.cleartk.util.ae

V

value - Variable in class org.cleartk.ml.baseline.SingleOutcomeClassifierBuilder
value - Variable in class org.cleartk.ml.Feature
value - Variable in class org.cleartk.ml.util.featurevector.FeatureVector.Entry
valueOf(String) - Static method in enum org.cleartk.ml.feature.function.CapitalTypeFeatureFunction.CapitalType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.cleartk.ml.feature.function.CharacterCategoryPatternFunction.PatternType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.cleartk.ml.feature.function.CharacterNgramFeatureFunction.Orientation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.cleartk.ml.feature.function.FeatureFunctionExtractor.BaseFeatures: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.cleartk.ml.feature.function.NumericTypeFeatureFunction.NumericType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.CombineScoreMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.cleartk.util.ae.UriToXmiCasAnnotator.XmlScheme: Returns the enum constant of this type with the specified name.
values() - Static method in enum org.cleartk.ml.feature.function.CapitalTypeFeatureFunction.CapitalType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.cleartk.ml.feature.function.CharacterCategoryPatternFunction.PatternType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.cleartk.ml.feature.function.CharacterNgramFeatureFunction.Orientation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.cleartk.ml.feature.function.FeatureFunctionExtractor.BaseFeatures: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.cleartk.ml.feature.function.NumericTypeFeatureFunction.NumericType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.cleartk.ml.feature.selection.MutualInformationFeatureSelectionExtractor.CombineScoreMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.cleartk.util.ae.UriToXmiCasAnnotator.XmlScheme: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Method in class org.cleartk.util.collection.CompressedStringBiMap
variance() - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat
variancePop() - Method in class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat
ViewUriUtil() - Constructor for class org.cleartk.util.ViewUriUtil
viterbi(List<List<Feature>>) - Method in class org.cleartk.ml.viterbi.ViterbiClassifier: This implementation of Viterbi requires at most stackSize * sequenceLength calls to the classifier.
ViterbiClassifier(Classifier<OUTCOME_TYPE>, OutcomeFeatureExtractor[]) - Constructor for class org.cleartk.ml.viterbi.ViterbiClassifier
ViterbiClassifierBuilder() - Constructor for class org.cleartk.ml.viterbi.ViterbiClassifierBuilder
ViterbiDataWriter(File, OutcomeFeatureExtractor[]) - Constructor for class org.cleartk.ml.viterbi.ViterbiDataWriter
ViterbiDataWriterFactory() - Constructor for class org.cleartk.ml.viterbi.ViterbiDataWriterFactory

W

WhiteSpaceExtractor() - Constructor for class org.cleartk.ml.feature.extractor.WhiteSpaceExtractor
WhiteSpacePattern - Static variable in class org.cleartk.ml.feature.extractor.WhiteSpaceExtractor
WhiteSpaceRegex - Static variable in class org.cleartk.ml.feature.extractor.WhiteSpaceExtractor
write(Instance<OUTCOME_TYPE>) - Method in class org.cleartk.ml.baseline.OutcomeOnlyDataWriter
write(Instance<OUTCOME_TYPE>) - Method in interface org.cleartk.ml.DataWriter
write(Instance<OUTCOME_T>) - Method in class org.cleartk.ml.feature.transform.InstanceDataWriter
write(Instance<OUTCOME_TYPE>) - Method in class org.cleartk.ml.jar.DataWriter_ImplBase
write(List<Instance<OUTCOME_TYPE>>) - Method in class org.cleartk.ml.jar.SequenceDataWriter_ImplBase
write(List<Instance<OUTCOME_TYPE>>) - Method in interface org.cleartk.ml.SequenceDataWriter
write(Instance<T>) - Method in class org.cleartk.ml.util.PublicFieldDataWriter
write(List<Instance<T>>) - Method in class org.cleartk.ml.util.PublicFieldSequenceDataWriter
write(List<Instance<OUTCOME_TYPE>>) - Method in class org.cleartk.ml.viterbi.ViterbiDataWriter
write(Writer) - Method in class org.cleartk.util.collection.CompressedStringBiMap
write(Writer, boolean) - Method in class org.cleartk.util.collection.CompressedStringBiMap
write(File) - Method in class org.cleartk.util.collection.GenericStringMapper
write(Writer) - Method in class org.cleartk.util.collection.GenericStringMapper
write(File) - Method in interface org.cleartk.util.collection.Writable
write(Writer) - Method in interface org.cleartk.util.collection.Writable
writeAnnotation(JCas, Annotation) - Method in class org.cleartk.util.ae.linewriter.annotation.CoveredTextAnnotationWriter
writeAnnotation(JCas, ANNOTATION_TYPE) - Method in interface org.cleartk.util.ae.linewriter.AnnotationWriter
writeBlock(JCas, Annotation) - Method in class org.cleartk.util.ae.linewriter.block.BlankLineBlockWriter
writeBlock(JCas, Annotation) - Method in class org.cleartk.util.ae.linewriter.block.DocumentIdBlockWriter
writeBlock(JCas, Annotation) - Method in class org.cleartk.util.ae.linewriter.block.DoNothingBlockWriter
writeBlock(JCas, BLOCK_TYPE) - Method in interface org.cleartk.util.ae.linewriter.BlockWriter
writeEncoded(ENCODED_FEATURES_TYPE, ENCODED_OUTCOME_TYPE) - Method in class org.cleartk.ml.jar.DataWriter_ImplBase: Write the encoded features and encoded outcome to the output directory.
writeEncoded(ENCODED_FEATURES_TYPE, ENCODED_OUTCOME_TYPE) - Method in class org.cleartk.ml.jar.SequenceDataWriter_ImplBase: Write the encoded features and encoded outcome to the output directory.
writeEndSequence() - Method in class org.cleartk.ml.jar.SequenceDataWriter_ImplBase: Write the marker for the end of a sequence.
writeOutcome(File, OUTCOME_TYPE) - Method in class org.cleartk.ml.baseline.SingleOutcomeClassifierBuilder
wrongAnnotationType(Class<? extends Annotation>, Annotation) - Static method in exception org.cleartk.ml.feature.extractor.CleartkExtractorException
wrongNumberOfAnnotations(Class<? extends Annotation>, int, int) - Static method in exception org.cleartk.ml.feature.extractor.CleartkExtractorException

X

XCAS - Static variable in class org.cleartk.util.cr.XReader
XMI - Static variable in class org.cleartk.util.cr.XReader
XmiWriter - Class in org.cleartk.util.ae: This is a simple annotator for writing out XMI files, used by the parsing examples.
XmiWriter() - Constructor for class org.cleartk.util.ae.XmiWriter
XReader() - Constructor for class org.cleartk.util.cr.XReader

Z

ZeroMeanUnitStddevExtractor<OUTCOME_T,FOCUS_T extends Annotation> - Class in org.cleartk.ml.feature.transform.extractor: Scales features produced by its subextractor to have mean=0, stddev=1 for a given feature
ZeroMeanUnitStddevExtractor(String) - Constructor for class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor
ZeroMeanUnitStddevExtractor(String, FeatureExtractor1<FOCUS_T>) - Constructor for class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor
ZeroMeanUnitStddevExtractor.MeanStddevTuple - Class in org.cleartk.ml.feature.transform.extractor
ZeroMeanUnitStddevExtractor.MeanStddevTuple(double, double) - Constructor for class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanStddevTuple
ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat - Class in org.cleartk.ml.feature.transform.extractor
ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat() - Constructor for class org.cleartk.ml.feature.transform.extractor.ZeroMeanUnitStddevExtractor.MeanVarianceRunningStat

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