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

## A

absNorm() - Method in interface cc.mallet.types.ConstantMatrix
absNorm() - Method in class cc.mallet.types.DenseMatrix
absNorm(double[]) - Static method in class cc.mallet.types.MatrixOps
absNorm() - Method in class cc.mallet.types.SparseMatrixn
absNorm() - Method in class cc.mallet.types.SparseVector
absNormalize() - Method in class cc.mallet.types.DenseMatrix
absNormalize() - Method in interface cc.mallet.types.Matrix
absNormalize(double[]) - Static method in class cc.mallet.types.MatrixOps
absNormalize() - Method in class cc.mallet.types.SparseMatrixn
absoluteDifference(Dirichlet) - Method in class cc.mallet.types.Dirichlet
  Compute the L1 residual between two dirichlets
AbstractBeliefPropagation - Class in cc.mallet.grmm.inference
  Abstract base class for umplementations of belief propagation for general factor graphs.
AbstractBeliefPropagation() - Constructor for class cc.mallet.grmm.inference.AbstractBeliefPropagation
AbstractBeliefPropagation(AbstractBeliefPropagation.MessageStrategy) - Constructor for class cc.mallet.grmm.inference.AbstractBeliefPropagation
AbstractBeliefPropagation.AbstractMessageStrategy - Class in cc.mallet.grmm.inference
AbstractBeliefPropagation.AbstractMessageStrategy() - Constructor for class cc.mallet.grmm.inference.AbstractBeliefPropagation.AbstractMessageStrategy
AbstractBeliefPropagation.MaxProductMessageStrategy - Class in cc.mallet.grmm.inference
AbstractBeliefPropagation.MaxProductMessageStrategy() - Constructor for class cc.mallet.grmm.inference.AbstractBeliefPropagation.MaxProductMessageStrategy
AbstractBeliefPropagation.MessageStrategy - Interface in cc.mallet.grmm.inference
AbstractBeliefPropagation.SumProductMessageStrategy - Class in cc.mallet.grmm.inference
AbstractBeliefPropagation.SumProductMessageStrategy() - Constructor for class cc.mallet.grmm.inference.AbstractBeliefPropagation.SumProductMessageStrategy
AbstractBeliefPropagation.SumProductMessageStrategy(double) - Constructor for class cc.mallet.grmm.inference.AbstractBeliefPropagation.SumProductMessageStrategy
AbstractFactor - Class in cc.mallet.grmm.types
  An Abstract class from which new Factor classes can be subclassed.
AbstractFactor() - Constructor for class cc.mallet.grmm.types.AbstractFactor
AbstractFactor(VarSet) - Constructor for class cc.mallet.grmm.types.AbstractFactor
AbstractInferencer - Class in cc.mallet.grmm.inference
  Abstract base class for inferencers.
AbstractInferencer() - Constructor for class cc.mallet.grmm.inference.AbstractInferencer
AbstractMessageStrategy - Class in cc.mallet.grmm.inference.gbp
  Created: May 29, 2005
AbstractMessageStrategy() - Constructor for class cc.mallet.grmm.inference.gbp.AbstractMessageStrategy
AbstractTableFactor - Class in cc.mallet.grmm.types
  Class for a multivariate multinomial distribution.
AbstractTableFactor(BidirectionalIntObjectMap) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
AbstractTableFactor(Variable) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Creates an identity potential over the given variable.
AbstractTableFactor(Variable, double[]) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
AbstractTableFactor() - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Creates an identity potential over NO variables.
AbstractTableFactor(Variable[]) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Creates an identity potential with the given variables.
AbstractTableFactor(Collection) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Creates an identity potential with the given variables.
AbstractTableFactor(Variable[], double[]) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Creates a potential with the given variables and the given probabilities.
AbstractTableFactor(VarSet, double[]) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Creates a potential with the given variables and the given probabilities.
AbstractTableFactor(Variable[], Matrix) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Creates a potential with the given variables and the given probabilities.
AbstractTableFactor(AbstractTableFactor) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Copy constructor.
AbstractTableFactor(VarSet, Matrix) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Creates a potential with the given variables and the given probabilities.
AbstractTableFactor(AbstractTableFactor, double[]) - Constructor for class cc.mallet.grmm.types.AbstractTableFactor
  Creates a potential with the same variables as another, but different probabilites.
accept(File) - Method in class cc.mallet.util.DirectoryFilter
accept(File) - Method in class cc.mallet.util.RegexFileFilter
accuracyAtCoverage(double) - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
  accuracy at a given coverage percentage
accuracyAtCoverage(double) - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
AccuracyCoverage - Class in cc.mallet.classify.evaluate
  Methods for calculating and displaying the accuracy v.
AccuracyCoverage(Trial, int, String, String) - Constructor for class cc.mallet.classify.evaluate.AccuracyCoverage
  Constructs object, sorts classifications, and creates accuracyValues array
AccuracyCoverage(Trial, String, String) - Constructor for class cc.mallet.classify.evaluate.AccuracyCoverage
AccuracyCoverage(Trial, String) - Constructor for class cc.mallet.classify.evaluate.AccuracyCoverage
AccuracyCoverage(Classifier, InstanceList, String) - Constructor for class cc.mallet.classify.evaluate.AccuracyCoverage
AccuracyCoverage(Classifier, InstanceList, int, String) - Constructor for class cc.mallet.classify.evaluate.AccuracyCoverage
AccuracyCoverage.ClassificationComparator - Class in cc.mallet.classify.evaluate
AccuracyCoverage.ClassificationComparator() - Constructor for class cc.mallet.classify.evaluate.AccuracyCoverage.ClassificationComparator
AccuracyCoverageEvaluator - Class in cc.mallet.extract
  Constructs Accuracy-coverage graph using confidence values to sort Fields.
AccuracyCoverageEvaluator(int) - Constructor for class cc.mallet.extract.AccuracyCoverageEvaluator
accuracyCoverageValuesToString() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
AccuracyEvaluator - Class in cc.mallet.cluster.evaluate
  Accuracy of a clustering is (truePositive + trueNegative) / (numberPairwiseComparisons)
AccuracyEvaluator() - Constructor for class cc.mallet.cluster.evaluate.AccuracyEvaluator
accuracyRecallValuesToString(int) - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
accuracyValues() - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
ACRF - Class in cc.mallet.grmm.learning
  Class for Arbitrary CRFs.
ACRF(Pipe, ACRF.Template[]) - Constructor for class cc.mallet.grmm.learning.ACRF
  Create a ACRF for a 1-d sequence.
ACRF.BigramTemplate - Class in cc.mallet.grmm.learning
  A template that adds edges between adjacent nodes in a label sequence for one factor.
ACRF.BigramTemplate(int) - Constructor for class cc.mallet.grmm.learning.ACRF.BigramTemplate
ACRF.FixedFactorTemplate - Class in cc.mallet.grmm.learning
ACRF.FixedFactorTemplate() - Constructor for class cc.mallet.grmm.learning.ACRF.FixedFactorTemplate
ACRF.GraphPostProcessor - Interface in cc.mallet.grmm.learning
  Interface for making global transformations to an unrolled graph after it has been generated.
ACRF.MaximizableACRF - Class in cc.mallet.grmm.learning
ACRF.MaximizableACRF(InstanceList) - Constructor for class cc.mallet.grmm.learning.ACRF.MaximizableACRF
ACRF.PairwiseFactorTemplate - Class in cc.mallet.grmm.learning
  A template that adds edges between cotemporal nodes of a given pair of factors.
ACRF.PairwiseFactorTemplate(int, int) - Constructor for class cc.mallet.grmm.learning.ACRF.PairwiseFactorTemplate
ACRF.SequenceTemplate - Class in cc.mallet.grmm.learning
  Abstract class for Templates that expect a (FeatureVectorSequence, LabelsSequence) for their instances.
ACRF.SequenceTemplate() - Constructor for class cc.mallet.grmm.learning.ACRF.SequenceTemplate
ACRF.Template - Class in cc.mallet.grmm.learning
  A type of clique in the model.
ACRF.Template() - Constructor for class cc.mallet.grmm.learning.ACRF.Template
ACRF.UnigramTemplate - Class in cc.mallet.grmm.learning
  A template that adds node potentials for a given factor.
ACRF.UnigramTemplate(int) - Constructor for class cc.mallet.grmm.learning.ACRF.UnigramTemplate
ACRF.UnrolledGraph - Class in cc.mallet.grmm.learning
ACRF.UnrolledGraph(Instance, ACRF.Template[], ACRF.Template[]) - Constructor for class cc.mallet.grmm.learning.ACRF.UnrolledGraph
ACRF.UnrolledGraph(Instance, ACRF.Template[], List, boolean) - Constructor for class cc.mallet.grmm.learning.ACRF.UnrolledGraph
  Creates a graphical model for a given instance.
ACRF.UnrolledVarSet - Class in cc.mallet.grmm.learning
  A clique in the unrolled graphical model (an instantiation of some Template).
ACRF.UnrolledVarSet(ACRF.UnrolledGraph, ACRF.Template, Variable[], FeatureVector) - Constructor for class cc.mallet.grmm.learning.ACRF.UnrolledVarSet
ACRFEvaluator - Class in cc.mallet.grmm.learning
  Created: Sun Jan 25 23:28:45 2004
ACRFEvaluator() - Constructor for class cc.mallet.grmm.learning.ACRFEvaluator
ACRFExtractor - Class in cc.mallet.grmm.learning.extract
  Created: Mar 1, 2005
ACRFExtractor(ACRF, Pipe, Pipe) - Constructor for class cc.mallet.grmm.learning.extract.ACRFExtractor
ACRFExtractorTrainer - Class in cc.mallet.grmm.learning.extract
  Created: Mar 31, 2005
ACRFExtractorTrainer() - Constructor for class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
AcrfExtractorTui - Class in cc.mallet.grmm.learning.extract
AcrfExtractorTui() - Constructor for class cc.mallet.grmm.learning.extract.AcrfExtractorTui
AcrfSerialEvaluator - Class in cc.mallet.grmm.learning
  Created: Aug 24, 2005
AcrfSerialEvaluator(List) - Constructor for class cc.mallet.grmm.learning.AcrfSerialEvaluator
ACRFTrainer - Interface in cc.mallet.grmm.learning
  $Id: ACRFTrainer.java,v 1.1 2007/10/22 21:37:43 mccallum Exp $
actionPerformed(ActionEvent) - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
AdaBoost - Class in cc.mallet.classify
  AdaBoost Robert E.
AdaBoost(Pipe, Classifier[], double[]) - Constructor for class cc.mallet.classify.AdaBoost
AdaBoostM2 - Class in cc.mallet.classify
  AdaBoostM2
AdaBoostM2(Pipe, Classifier[], double[]) - Constructor for class cc.mallet.classify.AdaBoostM2
AdaBoostM2Trainer - Class in cc.mallet.classify
  This version of AdaBoost can handle multi-class problems.
AdaBoostM2Trainer(ClassifierTrainer, int) - Constructor for class cc.mallet.classify.AdaBoostM2Trainer
AdaBoostM2Trainer(ClassifierTrainer) - Constructor for class cc.mallet.classify.AdaBoostM2Trainer
AdaBoostTrainer - Class in cc.mallet.classify
  This version of AdaBoost should be used only for binary classification.
AdaBoostTrainer(ClassifierTrainer, int) - Constructor for class cc.mallet.classify.AdaBoostTrainer
AdaBoostTrainer(ClassifierTrainer) - Constructor for class cc.mallet.classify.AdaBoostTrainer
add(String) - Method in class cc.mallet.classify.evaluate.Graph.Legend
add(Classification) - Method in class cc.mallet.classify.Trial
add(int, Classification) - Method in class cc.mallet.classify.Trial
add(Object) - Method in class cc.mallet.grmm.types.BitVarSet
add(Object) - Method in class cc.mallet.grmm.types.HashVarSet
add(Object, boolean) - Method in class cc.mallet.grmm.types.HashVarSet
add(Object) - Method in class cc.mallet.grmm.types.ListVarSet
add(Object) - Method in class cc.mallet.grmm.types.Tree
add(Variable) - Method in class cc.mallet.grmm.types.Universe
add(Object) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
add(int, int, Object) - Method in class cc.mallet.grmm.util.CSIntInt2ObjectMultiMap
add(Object) - Method in class cc.mallet.grmm.util.THashMultiMap
  Adds `key` as a key with an empty list as a value.
add(FeatureVector) - Method in class cc.mallet.types.AugmentableFeatureVector
  Adds all indices that are present in some other feature vector with value 1.0.
add(FeatureVector, String) - Method in class cc.mallet.types.AugmentableFeatureVector
  Adds all features from some other feature vector with weight 1.0.
add(FeatureVector, String, boolean) - Method in class cc.mallet.types.AugmentableFeatureVector
  Adds all features from some other feature vector with weight 1.0.
add(int, double) - Method in class cc.mallet.types.AugmentableFeatureVector
add(Object, double) - Method in class cc.mallet.types.AugmentableFeatureVector
add(int) - Method in class cc.mallet.types.AugmentableFeatureVector
add(FeatureConjunction) - Method in class cc.mallet.types.FeatureConjunction.List
add(Object) - Method in class cc.mallet.types.FeatureSelection
add(int) - Method in class cc.mallet.types.FeatureSelection
add(int) - Method in class cc.mallet.types.FeatureSequence
add(Object) - Method in class cc.mallet.types.FeatureSequence
add(Object, Object, Object, Object, double) - Method in class cc.mallet.types.InstanceList
  Deprecated. Use trainingset.addThruPipe (new Instance(data,target,name,source)) instead.
add(Object, Object, Object, Object) - Method in class cc.mallet.types.InstanceList
  Deprecated. Use trainingset.add (new Instance(data,target,name,source)) instead.
add(Instance) - Method in class cc.mallet.types.InstanceList
  Appends the instance to this list without passing the instance through the InstanceList's pipe.
add(Instance, double) - Method in class cc.mallet.types.InstanceList
  Appends the instance to this list without passing it through this InstanceList's pipe, assigning it the specified weight.
add(int, Instance) - Method in class cc.mallet.types.InstanceList
add(Instance, double) - Method in class cc.mallet.types.MultiInstanceList
add(Instance) - Method in class cc.mallet.types.MultiInstanceList
add(int, Instance) - Method in class cc.mallet.types.MultiInstanceList
add(Instance) - Method in class cc.mallet.types.PagedInstanceList
  Appends the instance to this list.
add(Classification) - Method in class cc.mallet.types.ROCData
  Adds classification results to the ROC data
add(Trial) - Method in class cc.mallet.types.ROCData
  Adds trial results to the ROC data
add(ROCData) - Method in class cc.mallet.types.ROCData
  Adds existing ROC data to this ROC data
add(String) - Method in class cc.mallet.types.TokenSequence
add(Object) - Method in interface cc.mallet.util.Addable
add(CommandOption) - Method in class cc.mallet.util.CommandOption.List
add(CommandOption[]) - Method in class cc.mallet.util.CommandOption.List
add(CommandOption.List) - Method in class cc.mallet.util.CommandOption.List
add(Class) - Method in class cc.mallet.util.CommandOption.List
add(double) - Method in class cc.mallet.util.DoubleList
add(String, Object, PropertyList) - Static method in class cc.mallet.util.PropertyList
add(String, String, PropertyList) - Static method in class cc.mallet.util.PropertyList
add(String, double, PropertyList) - Static method in class cc.mallet.util.PropertyList
Addable - Interface in cc.mallet.util
addAll(Collection<? extends Classification>) - Method in class cc.mallet.classify.Trial
addAll(int, Collection<? extends Classification>) - Method in class cc.mallet.classify.Trial
addAll(Collection) - Method in class cc.mallet.grmm.types.HashVarSet
addAll(Collection) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
addAll(Collection<? extends Instance>) - Method in class cc.mallet.types.InstanceList
addAll(int, Collection<? extends Instance>) - Method in class cc.mallet.types.InstanceList
addAll(Object[]) - Method in class cc.mallet.types.TokenSequence
addAllFactors(FactorGraph, List) - Static method in class cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator
AddClassifierTokenPredictions - Class in cc.mallet.pipe
  This pipe uses a Classifier to label each token (i.e., using 0-th order Markov assumption), then adds the predictions as features to each token.
AddClassifierTokenPredictions(InstanceList) - Constructor for class cc.mallet.pipe.AddClassifierTokenPredictions
AddClassifierTokenPredictions(InstanceList, InstanceList) - Constructor for class cc.mallet.pipe.AddClassifierTokenPredictions
AddClassifierTokenPredictions(AddClassifierTokenPredictions.TokenClassifiers, int[], boolean, InstanceList) - Constructor for class cc.mallet.pipe.AddClassifierTokenPredictions
AddClassifierTokenPredictions.TokenClassifiers - Class in cc.mallet.pipe
  This inner class represents the trained token classifiers.
AddClassifierTokenPredictions.TokenClassifiers(InstanceList) - Constructor for class cc.mallet.pipe.AddClassifierTokenPredictions.TokenClassifiers
  Train a token classifier using the given Instances with 5-fold cross validation
AddClassifierTokenPredictions.TokenClassifiers(InstanceList, int, int) - Constructor for class cc.mallet.pipe.AddClassifierTokenPredictions.TokenClassifiers
AddClassifierTokenPredictions.TokenClassifiers(ClassifierTrainer, InstanceList, int, int) - Constructor for class cc.mallet.pipe.AddClassifierTokenPredictions.TokenClassifiers
addClique(ACRF.UnrolledVarSet) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
addConjunction(String, Alphabet, int[], boolean[]) - Method in class cc.mallet.pipe.AugmentableFeatureVectorAddConjunctions
addDataToGraph(double[], int, String) - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
addDocumentExtraction(DocumentExtraction) - Method in class cc.mallet.extract.Extraction
addDocuments(InstanceList, int, int, int, String, Randoms) - Method in class cc.mallet.topics.LDA
  Deprecated.
addEvaluator(TransducerEvaluator) - Method in class cc.mallet.fst.TransducerTrainer
addEvaluators(Collection<TransducerEvaluator>) - Method in class cc.mallet.fst.TransducerTrainer
addEvidence(FactorGraph, Assignment) - Static method in class cc.mallet.grmm.util.Models
  Returns a new factor graph, the same as a given one, except that all the nodes in the given Assignment are clamped as evidence.
addEvidence(FactorGraph, Assignment, Map) - Static method in class cc.mallet.grmm.util.Models
addEvidence(UndirectedModel, Assignment) - Static method in class cc.mallet.grmm.util.Models
addFactor(Variable, Variable, double[]) - Method in class cc.mallet.grmm.types.FactorGraph
addFactor(Factor) - Method in class cc.mallet.grmm.types.FactorGraph
  Adds a factor to the model.
addFactor(Factor) - Method in class cc.mallet.grmm.types.UndirectedModel
addFeaturesClassEntropyThreshold - Variable in class cc.mallet.classify.DecisionTree
addFeatureWeightsTo(double[]) - Method in class cc.mallet.types.FeatureSequence
addFeatureWeightsTo(double[], double) - Method in class cc.mallet.types.FeatureSequence
addFiller(LabeledSpan) - Method in class cc.mallet.extract.Field
addFixedPotential(ACRF.Template) - Method in class cc.mallet.grmm.learning.ACRF
addFixedPotentials(ACRF.Template[]) - Method in class cc.mallet.grmm.learning.ACRF
addFullyConnectedStates(String[]) - Method in class cc.mallet.fst.CRF
  Add a group of states that are fully connected with each other, with parameters equal zero, and labels on their out-going arcs the same name as their destination state names.
addFullyConnectedStates(String[]) - Method in class cc.mallet.fst.HMM
  Add a group of states that are fully connected with each other, with parameters equal zero, and labels on their out-going arcs the same name as their destination state names.
addFullyConnectedStatesForBiLabels() - Method in class cc.mallet.fst.CRF
addFullyConnectedStatesForBiLabels() - Method in class cc.mallet.fst.HMM
addFullyConnectedStatesForLabels() - Method in class cc.mallet.fst.CRF
addFullyConnectedStatesForLabels() - Method in class cc.mallet.fst.HMM
addFullyConnectedStatesForThreeQuarterLabels(InstanceList) - Method in class cc.mallet.fst.CRF
addFullyConnectedStatesForThreeQuarterLabels(InstanceList) - Method in class cc.mallet.fst.HMM
addFullyConnectedStatesForTriLabels() - Method in class cc.mallet.fst.CRF
addFullyConnectedStatesForTriLabels() - Method in class cc.mallet.fst.HMM
addInstances(InstanceList) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
addInstances(InstanceList, List<LabelSequence>) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
addInstances(InstanceList, int) - Method in class cc.mallet.topics.NPTopicModel
addInstances(InstanceList) - Method in class cc.mallet.topics.ParallelTopicModel
addInstances(InstanceList[]) - Method in class cc.mallet.topics.PolylingualTopicModel
addInstances(InstanceList) - Method in class cc.mallet.topics.SimpleLDA
addInstantiatedCliques(ACRF.UnrolledGraph, FeatureVectorSequence, LabelsAssignment) - Method in class cc.mallet.grmm.examples.CrossTemplate1
addInstantiatedCliques(ACRF.UnrolledGraph, FeatureVectorSequence, LabelsAssignment) - Method in class cc.mallet.grmm.learning.ACRF.BigramTemplate
addInstantiatedCliques(ACRF.UnrolledGraph, FeatureVectorSequence, LabelsAssignment) - Method in class cc.mallet.grmm.learning.ACRF.PairwiseFactorTemplate
addInstantiatedCliques(ACRF.UnrolledGraph, FeatureVectorSequence, LabelsAssignment) - Method in class cc.mallet.grmm.learning.ACRF.SequenceTemplate
  Adds all instiated cliques for an instance.
addInstantiatedCliques(ACRF.UnrolledGraph, Instance) - Method in class cc.mallet.grmm.learning.ACRF.SequenceTemplate
addInstantiatedCliques(ACRF.UnrolledGraph, Instance) - Method in class cc.mallet.grmm.learning.ACRF.Template
  Adds all instiated cliques for an instance.
addInstantiatedCliques(ACRF.UnrolledGraph, FeatureVectorSequence, LabelsAssignment) - Method in class cc.mallet.grmm.learning.ACRF.UnigramTemplate
addInstantiatedCliques(ACRF.UnrolledGraph, FeatureVectorSequence, LabelsAssignment) - Method in class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
addItem(String, int, Color) - Method in class cc.mallet.classify.evaluate.Graph
addItem(String, int) - Method in class cc.mallet.classify.evaluate.Graph
addItemVector(Vector, String) - Method in class cc.mallet.classify.evaluate.Graph
  Adds a new data series
addLogProbabilities(double[]) - Method in class cc.mallet.types.Multinomial.Logged
addMultinomial(Multinomial) - Method in class cc.mallet.types.Dirichlet.Estimator
addNode(Object, Object) - Method in class cc.mallet.grmm.inference.JunctionTree
addNode(Object, Object) - Method in class cc.mallet.grmm.types.Tree
addOrderNStates(InstanceList, int[], boolean[], String, Pattern, Pattern, boolean) - Method in class cc.mallet.fst.CRF
  Assumes that the CRF's output alphabet contains `String`s.
addOrderNStates(InstanceList, int[], boolean[], String, Pattern, Pattern, boolean) - Method in class cc.mallet.fst.HMM
  Assumes that the HMM's output alphabet contains `String`s.
addProbabilities(double[]) - Method in class cc.mallet.types.Multinomial.Logged
addProbabilitiesTo(double[]) - Method in class cc.mallet.types.Multinomial
addPrunedWordsToStoplist(SimpleTokenizer, int) - Method in class cc.mallet.pipe.FeatureCountPipe
  Add all pruned words to the internal stoplist of a SimpleTokenizer.
addRandomNodePotentials(Random, FactorGraph) - Static method in class cc.mallet.grmm.inference.RandomGraphs
addRow(Variable[], int[]) - Method in class cc.mallet.grmm.types.Assignment
addRow(Variable[], double[]) - Method in class cc.mallet.grmm.types.Assignment
addRow(Variable[], Object[]) - Method in class cc.mallet.grmm.types.Assignment
addRow(Object[]) - Method in class cc.mallet.grmm.types.Assignment
addRow(Assignment) - Method in class cc.mallet.grmm.types.Assignment
addSelfTransitioningStateForAllLabels(String) - Method in class cc.mallet.fst.CRF
addSelfTransitioningStateForAllLabels(String) - Method in class cc.mallet.fst.HMM
addSomeUnsupportedWeights(InstanceList) - Method in class cc.mallet.grmm.learning.ACRF.Template
addStartState() - Method in class cc.mallet.fst.CRF
addStartState(String) - Method in class cc.mallet.fst.CRF
addState(String, double, double, String[], String[], String[][]) - Method in class cc.mallet.fst.CRF
addState(String, double, double, String[], String[], String[]) - Method in class cc.mallet.fst.CRF
addState(String, double, double, String[], String[]) - Method in class cc.mallet.fst.CRF
  Default gives separate parameters to each transition.
addState(String, String[]) - Method in class cc.mallet.fst.CRF
  Add a state with parameters equal zero, and labels on out-going arcs the same name as their destination state names.
addState(String, double, double, int[], int[], double[], String[]) - Method in class cc.mallet.fst.FeatureTransducer
addState(String, double, double, Object[], Object[], double[], String[]) - Method in class cc.mallet.fst.FeatureTransducer
addState(String, double, double, String[], String[]) - Method in class cc.mallet.fst.HMM
addState(String, String[]) - Method in class cc.mallet.fst.HMM
  Add a state with parameters equal zero, and labels on out-going arcs the same name as their destination state names.
addState(String, String) - Method in class cc.mallet.fst.semi_supervised.StateLabelMap
  Adds a state to the map.
addStatesForBiLabelsConnectedAsIn(InstanceList) - Method in class cc.mallet.fst.CRF
  Add states to create a second-order Markov model on labels, adding only those transitions the occur in the given trainingSet.
addStatesForBiLabelsConnectedAsIn(InstanceList) - Method in class cc.mallet.fst.HMM
  Add states to create a second-order Markov model on labels, adding only those transitions the occur in the given trainingSet.
addStatesForHalfLabelsConnectedAsIn(InstanceList) - Method in class cc.mallet.fst.CRF
  Add as many states as there are labels, but don't create separate weights for each source-destination pair of states.
addStatesForHalfLabelsConnectedAsIn(InstanceList) - Method in class cc.mallet.fst.HMM
  Add as many states as there are labels, but don't create separate weights for each source-destination pair of states.
addStatesForLabelsConnectedAsIn(InstanceList) - Method in class cc.mallet.fst.CRF
  Add states to create a first-order Markov model on labels, adding only those transitions the occur in the given trainingSet.
addStatesForLabelsConnectedAsIn(InstanceList) - Method in class cc.mallet.fst.HMM
  Add states to create a first-order Markov model on labels, adding only those transitions the occur in the given trainingSet.
addStatesForThreeQuarterLabelsConnectedAsIn(InstanceList) - Method in class cc.mallet.fst.CRF
  Add as many states as there are labels, but don't create separate observational-test-weights for each source-destination pair of states---instead have all the incoming transitions to a state share the same observational-feature-test weights.
addStatesForThreeQuarterLabelsConnectedAsIn(InstanceList) - Method in class cc.mallet.fst.HMM
  Add as many states as there are labels, but don't create separate observational-test-weights for each source-destination pair of states---instead have all the incoming transitions to a state share the same observational-feature-test weights.
addStopWords(String[]) - Method in class cc.mallet.pipe.TokenSequenceRemoveStopwords
addStopWords(File) - Method in class cc.mallet.pipe.TokenSequenceRemoveStopwords
  Add whitespace-separated tokens in file "wordlist" to the stoplist.
addThruPipe(Iterator<Instance>) - Method in class cc.mallet.types.InstanceList
  Adds to this list every instance generated by the iterator, passing each one through this InstanceList's pipe.
addThruPipe(Instance) - Method in class cc.mallet.types.InstanceList
  Adds the input instance to this list, after passing it through the InstanceList's pipe.
addTo(double[], double) - Method in class cc.mallet.types.AugmentableFeatureVector
addTo(double[]) - Method in class cc.mallet.types.AugmentableFeatureVector
addTo(double[]) - Method in class cc.mallet.types.DenseVector
addTo(double[], double) - Method in class cc.mallet.types.DenseVector
addTo(AugmentableFeatureVector, double, FeatureSelection) - Method in class cc.mallet.types.FeatureConjunction
addTo(AugmentableFeatureVector, double) - Method in class cc.mallet.types.FeatureConjunction
addTo(AugmentableFeatureVector) - Method in class cc.mallet.types.FeatureConjunction
addTo(AugmentableFeatureVector, double, FeatureSelection) - Method in class cc.mallet.types.FeatureConjunction.List
addTo(AugmentableFeatureVector, double) - Method in class cc.mallet.types.FeatureConjunction.List
addTo(double[]) - Method in class cc.mallet.types.Label
addTo(double[], double) - Method in class cc.mallet.types.Label
addTo(double[]) - Method in interface cc.mallet.types.Labeling
addTo(double[], double) - Method in interface cc.mallet.types.Labeling
addTo(double[], double) - Method in class cc.mallet.types.SparseVector
addTo(double[]) - Method in class cc.mallet.types.SparseVector
addTrial(Trial, String) - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
addTrial(Trial, int, String) - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
addWeight(int, String) - Method in class cc.mallet.fst.CRF.State
advance() - Method in interface cc.mallet.grmm.types.AssignmentIterator
afterFactorAdd(Factor) - Method in class cc.mallet.grmm.types.DirectedModel
afterFactorAdd(Factor) - Method in class cc.mallet.grmm.types.FactorGraph
  Performs operations on a factor after it has been added to the model, such as caching.
AgglomerativeNeighbor - Class in cc.mallet.cluster.neighbor_evaluator
  A `Neighbor` created by merging two clusters of the original Clustering.
AgglomerativeNeighbor(Clustering, Clustering, int[][]) - Constructor for class cc.mallet.cluster.neighbor_evaluator.AgglomerativeNeighbor
AgglomerativeNeighbor(Clustering, Clustering, int[], int[]) - Constructor for class cc.mallet.cluster.neighbor_evaluator.AgglomerativeNeighbor
AgglomerativeNeighbor(Clustering, Clustering, int, int) - Constructor for class cc.mallet.cluster.neighbor_evaluator.AgglomerativeNeighbor
AGIS - Class in cc.mallet.optimize
AGIS(Optimizable.ByGISUpdate, double) - Constructor for class cc.mallet.optimize.AGIS
AGIS(Optimizable.ByGISUpdate, double, boolean) - Constructor for class cc.mallet.optimize.AGIS
algorithms - Variable in class cc.mallet.grmm.test.TestInference
ALL_DIRECTORIES - Static variable in class cc.mallet.pipe.iterator.FileIterator
  Use as label names all the directory names in the filename.
ALL_DIRECTORIES - Static variable in class cc.mallet.pipe.iterator.FileListIterator
  Use as label names all the directory names in the filename.
ALL_DIRECTORIES - Static variable in class cc.mallet.pipe.iterator.UnlabeledFileIterator
  Use as label names all the directory names in the filename.
allAlgs - Variable in class cc.mallet.grmm.test.TestInference
allFactorsContaining(Collection) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns a collection of all factors that involve only the given variables.
allFactorsContaining(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
allFactorsOf(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns a list of all factors in the graph whose domain is exactly the specified var.
allFactorsOf(Collection) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns a list of all factors in the graph whose domain is exactly the specified Collection of Variables.
allL1MarginalDistance(FactorGraph, Inferencer, Inferencer) - Static method in class cc.mallet.grmm.inference.Utils
AllPairsIterator - Class in cc.mallet.cluster.iterator
  Iterate over all pairs of Instances.
AllPairsIterator(Clustering) - Constructor for class cc.mallet.cluster.iterator.AllPairsIterator
almostEquals(Factor) - Method in class cc.mallet.grmm.types.AbstractFactor
almostEquals(Factor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.Assignment
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.BetaFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.ConstantFactor
almostEquals(Factor) - Method in class cc.mallet.grmm.types.CPT
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.CPT
almostEquals(Factor) - Method in interface cc.mallet.grmm.types.Factor
  Returns whether this is almost equal to another potential.
almostEquals(Factor, double) - Method in interface cc.mallet.grmm.types.Factor
almostEquals(Factor) - Method in class cc.mallet.grmm.types.FactorGraph
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.FactorGraph
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.NormalFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.PottsTableFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.SkeletonFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.UniformFactor
almostEquals(Factor, double) - Method in class cc.mallet.grmm.types.UniNormalFactor
almostEquals(ConstantMatrix) - Method in class cc.mallet.types.DenseMatrix
almostEquals(double, double) - Static method in class cc.mallet.util.Maths
almostEquals(double, double, double) - Static method in class cc.mallet.util.Maths
almostEquals(double[], double[], double) - Static method in class cc.mallet.util.Maths
alpha - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice.LatticeNode
alpha - Variable in class cc.mallet.fst.semi_supervised.GELattice.LatticeNode
alpha - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
alpha - Variable in class cc.mallet.topics.MarginalProbEstimator
alpha - Variable in class cc.mallet.topics.NPTopicModel
alpha - Variable in class cc.mallet.topics.ParallelTopicModel
alpha - Variable in class cc.mallet.topics.PolylingualTopicModel
alpha - Variable in class cc.mallet.topics.SimpleLDA
alpha - Variable in class cc.mallet.topics.TopicInferencer
alpha - Variable in class cc.mallet.topics.WorkerRunnable
alpha(int) - Method in class cc.mallet.types.Dirichlet
alphabet - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
alphabet - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
alphabet - Variable in class cc.mallet.topics.NPTopicModel
alphabet - Variable in class cc.mallet.topics.ParallelTopicModel
alphabet - Variable in class cc.mallet.topics.SimpleLDA
Alphabet - Class in cc.mallet.types
  A mapping between integers and objects where the mapping in each direction is efficient.
Alphabet(int, Class) - Constructor for class cc.mallet.types.Alphabet
Alphabet(Class) - Constructor for class cc.mallet.types.Alphabet
Alphabet(int) - Constructor for class cc.mallet.types.Alphabet
Alphabet() - Constructor for class cc.mallet.types.Alphabet
Alphabet(Object[]) - Constructor for class cc.mallet.types.Alphabet
AlphabetCarrying - Interface in cc.mallet.types
  An interface for objects that contain one or more Alphabets.
AlphabetFactory - Class in cc.mallet.types
AlphabetFactory() - Constructor for class cc.mallet.types.AlphabetFactory
alphabetOfSize(int) - Static method in class cc.mallet.types.AlphabetFactory
  Create a dummy alphabet with `n` dimensions
alphabets - Variable in class cc.mallet.topics.PolylingualTopicModel
alphabetsMatch(AlphabetCarrying) - Method in class cc.mallet.classify.Classifier
alphabetsMatch(AlphabetCarrying) - Method in class cc.mallet.classify.NaiveBayesTrainer
alphabetsMatch(AlphabetCarrying) - Method in class cc.mallet.pipe.Pipe
alphabetsMatch(AlphabetCarrying, AlphabetCarrying) - Static method in class cc.mallet.types.Alphabet
  Convenience method that can often implement alphabetsMatch in classes that implement the AlphabetsCarrying interface.
alphabetsMatch(AlphabetCarrying) - Method in class cc.mallet.types.FeatureSequence
alphabetsMatch(AlphabetCarrying) - Method in class cc.mallet.types.FeatureVector
alphabetsMatch(AlphabetCarrying) - Method in class cc.mallet.types.Instance
alphaSum - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
alphaSum - Variable in class cc.mallet.topics.MarginalProbEstimator
alphaSum - Variable in class cc.mallet.topics.ParallelTopicModel
alphaSum - Variable in class cc.mallet.topics.PolylingualTopicModel
alphaSum - Variable in class cc.mallet.topics.SimpleLDA
alphaSum - Variable in class cc.mallet.topics.WorkerRunnable
any(TDoubleProcedure, double[]) - Static method in class cc.mallet.util.ArrayUtils
  Returns true if the procedure proc returns true for any element of the array v.
any(TObjectProcedure, Object[][]) - Static method in class cc.mallet.util.ArrayUtils
  Returns true if the procedure proc returns true for any element of the array v.
append(double[], double) - Static method in class cc.mallet.types.MatrixOps
append(int[], int[]) - Static method in class cc.mallet.util.ArrayUtils
  Returns a new array that is the concatenation of a1 and a2.
append(double[], double[]) - Static method in class cc.mallet.util.ArrayUtils
  Returns a new array that is the concatenation of a1 and a2.
append(int[], int) - Static method in class cc.mallet.util.ArrayUtils
  Returns a new array with a single element appended at the end.
append(boolean[], boolean) - Static method in class cc.mallet.util.ArrayUtils
  Returns a new array with a single element appended at the end.
append(Object[], Object) - Static method in class cc.mallet.util.ArrayUtils
  Returns a new array with a single element appended at the end.
append(PropertyList) - Method in class cc.mallet.util.PropertyList
apply(Transducer, Sequence, int) - Static method in class cc.mallet.fst.SimpleTagger
  Apply a transducer to an input sequence to produce the k highest-scoring output sequences.
appxAlgs - Variable in class cc.mallet.grmm.test.TestInference
argmax() - Method in class cc.mallet.grmm.types.AbstractFactor
argmax() - Method in class cc.mallet.grmm.types.AbstractTableFactor
argmax() - Method in class cc.mallet.grmm.types.CPT
argmax() - Method in interface cc.mallet.grmm.types.Factor
  Returns the assignment that maximizes this potential.
argmax() - Method in class cc.mallet.grmm.types.FactorGraph
argmax(double[]) - Static method in class cc.mallet.util.ArrayUtils
argmax(TObjectDoubleHashMap) - Static method in class cc.mallet.util.CollectionUtils
  Returns the key in map that has the greatest score
Array2FeatureVector - Class in cc.mallet.pipe
  Converts a Java array of numerical types to a FeatureVector, where the Alphabet is the data array index wrapped in an Integer object.
Array2FeatureVector(int) - Constructor for class cc.mallet.pipe.Array2FeatureVector
Array2FeatureVector() - Constructor for class cc.mallet.pipe.Array2FeatureVector
Array2FeatureVector(Alphabet, Alphabet) - Constructor for class cc.mallet.pipe.Array2FeatureVector
  Construct a pipe based on the dimensions of the data and target.
arrayCopyFrom(int, Matrix) - Method in class cc.mallet.types.DenseVector
arrayCopyFrom(double[]) - Method in class cc.mallet.types.DenseVector
  Copy values from an array into this vector.
arrayCopyFrom(double[], int) - Method in class cc.mallet.types.DenseVector
  Copy values from an array starting at a particular index into this vector.
arrayCopyFrom(double[], int) - Method in class cc.mallet.types.Matrix2
  Deprecated.
arrayCopyFrom(double[]) - Method in class cc.mallet.types.SparseVector
  Copy values from an array into this vector.
arrayCopyFrom(double[], int) - Method in class cc.mallet.types.SparseVector
  Copy values from an array starting at a particular location into this vector.
arrayCopyInto(double[], int) - Method in class cc.mallet.types.DenseVector
  Copy the contents of this vector into an array starting at a particular index.
arrayCopyInto(double[], int) - Method in class cc.mallet.types.Matrix2
  Deprecated.
arrayCopyInto(double[], int) - Method in class cc.mallet.types.SparseVector
  Copy the contents of this vector into an array starting at a particular location.
arrayCopyTo(int, Matrix) - Method in class cc.mallet.types.DenseVector
arrayCopyTo(int, double[]) - Method in class cc.mallet.types.DenseVector
ArrayDataAndTargetIterator - Class in cc.mallet.pipe.iterator
ArrayDataAndTargetIterator(List, List) - Constructor for class cc.mallet.pipe.iterator.ArrayDataAndTargetIterator
ArrayDataAndTargetIterator(Object[], Object[]) - Constructor for class cc.mallet.pipe.iterator.ArrayDataAndTargetIterator
ArrayIterator - Class in cc.mallet.pipe.iterator
ArrayIterator(List, Object) - Constructor for class cc.mallet.pipe.iterator.ArrayIterator
ArrayIterator(List) - Constructor for class cc.mallet.pipe.iterator.ArrayIterator
ArrayIterator(Object[], Object) - Constructor for class cc.mallet.pipe.iterator.ArrayIterator
ArrayIterator(Object[]) - Constructor for class cc.mallet.pipe.iterator.ArrayIterator
ArrayListSequence<E> - Class in cc.mallet.types
ArrayListSequence() - Constructor for class cc.mallet.types.ArrayListSequence
ArrayListUtils - Class in cc.mallet.util
ArrayListUtils() - Constructor for class cc.mallet.util.ArrayListUtils
ArraySequence<E> - Class in cc.mallet.types
ArraySequence(ArrayList<E>) - Constructor for class cc.mallet.types.ArraySequence
ArraySequence(E[], boolean) - Constructor for class cc.mallet.types.ArraySequence
ArraySequence(E[]) - Constructor for class cc.mallet.types.ArraySequence
ArraySequence(Sequence<E>, boolean) - Constructor for class cc.mallet.types.ArraySequence
ArrayUtils - Class in cc.mallet.util
  Static utility methods for arrays (like java.util.Arrays, but more useful).
asFactor(Inferencer) - Static method in class cc.mallet.grmm.types.Factors
  Adapter that allows an Inferencer to be treated as if it were a factor.
asJavaRandom() - Method in class cc.mallet.util.Randoms
  Deprecated.
asList() - Method in class cc.mallet.grmm.types.Assignment
  Returns a list of single-row assignments, one for each row in this assignment.
assertLabelExpNonNull() - Method in class cc.mallet.fst.semi_supervised.GECriteria
assertNotNaN() - Method in class cc.mallet.fst.CRF.Factors
assertNotNaNOrInfinite() - Method in class cc.mallet.fst.CRF.Factors
assignedVertexPtls - Variable in class cc.mallet.grmm.inference.AbstractBeliefPropagation
Assignment - Class in cc.mallet.grmm.types
  An assignment to a bunch of variables.
Assignment() - Constructor for class cc.mallet.grmm.types.Assignment
  Creates an empty assignment.
Assignment(Variable, int) - Constructor for class cc.mallet.grmm.types.Assignment
Assignment(Variable, double) - Constructor for class cc.mallet.grmm.types.Assignment
Assignment(Variable[], int[]) - Constructor for class cc.mallet.grmm.types.Assignment
  Creates an assignemnt for the given variables.
Assignment(Variable[], double[]) - Constructor for class cc.mallet.grmm.types.Assignment
  Creates an assignemnt for the given variables.
Assignment(List, int[]) - Constructor for class cc.mallet.grmm.types.Assignment
  Creates an assignemnt for the given variables.
Assignment(FactorGraph, int[]) - Constructor for class cc.mallet.grmm.types.Assignment
  Creates an assignment over all Variables in a model.
assignment() - Method in interface cc.mallet.grmm.types.AssignmentIterator
assignmentIterator() - Method in class cc.mallet.grmm.types.AbstractFactor
assignmentIterator() - Method in class cc.mallet.grmm.types.AbstractTableFactor
AssignmentIterator - Interface in cc.mallet.grmm.types
  Iterates over the assignments to a set of variables.
assignmentIterator() - Method in class cc.mallet.grmm.types.BitVarSet
assignmentIterator() - Method in class cc.mallet.grmm.types.CPT
assignmentIterator() - Method in interface cc.mallet.grmm.types.Factor
  Returns an iterator over all Assignmentss to this potential.
assignmentIterator() - Method in class cc.mallet.grmm.types.FactorGraph
  Returns an iterator over all assignments to all variables of this graphical model.
assignmentIterator() - Method in class cc.mallet.grmm.types.HashVarSet
assignmentIterator() - Method in class cc.mallet.grmm.types.ListVarSet
assignmentIterator() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
assignmentIterator() - Method in interface cc.mallet.grmm.types.VarSet
  Returns an iterator over the assignments to this clique.
asTable() - Method in class cc.mallet.grmm.types.AbstractFactor
asTable() - Method in class cc.mallet.grmm.types.AbstractTableFactor
asTable() - Method in class cc.mallet.grmm.types.Assignment
asTable() - Method in class cc.mallet.grmm.types.CPT
asTable() - Method in interface cc.mallet.grmm.types.Factor
asTable() - Method in class cc.mallet.grmm.types.FactorGraph
AStar - Class in cc.mallet.util.search
  Created by IntelliJ IDEA.
AStar(AStarState[], int) - Constructor for class cc.mallet.util.search.AStar
  Create an A* search iterator starting from the given initial states.
AStarNode - Class in cc.mallet.util.search
  Created by IntelliJ IDEA.
AStarNode(AStarState, AStarNode, double) - Constructor for class cc.mallet.util.search.AStarNode
  Create an A* search node with given state, parent, and cost.
AStarNode.NextNodeIterator - Class in cc.mallet.util.search
  Iterator over new A* search nodes generated by state transitions from this node's state.
AStarNode.NextNodeIterator() - Constructor for class cc.mallet.util.search.AStarNode.NextNodeIterator
AStarState - Interface in cc.mallet.util.search
  Created by IntelliJ IDEA.
AugmentableFeatureVector - Class in cc.mallet.types
AugmentableFeatureVector(Alphabet, int[], double[], int, int, boolean, boolean, boolean) - Constructor for class cc.mallet.types.AugmentableFeatureVector
  To make a binary vector, pass null for "values"
AugmentableFeatureVector(Alphabet, int[], double[], int, boolean, boolean) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(Alphabet, int[], double[], int, boolean) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(Alphabet, int[], double[], int) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(Alphabet, double[], int) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(Alphabet, double[]) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(Alphabet, int, boolean) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(Alphabet, boolean) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(Alphabet) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(FeatureVector) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(FeatureSequence, boolean) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(Alphabet, PropertyList, boolean, boolean) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVector(Alphabet, PropertyList, boolean) - Constructor for class cc.mallet.types.AugmentableFeatureVector
AugmentableFeatureVectorAddConjunctions - Class in cc.mallet.pipe
  Add specified conjunctions to each instance.
AugmentableFeatureVectorAddConjunctions() - Constructor for class cc.mallet.pipe.AugmentableFeatureVectorAddConjunctions
AugmentableFeatureVectorLogScale - Class in cc.mallet.pipe
  Given an AugmentableFeatureVector, set those values greater than or equal to 1 to log(value)+1.
AugmentableFeatureVectorLogScale() - Constructor for class cc.mallet.pipe.AugmentableFeatureVectorLogScale
average(Factor, Factor, double) - Static method in class cc.mallet.grmm.types.Factors
averageMessages(RegionGraph, MessageArray, MessageArray, double) - Method in class cc.mallet.grmm.inference.gbp.FullMessageStrategy
averageMessages(RegionGraph, MessageArray, MessageArray, double) - Method in interface cc.mallet.grmm.inference.gbp.MessageStrategy
averageMessages(RegionGraph, MessageArray, MessageArray, double) - Method in class cc.mallet.grmm.inference.gbp.SparseMessageSender
averageTokenAccuracy(InstanceList) - Method in class cc.mallet.fst.Transducer
  Runs inference across all the instances and returns the average token accuracy.
avgL1MarginalDistance(FactorGraph, Inferencer, Inferencer) - Static method in class cc.mallet.grmm.inference.Utils

## B

BackTrackLineSearch - Class in cc.mallet.optimize
BackTrackLineSearch(Optimizable.ByGradientValue) - Constructor for class cc.mallet.optimize.BackTrackLineSearch
backwardLattice(double[][], double[][][]) - Method in class cc.mallet.fst.semi_supervised.EntropyLattice
  Computes the backward entropies (H^beta).
BaggingClassifier - Class in cc.mallet.classify
BaggingClassifier(Pipe, Classifier[]) - Constructor for class cc.mallet.classify.BaggingClassifier
BaggingTrainer - Class in cc.mallet.classify
  Bagging Trainer.
BaggingTrainer(ClassifierTrainer.Factory, int) - Constructor for class cc.mallet.classify.BaggingTrainer
BaggingTrainer(ClassifierTrainer.Factory) - Constructor for class cc.mallet.classify.BaggingTrainer
BalancedWinnow - Class in cc.mallet.classify
  Classification methods of BalancedWinnow algorithm.
BalancedWinnow(Pipe, double[][]) - Constructor for class cc.mallet.classify.BalancedWinnow
  Passes along data pipe and weights from `BalancedWinnowTrainer`
BalancedWinnowTrainer - Class in cc.mallet.classify
  An implementation of the training methods of a BalancedWinnow on-line classifier.
BalancedWinnowTrainer() - Constructor for class cc.mallet.classify.BalancedWinnowTrainer
  Default constructor.
BalancedWinnowTrainer(double, double, int, double) - Constructor for class cc.mallet.classify.BalancedWinnowTrainer
bandCholesky(double[], int) - Static method in class cc.mallet.util.MVNormal
bandMatrixRoot(int, int) - Static method in class cc.mallet.util.MVNormal
  For testing band cholesky factorization
batchCachedGradient - Variable in class cc.mallet.fst.ThreadedOptimizable
  Gradient obtained from the optimizable for each batch
batchCachedValue - Variable in class cc.mallet.fst.ThreadedOptimizable
  Value obtained from the optimizable for each batch
batchTest(InstanceList, List<Sequence>, String, PrintStream) - Method in class cc.mallet.fst.MultiSegmentationEvaluator
  Tests segmentation using an ArrayList of predicted Sequences instead of a `Transducer`.
BCubedEvaluator - Class in cc.mallet.cluster.evaluate
  Evaluate a Clustering using the B-Cubed evaluation metric.
BCubedEvaluator() - Constructor for class cc.mallet.cluster.evaluate.BCubedEvaluator
beamWidth - Static variable in class cc.mallet.fst.SumLatticeBeam
beforeFactorAdd(Factor) - Method in class cc.mallet.grmm.types.DirectedModel
beforeFactorAdd(Factor) - Method in class cc.mallet.grmm.types.FactorGraph
  Performs checking of a factor before it is added to the model.
bestAssignment() - Method in class cc.mallet.grmm.inference.TRP
bestAssignment(InstanceList) - Method in class cc.mallet.grmm.learning.ACRF
bestAssignment(Instance) - Method in class cc.mallet.grmm.learning.ACRF
bestAssignment(FactorGraph, Inferencer) - Static method in class cc.mallet.grmm.util.Models
  Returns the highest-score Assignment in a model according to a given inferencer.
bestLabelIsCorrect() - Method in class cc.mallet.classify.Classification
bestOutputAlignment() - Method in class cc.mallet.fst.MaxLatticeDefault
bestOutputAlignments(int) - Method in class cc.mallet.fst.MaxLatticeDefault
bestOutputSequence() - Method in interface cc.mallet.fst.MaxLattice
bestOutputSequence() - Method in class cc.mallet.fst.MaxLatticeDefault
bestOutputSequences(int) - Method in interface cc.mallet.fst.MaxLattice
bestOutputSequences(int) - Method in class cc.mallet.fst.MaxLatticeDefault
bestStateAlignment() - Method in class cc.mallet.fst.MaxLatticeDefault
bestStateAlignments(int) - Method in class cc.mallet.fst.MaxLatticeDefault
  Perform the backward pass of Viterbi, returning the n-best sequences of States.
bestStateSequence() - Method in interface cc.mallet.fst.MaxLattice
bestStateSequence() - Method in class cc.mallet.fst.MaxLatticeDefault
bestStateSequences(int) - Method in interface cc.mallet.fst.MaxLattice
bestStateSequences(int) - Method in class cc.mallet.fst.MaxLatticeDefault
bestViterbiNodeSequences(int) - Method in class cc.mallet.fst.MaxLatticeDefault
  Perform the backward pass of Viterbi, returning the n-best sequences of ViterbiNodes.
bestWeight() - Method in class cc.mallet.fst.MaxLatticeDefault
beta - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice.LatticeNode
beta - Variable in class cc.mallet.fst.semi_supervised.GELattice.LatticeNode
beta - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
beta - Variable in class cc.mallet.topics.MarginalProbEstimator
beta - Variable in class cc.mallet.topics.NPTopicModel
beta - Variable in class cc.mallet.topics.ParallelTopicModel
beta - Variable in class cc.mallet.topics.SimpleLDA
beta - Variable in class cc.mallet.topics.TopicInferencer
beta - Variable in class cc.mallet.topics.WorkerRunnable
beta(double, double) - Static method in class cc.mallet.util.Maths
BetaFactor - Class in cc.mallet.grmm.types
  $Id: BetaFactor.java,v 1.1 2007/10/22 21:37:44 mccallum Exp $
BetaFactor(Variable, double, double) - Constructor for class cc.mallet.grmm.types.BetaFactor
BetaFactor(Variable, double, double, double, double) - Constructor for class cc.mallet.grmm.types.BetaFactor
betainv(double, double, double) - Static method in class cc.mallet.util.StatFunctions
betas - Variable in class cc.mallet.topics.PolylingualTopicModel
betaSum - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
betaSum - Variable in class cc.mallet.topics.MarginalProbEstimator
betaSum - Variable in class cc.mallet.topics.NPTopicModel
betaSum - Variable in class cc.mallet.topics.ParallelTopicModel
betaSum - Variable in class cc.mallet.topics.SimpleLDA
betaSum - Variable in class cc.mallet.topics.TopicInferencer
betaSum - Variable in class cc.mallet.topics.WorkerRunnable
betaSums - Variable in class cc.mallet.topics.PolylingualTopicModel
between(double, double) - Method in class cc.mallet.util.Univariate
BidirectionalIntObjectMap - Class in cc.mallet.grmm.types
  A mapping between integers and objects where the mapping in each direction is efficient.
BidirectionalIntObjectMap(int) - Constructor for class cc.mallet.grmm.types.BidirectionalIntObjectMap
BidirectionalIntObjectMap() - Constructor for class cc.mallet.grmm.types.BidirectionalIntObjectMap
BidirectionalIntObjectMap(BidirectionalIntObjectMap) - Constructor for class cc.mallet.grmm.types.BidirectionalIntObjectMap
BINARY_COUNT - Static variable in class cc.mallet.pipe.tsf.CountMatches
BinaryUnaryFactor - Class in cc.mallet.grmm.types
  A factor over a continuous variable theta and binary variables `var`.
BinaryUnaryFactor(Variable, Variable, Variable) - Constructor for class cc.mallet.grmm.types.BinaryUnaryFactor
BIOTokenizationFilter - Class in cc.mallet.extract
  Created: Nov 12, 2004
BIOTokenizationFilter() - Constructor for class cc.mallet.extract.BIOTokenizationFilter
BIOTokenizationFilterWithTokenIndices - Class in cc.mallet.extract
BIOTokenizationFilterWithTokenIndices() - Constructor for class cc.mallet.extract.BIOTokenizationFilterWithTokenIndices
BitVarSet - Class in cc.mallet.grmm.types
  A clique that uses very little time and memory based on the flyweight pattern.
BitVarSet(Universe, BitSet) - Constructor for class cc.mallet.grmm.types.BitVarSet
  Creates a BitSet clique given an alphabet of Variables, and a bitset that says which variables in the alphabet to include in the clique.
BitVarSet(Universe, Collection) - Constructor for class cc.mallet.grmm.types.BitVarSet
BitVarSet(VarSet) - Constructor for class cc.mallet.grmm.types.BitVarSet
BoltzmannPairFactor - Class in cc.mallet.grmm.types
  A factor over a continuous variable theta and binary variables `var`.
BoltzmannPairFactor(Variable, Variable, Variable) - Constructor for class cc.mallet.grmm.types.BoltzmannPairFactor
BoltzmannUnaryFactor - Class in cc.mallet.grmm.types
  A factor over a continuous variable theta and binary variables `var`.
BoltzmannUnaryFactor(Variable, Variable) - Constructor for class cc.mallet.grmm.types.BoltzmannUnaryFactor
Boostable - Interface in cc.mallet.classify
  This interface is a tag indicating that the classifier attends to the InstanceList.getInstanceWeight() weights when training.
BPRegionGenerator - Class in cc.mallet.grmm.inference.gbp
  Created: May 30, 2005
BPRegionGenerator() - Constructor for class cc.mallet.grmm.inference.gbp.BPRegionGenerator
BranchingPipe - Class in cc.mallet.pipe
  Deprecated.
BranchingPipe() - Constructor for class cc.mallet.pipe.BranchingPipe
  Deprecated.
BranchingPipe(Pipe[]) - Constructor for class cc.mallet.pipe.BranchingPipe
  Deprecated.
BranchingPipe(Collection<Pipe>) - Constructor for class cc.mallet.pipe.BranchingPipe
  Deprecated.
BruteForceInferencer - Class in cc.mallet.grmm.inference
  Computes the joint of a GraphicalModel by brute-force calculation.
BruteForceInferencer() - Constructor for class cc.mallet.grmm.inference.BruteForceInferencer
BshInterpreter - Class in cc.mallet.util
BshInterpreter(String) - Constructor for class cc.mallet.util.BshInterpreter
BshInterpreter() - Constructor for class cc.mallet.util.BshInterpreter
buildInitialTypeTopicCounts() - Method in class cc.mallet.topics.ParallelTopicModel
buildJunctionTree(FactorGraph) - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
  Constructs a junction tree from a given factor graph.
buildLocalTypeTopicCounts() - Method in class cc.mallet.topics.WorkerRunnable
  Once we have sampled the local counts, trash the "global" type topic counts and reuse the space to build a summary of the type topic counts specific to this worker's section of the corpus.
BulkLoader - Class in cc.mallet.util
  This class reads through a single file, breaking each line into data and (optional) name and label fields.
BulkLoader() - Constructor for class cc.mallet.util.BulkLoader
burninPeriod - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
burninPeriod - Variable in class cc.mallet.topics.ParallelTopicModel
burninPeriod - Variable in class cc.mallet.topics.PolylingualTopicModel

## C

C45 - Class in cc.mallet.classify
  A C4.5 Decision Tree classifier.
C45(Pipe, C45.Node) - Constructor for class cc.mallet.classify.C45
C45.Node - Class in cc.mallet.classify
C45.Node(InstanceList, C45.Node, int) - Constructor for class cc.mallet.classify.C45.Node
C45.Node(InstanceList, C45.Node, int, int[]) - Constructor for class cc.mallet.classify.C45.Node
C45Trainer - Class in cc.mallet.classify
  A C4.5 decision tree learner, approximtely.
C45Trainer() - Constructor for class cc.mallet.classify.C45Trainer
  Uses default values: not depth limited tree with a minimum of 2 instances in each leaf node
C45Trainer(int) - Constructor for class cc.mallet.classify.C45Trainer
  Construct a depth-limited tree with the given depth limit
C45Trainer(boolean) - Constructor for class cc.mallet.classify.C45Trainer
C45Trainer(int, boolean) - Constructor for class cc.mallet.classify.C45Trainer
cachedCoefficients - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
cachedCoefficients - Variable in class cc.mallet.topics.MarginalProbEstimator
cachedCoefficients - Variable in class cc.mallet.topics.WorkerRunnable
cachedGradient - Variable in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
cachedGradient - Variable in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
cachedGradient - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
cachedGradient - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
cachedGradientChangeStamp - Variable in class cc.mallet.fst.CRFCacheStaleIndicator
CachedMetric - Interface in cc.mallet.types
  Stores a hash for each object being compared for efficient computation.
cachedNumParametersStamp - Variable in class cc.mallet.fst.CRF
cachedValue - Variable in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
cachedValue - Variable in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
cachedValue - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
cachedValue - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
cachedValueChangeStamp - Variable in class cc.mallet.fst.CRFCacheStaleIndicator
cacheIndicator - Variable in class cc.mallet.fst.ThreadedOptimizable
CacheStaleIndicator - Interface in cc.mallet.fst
  Indicates when the value/gradient during training becomes stale.
calcGainRatios(InstanceList, int[], int) - Static method in class cc.mallet.types.GainRatio
  Calculates gain ratios for all (feature, split point) pairs snd returns array of:
calcPerLabelInfoGains(InstanceList) - Static method in class cc.mallet.types.PerLabelInfoGain
calculateExpectations(InstanceList, Transducer, Map<Integer, SumLattice>) - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Calculates the model expectation of all feature constraints.
calculateNCRP(TObjectDoubleHashMap<HierarchicalLDA.NCRPNode>, HierarchicalLDA.NCRPNode, double) - Method in class cc.mallet.topics.HierarchicalLDA
calculateWordLikelihood(TObjectDoubleHashMap<HierarchicalLDA.NCRPNode>, HierarchicalLDA.NCRPNode, double, TIntIntHashMap[], double[], int, int) - Method in class cc.mallet.topics.HierarchicalLDA
callEvaluator(ACRF, InstanceList, InstanceList, InstanceList, int, ACRFEvaluator) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
Calo2Classify - Class in cc.mallet.classify.tui
  Classify documents, run trials, print statistics from a vector file.
Calo2Classify() - Constructor for class cc.mallet.classify.tui.Calo2Classify
canIterateAllTransitions() - Method in class cc.mallet.fst.Transducer
  Some transducers are "generative", meaning that you can get a sequence out of them without giving them an input sequence.
cardinality() - Method in class cc.mallet.types.FeatureSelection
cc.mallet.classify - package cc.mallet.classify
  Classes for training and classifying instances.
cc.mallet.classify.evaluate - package cc.mallet.classify.evaluate
  Classes for computing and displaying the quaility of a classification trial, including accuracy, precision, and confusion matrix.
cc.mallet.classify.examples - package cc.mallet.classify.examples
  Example classes showing how to use classifiers.
cc.mallet.classify.tests - package cc.mallet.classify.tests
  JUnit tests for classifiers
cc.mallet.classify.tui - package cc.mallet.classify.tui
  Command line programs for document classification.
cc.mallet.cluster - package cc.mallet.cluster
  Unsupervised clustering of `Instance` objects within an `InstanceList`.
cc.mallet.cluster.clustering_scorer - package cc.mallet.cluster.clustering_scorer
cc.mallet.cluster.evaluate - package cc.mallet.cluster.evaluate
cc.mallet.cluster.evaluate.tests - package cc.mallet.cluster.evaluate.tests
cc.mallet.cluster.examples - package cc.mallet.cluster.examples
cc.mallet.cluster.iterator - package cc.mallet.cluster.iterator
cc.mallet.cluster.iterator.tests - package cc.mallet.cluster.iterator.tests
cc.mallet.cluster.neighbor_evaluator - package cc.mallet.cluster.neighbor_evaluator
cc.mallet.cluster.tui - package cc.mallet.cluster.tui
cc.mallet.cluster.util - package cc.mallet.cluster.util
cc.mallet.examples - package cc.mallet.examples
cc.mallet.extract - package cc.mallet.extract
  Unimplemented.
cc.mallet.extract.pipe - package cc.mallet.extract.pipe
cc.mallet.extract.test - package cc.mallet.extract.test
cc.mallet.fst - package cc.mallet.fst
  Transducers, including Conditional Random Fields (CRFs).
cc.mallet.fst.confidence - package cc.mallet.fst.confidence
cc.mallet.fst.semi_supervised - package cc.mallet.fst.semi_supervised
cc.mallet.fst.tests - package cc.mallet.fst.tests
  Tests for Transducers, including Conditional Random Fields (CRFs).
cc.mallet.grmm.examples - package cc.mallet.grmm.examples
cc.mallet.grmm.inference - package cc.mallet.grmm.inference
cc.mallet.grmm.inference.gbp - package cc.mallet.grmm.inference.gbp
cc.mallet.grmm.learning - package cc.mallet.grmm.learning
cc.mallet.grmm.learning.extract - package cc.mallet.grmm.learning.extract
cc.mallet.grmm.learning.templates - package cc.mallet.grmm.learning.templates
cc.mallet.grmm.test - package cc.mallet.grmm.test
cc.mallet.grmm.types - package cc.mallet.grmm.types
cc.mallet.grmm.util - package cc.mallet.grmm.util
cc.mallet.optimize - package cc.mallet.optimize
  Classes for finding the maximum of a function.
cc.mallet.optimize.tests - package cc.mallet.optimize.tests
  JUnit tests for maximize.
cc.mallet.pipe - package cc.mallet.pipe
  Classes for processing arbitrary data into instances.
cc.mallet.pipe.iterator - package cc.mallet.pipe.iterator
  Classes that generate instances from different kinds of input or data structures.
cc.mallet.pipe.iterator.tests - package cc.mallet.pipe.iterator.tests
cc.mallet.pipe.tests - package cc.mallet.pipe.tests
  JUnit tests for pipes.
cc.mallet.pipe.tsf - package cc.mallet.pipe.tsf
  TokenSequenceFeature Pipes.
cc.mallet.pipe.tsf.tests - package cc.mallet.pipe.tsf.tests
  JUnit tests for TokenSequenceFeature Pipes.
cc.mallet.share.casutton.ner - package cc.mallet.share.casutton.ner
cc.mallet.share.mccallum.ner - package cc.mallet.share.mccallum.ner
  Named entity recognizer.
cc.mallet.share.upenn - package cc.mallet.share.upenn
  Utilities that currently include a command line wrapper for the maxent classifier.
cc.mallet.share.upenn.ner - package cc.mallet.share.upenn.ner
cc.mallet.share.weili.ner - package cc.mallet.share.weili.ner
cc.mallet.share.weili.ner.enron - package cc.mallet.share.weili.ner.enron
cc.mallet.topics - package cc.mallet.topics
cc.mallet.topics.tui - package cc.mallet.topics.tui
cc.mallet.types - package cc.mallet.types
  Fundamental MALLET types, including FeatureVector, Instance, Label etc.
cc.mallet.types.tests - package cc.mallet.types.tests
  JUnit tests for Fundamental MALLET types.
cc.mallet.util - package cc.mallet.util
  Miscellaneous utilities including command line processing, math functions, lexing, logging.
cc.mallet.util.resources.wn - package cc.mallet.util.resources.wn
cc.mallet.util.search - package cc.mallet.util.search
cc.mallet.util.tests - package cc.mallet.util.tests
  JUnit tests for the miscellaneous utilities.
CERTAIN_WEIGHT - Static variable in class cc.mallet.fst.Transducer
ChainedInstanceIterator - Class in cc.mallet.types
  Deprecated.
ChainedInstanceIterator(Iterator<Instance>, ChainedInstanceIterator) - Constructor for class cc.mallet.types.ChainedInstanceIterator
  Deprecated. Both source and target may be null.
changePriority(QueueElement, double) - Method in class cc.mallet.util.search.MinHeap
changePriority(QueueElement, double) - Method in interface cc.mallet.util.search.PriorityQueue
  Change the priority of queue element `e` to `priority`.
CharSequence2CharNGrams - Class in cc.mallet.pipe
  Transform a character sequence into a token sequence of character N grams.
CharSequence2CharNGrams(int, boolean) - Constructor for class cc.mallet.pipe.CharSequence2CharNGrams
CharSequence2TokenSequence - Class in cc.mallet.pipe
  Pipe that tokenizes a character sequence.
CharSequence2TokenSequence(CharSequenceLexer) - Constructor for class cc.mallet.pipe.CharSequence2TokenSequence
CharSequence2TokenSequence(String) - Constructor for class cc.mallet.pipe.CharSequence2TokenSequence
CharSequence2TokenSequence(Pattern) - Constructor for class cc.mallet.pipe.CharSequence2TokenSequence
CharSequence2TokenSequence() - Constructor for class cc.mallet.pipe.CharSequence2TokenSequence
CharSequenceArray2TokenSequence - Class in cc.mallet.pipe
  Transform an array of character Sequences into a token sequence.
CharSequenceArray2TokenSequence() - Constructor for class cc.mallet.pipe.CharSequenceArray2TokenSequence
CharSequenceLexer - Class in cc.mallet.util
CharSequenceLexer() - Constructor for class cc.mallet.util.CharSequenceLexer
CharSequenceLexer(Pattern) - Constructor for class cc.mallet.util.CharSequenceLexer
CharSequenceLexer(String) - Constructor for class cc.mallet.util.CharSequenceLexer
CharSequenceLexer(CharSequence, Pattern) - Constructor for class cc.mallet.util.CharSequenceLexer
CharSequenceLexer(CharSequence, String) - Constructor for class cc.mallet.util.CharSequenceLexer
CharSequenceLowercase - Class in cc.mallet.pipe
  Replace the data string with a lowercased version.
CharSequenceLowercase() - Constructor for class cc.mallet.pipe.CharSequenceLowercase
CharSequenceRemoveHTML - Class in cc.mallet.pipe
  This pipe removes HTML from a CharSequence.
CharSequenceRemoveHTML() - Constructor for class cc.mallet.pipe.CharSequenceRemoveHTML
CharSequenceRemoveUUEncodedBlocks - Class in cc.mallet.pipe
CharSequenceRemoveUUEncodedBlocks() - Constructor for class cc.mallet.pipe.CharSequenceRemoveUUEncodedBlocks
CharSequenceReplace - Class in cc.mallet.pipe
  Given a string, repeatedly look for matches of the regex, and replace the entire match with the given replacement string.
CharSequenceReplace(Pattern, String) - Constructor for class cc.mallet.pipe.CharSequenceReplace
CharSubsequence - Class in cc.mallet.pipe
  Given a string, return only the portion of the string inside a regex parenthesized group.
CharSubsequence(Pattern, int) - Constructor for class cc.mallet.pipe.CharSubsequence
CharSubsequence(Pattern) - Constructor for class cc.mallet.pipe.CharSubsequence
check(double[][], double[][][], int, int, FeatureVectorSequence) - Method in class cc.mallet.fst.semi_supervised.GELattice
  Verifies the correctness of the lattice computations.
checkBreakeven(double) - Method in class cc.mallet.types.Dirichlet
checkWithinRange(double, double, double) - Static method in class cc.mallet.util.Maths
  Checks if `min <= value <= max`.
cholesky(double[], int) - Static method in class cc.mallet.util.MVNormal
  Simple Cholesky decomposition, with no checks on squareness, symmetricality, or positive definiteness.
Classification - Class in cc.mallet.classify
  The result of classifying a single instance.
Classification(Instance, Classifier, Labeling) - Constructor for class cc.mallet.classify.Classification
Classification2ConfidencePredictingFeatureVector - Class in cc.mallet.pipe
  Pipe features from underlying classifier to the confidence prediction instance list
Classification2ConfidencePredictingFeatureVector() - Constructor for class cc.mallet.pipe.Classification2ConfidencePredictingFeatureVector
Classifier - Class in cc.mallet.classify
  Abstract parent of all Classifiers.
Classifier() - Constructor for class cc.mallet.classify.Classifier
  For serialization only.
Classifier(Pipe) - Constructor for class cc.mallet.classify.Classifier
Classifier2Info - Class in cc.mallet.classify.tui
  Diagnostic facilities for a classifier.
Classifier2Info() - Constructor for class cc.mallet.classify.tui.Classifier2Info
ClassifierAccuracyEvaluator - Class in cc.mallet.classify
ClassifierAccuracyEvaluator(InstanceList[], String[]) - Constructor for class cc.mallet.classify.ClassifierAccuracyEvaluator
ClassifierAccuracyEvaluator(InstanceList, String) - Constructor for class cc.mallet.classify.ClassifierAccuracyEvaluator
ClassifierAccuracyEvaluator(InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.classify.ClassifierAccuracyEvaluator
ClassifierAccuracyEvaluator(InstanceList, String, InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.classify.ClassifierAccuracyEvaluator
ClassifierEnsemble - Class in cc.mallet.classify
  Classifer for an ensemble of classifers, combined with learned weights.
ClassifierEnsemble(Classifier[], double[]) - Constructor for class cc.mallet.classify.ClassifierEnsemble
ClassifierEnsembleTrainer - Class in cc.mallet.classify
ClassifierEnsembleTrainer(Classifier[]) - Constructor for class cc.mallet.classify.ClassifierEnsembleTrainer
ClassifierEvaluator - Class in cc.mallet.classify
ClassifierEvaluator(InstanceList[], String[]) - Constructor for class cc.mallet.classify.ClassifierEvaluator
ClassifierEvaluator(InstanceList, String) - Constructor for class cc.mallet.classify.ClassifierEvaluator
ClassifierEvaluator(InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.classify.ClassifierEvaluator
ClassifierEvaluator(InstanceList, String, InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.classify.ClassifierEvaluator
ClassifierTrainer<C extends Classifier> - Class in cc.mallet.classify
  Each ClassifierTrainer trains one Classifier based on various interfaces for consuming training data.
ClassifierTrainer() - Constructor for class cc.mallet.classify.ClassifierTrainer
ClassifierTrainer.ByActiveLearning<C extends Classifier> - Interface in cc.mallet.classify
  For active learning, in which this trainer will select certain instances and request that the Labeler instance label them.
ClassifierTrainer.ByIncrements<C extends Classifier> - Interface in cc.mallet.classify
  For various kinds of online learning by batches, where training instances are presented, consumed for learning immediately.
ClassifierTrainer.ByInstanceIncrements<C extends Classifier> - Interface in cc.mallet.classify
  For online learning that can operate on one instance at a time.
ClassifierTrainer.ByOptimization<C extends Classifier> - Interface in cc.mallet.classify
ClassifierTrainer.Factory<CT extends ClassifierTrainer<? extends Classifier>> - Class in cc.mallet.classify
  Instances of a Factory know how to create new ClassifierTrainers to apply to new Classifiers.
ClassifierTrainer.Factory() - Constructor for class cc.mallet.classify.ClassifierTrainer.Factory
classify(Instance) - Method in class cc.mallet.classify.AdaBoost
classify(Instance, int) - Method in class cc.mallet.classify.AdaBoost
  Classify the given instance using only the first `numWeakClassifiersToUse` classifiers trained during boosting
classify(Instance) - Method in class cc.mallet.classify.AdaBoostM2
classify(Instance, int) - Method in class cc.mallet.classify.AdaBoostM2
  Classify the given instance using only the first `numWeakClassifiersToUse` classifiers trained during boosting
classify(Instance) - Method in class cc.mallet.classify.BaggingClassifier
classify(Instance) - Method in class cc.mallet.classify.BalancedWinnow
  Classifies an instance using BalancedWinnow's weights
classify(Instance) - Method in class cc.mallet.classify.C45
classify(InstanceList) - Method in class cc.mallet.classify.Classifier
classify(Instance[]) - Method in class cc.mallet.classify.Classifier
classify(Instance) - Method in class cc.mallet.classify.Classifier
classify(Object) - Method in class cc.mallet.classify.Classifier
  Pipe the object through this classifier's pipe, then classify the resulting instance.
classify(Instance) - Method in class cc.mallet.classify.ClassifierEnsemble
classify(Instance) - Method in class cc.mallet.classify.ConfidencePredictingClassifier
classify(Instance) - Method in class cc.mallet.classify.DecisionTree
classify(Instance) - Method in class cc.mallet.classify.MaxEnt
classify(Instance) - Method in class cc.mallet.classify.MCMaxEnt
classify(Instance) - Method in class cc.mallet.classify.NaiveBayes
  Classify an instance using NaiveBayes according to the trained data.
classify(Instance) - Method in class cc.mallet.classify.RankMaxEnt
classify(Instance) - Method in class cc.mallet.classify.Winnow
  Classifies an instance using Winnow's weights
classify(Instance) - Method in class cc.mallet.pipe.AddClassifierTokenPredictions.TokenClassifiers
classify(Instance, boolean) - Method in class cc.mallet.pipe.AddClassifierTokenPredictions.TokenClassifiers
classify(Classifier, String[]) - Static method in class cc.mallet.share.upenn.MaxEntShell
  Compute the maxent classification of an instance.
classify(Classifier, String[][]) - Static method in class cc.mallet.share.upenn.MaxEntShell
  Compute the maxent classifications of an array of instances
classify(Classifier, Iterator<Instance>) - Static method in class cc.mallet.share.upenn.MaxEntShell
  Compute the maxent classifications for unlabeled instances given by an iterator.
ClassifyingNeighborEvaluator - Class in cc.mallet.cluster.neighbor_evaluator
  A `NeighborEvaluator` that is backed by a `Classifier`.
ClassifyingNeighborEvaluator(Classifier, String) - Constructor for class cc.mallet.cluster.neighbor_evaluator.ClassifyingNeighborEvaluator
classShortName(Object) - Static method in class cc.mallet.grmm.util.GeneralUtils
cleanFields(FieldCleaner) - Method in class cc.mallet.extract.Extraction
cleanFieldValue(String) - Method in interface cc.mallet.extract.FieldCleaner
  Returns a post-processed version of a field.
cleanFieldValue(String) - Method in class cc.mallet.extract.RegexFieldCleaner
clear() - Method in class cc.mallet.grmm.types.BitVarSet
clear() - Method in class cc.mallet.grmm.types.FactorGraph
  Removes all potentias from this model.
clear() - Method in class cc.mallet.grmm.types.HashVarSet
clear() - Method in class cc.mallet.grmm.types.ListVarSet
clear() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
clear() - Method in class cc.mallet.grmm.util.CSIntInt2ObjectMultiMap
clear() - Method in class cc.mallet.types.CrossValidationIterator
  Calls clear on each fold.
clear() - Method in class cc.mallet.types.InstanceList
clear() - Method in class cc.mallet.types.MultiInstanceList
clear() - Method in class cc.mallet.types.PagedInstanceList
clearSource() - Method in class cc.mallet.types.Instance
clone() - Method in class cc.mallet.grmm.inference.TRP
clone() - Method in class cc.mallet.grmm.inference.TRP.ConvergenceTerminator
clone() - Method in class cc.mallet.grmm.inference.TRP.DefaultConvergenceTerminator
clone() - Method in class cc.mallet.grmm.inference.TRP.IterationTerminator
clone() - Method in interface cc.mallet.grmm.inference.TRP.TerminationCondition
clone() - Method in class cc.mallet.grmm.types.AbstractTableFactor
clone() - Method in class cc.mallet.grmm.types.HashVarSet
clone() - Method in class cc.mallet.types.Alphabet
clone() - Method in class cc.mallet.types.FeatureSelection
clone() - Method in class cc.mallet.types.Instance
clone() - Method in class cc.mallet.types.InstanceList
clone() - Method in class cc.mallet.types.Matrixn
clone() - Method in class cc.mallet.types.MultiInstanceList
clone() - Method in class cc.mallet.types.Multinomial.Estimator
clone() - Method in class cc.mallet.types.SparseMatrixn
clone() - Method in class cc.mallet.util.DoubleList
cloneDoubleList() - Method in class cc.mallet.util.DoubleList
cloneEmpty() - Method in class cc.mallet.types.InstanceList
cloneEmpty() - Method in class cc.mallet.types.MultiInstanceList
cloneEmpty() - Method in class cc.mallet.types.PagedInstanceList
cloneEmptyInto(InstanceList) - Method in class cc.mallet.types.InstanceList
cloneEmptyInto(InstanceList) - Method in class cc.mallet.types.MultiInstanceList
cloneMatrix() - Method in class cc.mallet.types.AugmentableFeatureVector
cloneMatrix() - Method in interface cc.mallet.types.ConstantMatrix
cloneMatrix() - Method in class cc.mallet.types.DenseMatrix
cloneMatrix() - Method in class cc.mallet.types.DenseVector
cloneMatrix() - Method in class cc.mallet.types.FeatureVector
cloneMatrix() - Method in class cc.mallet.types.HashedSparseVector
cloneMatrix() - Method in class cc.mallet.types.IndexedSparseVector
cloneMatrix() - Method in class cc.mallet.types.Matrix2
  Deprecated.
cloneMatrix() - Method in class cc.mallet.types.Matrixn
cloneMatrix() - Method in class cc.mallet.types.SparseMatrixn
cloneMatrix() - Method in class cc.mallet.types.SparseVector
  CLONING
cloneMatrix2() - Method in class cc.mallet.types.Matrix2
  Deprecated.
cloneMatrixZeroed() - Method in class cc.mallet.types.AugmentableFeatureVector
cloneMatrixZeroed() - Method in class cc.mallet.types.FeatureVector
cloneMatrixZeroed() - Method in class cc.mallet.types.HashedSparseVector
cloneMatrixZeroed() - Method in class cc.mallet.types.IndexedSparseVector
cloneMatrixZeroed() - Method in class cc.mallet.types.SparseVector
cloneViaSerialization(Serializable) - Static method in class cc.mallet.types.tests.TestSerializable
  Clones a given object by serializing it to a byte array and reading it back.
cluster(InstanceList) - Method in class cc.mallet.cluster.Clusterer
  Return a clustering of an InstanceList
cluster(InstanceList) - Method in class cc.mallet.cluster.HillClimbingClusterer
  While not converged, calls `improveClustering` to modify the current predicted `Clustering`.
cluster(InstanceList, int, Clustering) - Method in class cc.mallet.cluster.HillClimbingClusterer
  While not converged, call `improveClustering` to modify the current predicted `Clustering`.
cluster(InstanceList) - Method in class cc.mallet.cluster.KMeans
  Cluster instances
Clusterer - Class in cc.mallet.cluster
  An abstract class for clustering a set of points.
Clusterer(Pipe) - Constructor for class cc.mallet.cluster.Clusterer
  Creates a new `Clusterer` instance.
Clustering - Class in cc.mallet.cluster
Clustering(InstanceList, int, int[]) - Constructor for class cc.mallet.cluster.Clustering
  Clustering constructor.
clustering - Variable in class cc.mallet.cluster.iterator.NeighborIterator
ClusteringEvaluator - Class in cc.mallet.cluster.evaluate
  Evaluates a predicted Clustering against a true Clustering.
ClusteringEvaluator() - Constructor for class cc.mallet.cluster.evaluate.ClusteringEvaluator
ClusteringEvaluators - Class in cc.mallet.cluster.evaluate
  A list of `ClusteringEvaluators`.
ClusteringEvaluators(ClusteringEvaluator[]) - Constructor for class cc.mallet.cluster.evaluate.ClusteringEvaluators
Clusterings - Class in cc.mallet.cluster
Clusterings(Clustering[]) - Constructor for class cc.mallet.cluster.Clusterings
Clusterings2Clusterer - Class in cc.mallet.cluster.tui
Clusterings2Clusterer() - Constructor for class cc.mallet.cluster.tui.Clusterings2Clusterer
Clusterings2Clusterer.ClusteringPipe - Class in cc.mallet.cluster.tui
Clusterings2Clusterer.ClusteringPipe(int[], int[], int[]) - Constructor for class cc.mallet.cluster.tui.Clusterings2Clusterer.ClusteringPipe
Clusterings2Clusterings - Class in cc.mallet.cluster.tui
Clusterings2Clusterings() - Constructor for class cc.mallet.cluster.tui.Clusterings2Clusterings
Clusterings2Info - Class in cc.mallet.cluster.tui
Clusterings2Info() - Constructor for class cc.mallet.cluster.tui.Clusterings2Info
ClusteringScorer - Interface in cc.mallet.cluster.clustering_scorer
  Assign a score to a Clustering.
clusterKBest(InstanceList, int) - Method in class cc.mallet.cluster.HillClimbingClusterer
clusterKBest(InstanceList, int, Clustering, int) - Method in class cc.mallet.cluster.HillClimbingClusterer
  Return the K most recent solutions.
clusterKBest(InstanceList, int) - Method in class cc.mallet.cluster.KBestClusterer
clusterPotentials() - Method in class cc.mallet.grmm.inference.JunctionTree
  Returns a collection of all the potentials of cliques in the junction tree.
ClusterSampleIterator - Class in cc.mallet.cluster.iterator
  Sample clusters of Instances.
ClusterSampleIterator(Clustering, Randoms, double, int) - Constructor for class cc.mallet.cluster.iterator.ClusterSampleIterator
ClusterUtils - Class in cc.mallet.cluster.util
  Utility functions for Clusterings.
ClusterUtils() - Constructor for class cc.mallet.cluster.util.ClusterUtils
ClusterVariationalRegionGenerator - Class in cc.mallet.grmm.inference.gbp
  Created: Jun 1, 2005
ClusterVariationalRegionGenerator() - Constructor for class cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator
ClusterVariationalRegionGenerator(ClusterVariationalRegionGenerator.BaseRegionComputer) - Constructor for class cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator
ClusterVariationalRegionGenerator.BaseRegionComputer - Interface in cc.mallet.grmm.inference.gbp
ClusterVariationalRegionGenerator.ByFactorRegionComputer - Class in cc.mallet.grmm.inference.gbp
  Region computer where each top-level region consists of a single factor node.
ClusterVariationalRegionGenerator.ByFactorRegionComputer() - Constructor for class cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator.ByFactorRegionComputer
ClusterVariationalRegionGenerator.Grid2x2RegionComputer - Class in cc.mallet.grmm.inference.gbp
ClusterVariationalRegionGenerator.Grid2x2RegionComputer() - Constructor for class cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator.Grid2x2RegionComputer
collectAlphaStatistics() - Method in class cc.mallet.topics.WorkerRunnable
collectConstraints(InstanceList) - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
CollectionUtils - Class in cc.mallet.util
  * Created: Sun Jan 25 01:04:29 2004
CollectionUtils.Fn - Interface in cc.mallet.util
color(int) - Method in class cc.mallet.classify.evaluate.Graph.Legend
ColorUtils - Class in cc.mallet.util
  Utilities for dealing with RGB-style colors.
ColorUtils() - Constructor for class cc.mallet.util.ColorUtils
columnPlusEquals(int, double) - Method in class cc.mallet.types.DenseVector
columnPlusEquals(int, double) - Method in class cc.mallet.types.HashedSparseVector
columnPlusEquals(int, double) - Method in class cc.mallet.types.IndexedSparseVector
columnPlusEquals(int, Vector, double) - Method in class cc.mallet.types.Matrix2
  Deprecated.
columnPlusEquals(int, double, double) - Method in class cc.mallet.types.Matrix2
  Deprecated.
combine(double[]) - Method in class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator.Average
combine(double[]) - Method in interface cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator.CombiningStrategy
combine(double[]) - Method in class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator.Maximum
combine(double[]) - Method in class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator.Minimum
combine(double[]) - Method in class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator.Average
combine(double[]) - Method in interface cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator.CombiningStrategy
combine(double[]) - Method in class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator.Maximum
combine(double[]) - Method in class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator.Minimum
combineGradients(Collection<double[]>, double[]) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
  Adds gradients from all batches.
combineGradients(Collection<double[]>, double[]) - Method in interface cc.mallet.optimize.Optimizable.ByCombiningBatchGradient
combineLists(InstanceList, InstanceList) - Static method in class cc.mallet.cluster.util.ClusterUtils
CommandOption - Class in cc.mallet.util
CommandOption(Class, String, String, Class, boolean, String, String) - Constructor for class cc.mallet.util.CommandOption
CommandOption(Class, String, String, Class, boolean, String) - Constructor for class cc.mallet.util.CommandOption
  Deprecated.
CommandOption.Boolean - Class in cc.mallet.util
CommandOption.Boolean(Class, String, String, boolean, boolean, String, String) - Constructor for class cc.mallet.util.CommandOption.Boolean
CommandOption.Double - Class in cc.mallet.util
CommandOption.Double(Class, String, String, boolean, double, String, String) - Constructor for class cc.mallet.util.CommandOption.Double
CommandOption.DoubleArray - Class in cc.mallet.util
CommandOption.DoubleArray(Class, String, String, boolean, double[], String, String) - Constructor for class cc.mallet.util.CommandOption.DoubleArray
CommandOption.File - Class in cc.mallet.util
CommandOption.File(Class, String, String, boolean, File, String, String) - Constructor for class cc.mallet.util.CommandOption.File
CommandOption.Integer - Class in cc.mallet.util
CommandOption.Integer(Class, String, String, boolean, int, String, String) - Constructor for class cc.mallet.util.CommandOption.Integer
CommandOption.IntegerArray - Class in cc.mallet.util
CommandOption.IntegerArray(Class, String, String, boolean, int[], String, String) - Constructor for class cc.mallet.util.CommandOption.IntegerArray
CommandOption.List - Class in cc.mallet.util
CommandOption.List(String, CommandOption[]) - Constructor for class cc.mallet.util.CommandOption.List
CommandOption.ListProviding - Interface in cc.mallet.util
  For objects that can provide CommandOption.List's (which can be merged into other lists.
CommandOption.Object - Class in cc.mallet.util
CommandOption.Object(Class, String, String, boolean, Object, String, String) - Constructor for class cc.mallet.util.CommandOption.Object
CommandOption.ObjectFromBean - Class in cc.mallet.util
CommandOption.ObjectFromBean(Class, String, String, boolean, Object, String, String) - Constructor for class cc.mallet.util.CommandOption.ObjectFromBean
CommandOption.Set - Class in cc.mallet.util
CommandOption.Set(Class, String, String, boolean, String[], int, String, String) - Constructor for class cc.mallet.util.CommandOption.Set
CommandOption.SpacedStrings - Class in cc.mallet.util
CommandOption.SpacedStrings(Class, String, String, boolean, String[], String, String) - Constructor for class cc.mallet.util.CommandOption.SpacedStrings
CommandOption.String - Class in cc.mallet.util
CommandOption.String(Class, String, String, boolean, String, String, String) - Constructor for class cc.mallet.util.CommandOption.String
commonPrefix(String[]) - Static method in class cc.mallet.util.Strings
commonPrefixIndex(String[]) - Static method in class cc.mallet.util.Strings
compact() - Method in class cc.mallet.grmm.inference.JunctionTree
compare(Object, Object) - Method in class cc.mallet.classify.evaluate.AccuracyCoverage.ClassificationComparator
compare(double, int, int, int) - Static method in class cc.mallet.types.Dirichlet
compare(double) - Method in class cc.mallet.util.Univariate
compareTo(Object) - Method in class cc.mallet.fst.confidence.InstanceWithConfidence
compareTo(Object) - Method in class cc.mallet.fst.confidence.PipedInstanceWithConfidence
compareTo(Object) - Method in class cc.mallet.fst.Segment
compareTo(Object) - Method in class cc.mallet.grmm.types.Variable
compareTo(Object) - Method in class cc.mallet.types.IDSorter
compareTo(Object) - Method in class cc.mallet.types.Label
completionCost() - Method in class cc.mallet.util.search.AStarNode
  Get the completion cost for the underlying state.
completionCost() - Method in interface cc.mallet.util.search.AStarState
  Get the cost to completion.
computeAssignment(Assignment, VarSet) - Method in class cc.mallet.grmm.learning.ACRF.Template
computeBaseRegions(FactorGraph) - Method in interface cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator.BaseRegionComputer
  Returns a list of top-level regions for use in the cluster variational method.
computeBaseRegions(FactorGraph) - Method in class cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator.ByFactorRegionComputer
computeBaseRegions(FactorGraph) - Method in class cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator.Grid2x2RegionComputer
computeBin(FeatureVector) - Method in interface cc.mallet.grmm.learning.templates.SimilarTokensTemplate.FeatureVectorBinner
computeBin(FeatureVector) - Method in class cc.mallet.grmm.learning.templates.SimilarTokensTemplate.WordFeatureBinner
computeCostAndPrune() - Method in class cc.mallet.classify.C45.Node
computeCurrentResids() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
computeExpectations() - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
  Resets, computes and fills expectations from all instances, also updating the entropy value.
computeFactor(ACRF.UnrolledVarSet) - Method in class cc.mallet.grmm.learning.ACRF.FixedFactorTemplate
computeFactor(ACRF.UnrolledVarSet) - Method in class cc.mallet.grmm.learning.ACRF.Template
computeGradient(FeatureVectorSequence, double[][], double[][][]) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
  Fills gradient from a single instance.
computeGradient(Map<Integer, SumLattice>) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
  Resets, computes and fills gradient from all instances.
computeLogLikelihood() - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.AbstractInferencer
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.BruteForceInferencer
computeMarginals(JunctionTree) - Method in class cc.mallet.grmm.inference.BruteForceInferencer
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
computeMarginals(FactorGraph) - Method in interface cc.mallet.grmm.inference.Inferencer
  Computes marginal distributions for a factor graph.
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
computeMarginals(JunctionTree) - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.LoopyBP
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.ResidualBP
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.SamplingInferencer
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.TreeBP
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.TRP
computeMarginals(FactorGraph) - Method in class cc.mallet.grmm.inference.VariableElimination
computeNormalizationFactor(FactorGraph) - Method in class cc.mallet.grmm.inference.VariableElimination
  Computes the normalization constant for a model.
computeSizes(Factor) - Static method in class cc.mallet.grmm.types.Factors
computeTestResults(InstanceList, List) - Static method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.LogEvaluator
computeVars(Factor) - Static method in class cc.mallet.grmm.types.Factors
ConcatenatedInstanceIterator - Class in cc.mallet.pipe.iterator
ConcatenatedInstanceIterator(Iterator<Instance>[]) - Constructor for class cc.mallet.pipe.iterator.ConcatenatedInstanceIterator
concatenatePipes(Pipe, Pipe) - Static method in class cc.mallet.pipe.PipeUtils
confidence() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator.EntityConfidence
ConfidenceCorrectorEvaluator - Class in cc.mallet.fst.confidence
  Calculates the effectiveness of "constrained viterbi" in propagating corrections in one segment of a sequence to other segments.
ConfidenceCorrectorEvaluator(Object[], Object[]) - Constructor for class cc.mallet.fst.confidence.ConfidenceCorrectorEvaluator
ConfidenceEvaluator - Class in cc.mallet.fst.confidence
ConfidenceEvaluator(Vector, int) - Constructor for class cc.mallet.fst.confidence.ConfidenceEvaluator
ConfidenceEvaluator(Vector) - Constructor for class cc.mallet.fst.confidence.ConfidenceEvaluator
ConfidenceEvaluator(Segment[], boolean) - Constructor for class cc.mallet.fst.confidence.ConfidenceEvaluator
ConfidenceEvaluator(InstanceWithConfidence[], boolean) - Constructor for class cc.mallet.fst.confidence.ConfidenceEvaluator
ConfidenceEvaluator(PipedInstanceWithConfidence[], boolean) - Constructor for class cc.mallet.fst.confidence.ConfidenceEvaluator
ConfidenceEvaluator.EntityConfidence - Class in cc.mallet.fst.confidence
  a simple class to store a confidence score and whether or not this labeling is correct
ConfidenceEvaluator.EntityConfidence(double, boolean, String) - Constructor for class cc.mallet.fst.confidence.ConfidenceEvaluator.EntityConfidence
ConfidenceEvaluator.EntityConfidence(double, boolean, Sequence, int, int) - Constructor for class cc.mallet.fst.confidence.ConfidenceEvaluator.EntityConfidence
ConfidencePredictingClassifier - Class in cc.mallet.classify
ConfidencePredictingClassifier(Classifier, Classifier) - Constructor for class cc.mallet.classify.ConfidencePredictingClassifier
ConfidencePredictingClassifierTrainer - Class in cc.mallet.classify
ConfidencePredictingClassifierTrainer(ClassifierTrainer, InstanceList, Pipe) - Constructor for class cc.mallet.classify.ConfidencePredictingClassifierTrainer
ConfidencePredictingClassifierTrainer(ClassifierTrainer, InstanceList) - Constructor for class cc.mallet.classify.ConfidencePredictingClassifierTrainer
ConfidenceTokenizationFilter - Class in cc.mallet.extract
  Created: Oct 26, 2005
ConfidenceTokenizationFilter(ExtractionConfidenceEstimator, TokenizationFilter) - Constructor for class cc.mallet.extract.ConfidenceTokenizationFilter
confusion - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
ConfusionMatrix - Class in cc.mallet.classify.evaluate
  Calculates and prints confusion matrix, accuracy, and precision for a given clasification trial.
ConfusionMatrix(Trial) - Constructor for class cc.mallet.classify.evaluate.ConfusionMatrix
  Constructs matrix and calculates values
ConjugateGradient - Class in cc.mallet.optimize
ConjugateGradient(Optimizable.ByGradientValue, double) - Constructor for class cc.mallet.optimize.ConjugateGradient
ConjugateGradient(Optimizable.ByGradientValue) - Constructor for class cc.mallet.optimize.ConjugateGradient
ConllNer2003Sentence2TokenSequence - Class in cc.mallet.share.casutton.ner
  Reads a data file in CoNLL 2003 format, and makes some simple transformations.
ConllNer2003Sentence2TokenSequence() - Constructor for class cc.mallet.share.casutton.ner.ConllNer2003Sentence2TokenSequence
ConllNer2003Sentence2TokenSequence(boolean, boolean) - Constructor for class cc.mallet.share.casutton.ner.ConllNer2003Sentence2TokenSequence
ConllNer2003Sentence2TokenSequence - Class in cc.mallet.share.mccallum.ner
ConllNer2003Sentence2TokenSequence() - Constructor for class cc.mallet.share.mccallum.ner.ConllNer2003Sentence2TokenSequence
ConllNer2003Sentence2TokenSequence(boolean) - Constructor for class cc.mallet.share.mccallum.ner.ConllNer2003Sentence2TokenSequence
constant(int[], double) - Static method in class cc.mallet.grmm.util.Matrices
ConstantFactor - Class in cc.mallet.grmm.types
  $Id: ConstantFactor.java,v 1.1 2007/10/22 21:37:44 mccallum Exp $
ConstantFactor(double) - Constructor for class cc.mallet.grmm.types.ConstantFactor
ConstantMatrix - Interface in cc.mallet.types
ConstrainedForwardBackwardConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of a `Segment` extracted by a `Transducer` by performing a "constrained lattice" calculation.
ConstrainedForwardBackwardConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.ConstrainedForwardBackwardConfidenceEstimator
ConstrainedViterbiTransducerCorrector - Class in cc.mallet.fst.confidence
  Corrects a subset of the `Segment`s produced by a `Transducer`.
ConstrainedViterbiTransducerCorrector(TransducerConfidenceEstimator, Transducer) - Constructor for class cc.mallet.fst.confidence.ConstrainedViterbiTransducerCorrector
ConstrainedViterbiTransducerCorrector(Transducer) - Constructor for class cc.mallet.fst.confidence.ConstrainedViterbiTransducerCorrector
constraintBits - Variable in class cc.mallet.fst.semi_supervised.GECriteria
constraints - Variable in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
constraints - Variable in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
constraints - Variable in class cc.mallet.fst.CRFTrainerByStochasticGradient
constraints - Variable in class cc.mallet.fst.semi_supervised.GECriteria
constraintsFile - Static variable in class cc.mallet.classify.tui.Vectors2FeatureConstraints
constructLabeledSpans(LabelAlphabet, Object, Label, Tokenization, Sequence) - Method in class cc.mallet.extract.BIOTokenizationFilter
constructLabeledSpans(LabelAlphabet, Object, Label, Tokenization, Sequence) - Method in class cc.mallet.extract.ConfidenceTokenizationFilter
constructLabeledSpans(LabelAlphabet, Object, Label, Tokenization, Sequence) - Method in class cc.mallet.extract.DefaultTokenizationFilter
constructLabeledSpans(LabelAlphabet, Object, Label, Tokenization, Sequence) - Method in class cc.mallet.extract.HierarchicalTokenizationFilter
constructLabeledSpans(LabelAlphabet, Object, Label, Tokenization, Sequence) - Method in interface cc.mallet.extract.TokenizationFilter
  Converts a the sequence of labels into a set of labeled spans.
constructRegionGraph(FactorGraph) - Method in class cc.mallet.grmm.inference.gbp.BPRegionGenerator
constructRegionGraph(FactorGraph) - Method in class cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator
constructRegionGraph(FactorGraph) - Method in class cc.mallet.grmm.inference.gbp.Kikuchi4SquareRegionGenerator
constructRegionGraph(FactorGraph) - Method in interface cc.mallet.grmm.inference.gbp.RegionGraphGenerator
  Construct a region graph from an artbitrary model.
contains(Object) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
contains(Object) - Method in class cc.mallet.grmm.types.BitVarSet
contains(Object) - Method in class cc.mallet.grmm.types.HashVarSet
contains(Object) - Method in class cc.mallet.grmm.types.ListVarSet
contains(Object) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
contains(Object) - Method in class cc.mallet.types.Alphabet
contains(Object) - Method in class cc.mallet.types.FeatureSelection
contains(int) - Method in class cc.mallet.types.FeatureSelection
contains(Object) - Method in class cc.mallet.types.FeatureVector
contains(Object) - Method in class cc.mallet.types.MultiInstanceList
contains(QueueElement) - Method in class cc.mallet.util.search.MinHeap
contains(QueueElement) - Method in interface cc.mallet.util.search.PriorityQueue
  Does the queue contain an element?
containsAll(Collection) - Method in class cc.mallet.grmm.types.BitVarSet
containsAll(BitVarSet) - Method in class cc.mallet.grmm.types.BitVarSet
  Efficient version of containsAll() for BitSetCliques.
containsAll(Collection) - Method in class cc.mallet.grmm.types.HashVarSet
containsAll(Collection) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
containsObject(Object) - Method in class cc.mallet.grmm.types.Tree
containsVar(Variable) - Method in class cc.mallet.grmm.types.AbstractFactor
containsVar(Variable) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Returns true iff this potential is over the given variable
containsVar(Variable) - Method in class cc.mallet.grmm.types.Assignment
  Returns true if this assignment specifies a value for `var`
containsVar(Variable) - Method in class cc.mallet.grmm.types.CPT
containsVar(Variable) - Method in interface cc.mallet.grmm.types.Factor
  Returns whether the potential is over the given variable.
containsVar(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns whether this variable is part of the model.
contentsAsCharSequence(Reader) - Static method in class cc.mallet.util.IoUtils
contentsAsString(File) - Static method in class cc.mallet.util.IoUtils
CONTINUOUS - Static variable in class cc.mallet.grmm.types.Variable
  Number of outcomes for a continous variable.
continuousVarsOf(Factor) - Static method in class cc.mallet.grmm.types.Factors
converged - Variable in class cc.mallet.cluster.GreedyAgglomerative
  True if should stop clustering.
converged(Clustering) - Method in class cc.mallet.cluster.GreedyAgglomerative
converged(Clustering) - Method in class cc.mallet.cluster.GreedyAgglomerativeByDensity
converged(Clustering) - Method in class cc.mallet.cluster.HillClimbingClusterer
converged - Variable in class cc.mallet.fst.CRFTrainerByStochasticGradient
convert(InstanceList, Noop) - Static method in class cc.mallet.pipe.AddClassifierTokenPredictions
  Converts each instance containing a FeatureVectorSequence to multiple instances, each containing an AugmentableFeatureVector as data.
convert(Instance, Noop) - Static method in class cc.mallet.pipe.AddClassifierTokenPredictions
copyAndMergeClusters(Clustering, int, int) - Static method in class cc.mallet.cluster.util.ClusterUtils
copyAndMergeInstances(Clustering, int, int) - Static method in class cc.mallet.cluster.util.ClusterUtils
copyAndMergeInstances(Clustering, int[]) - Static method in class cc.mallet.cluster.util.ClusterUtils
copyOldMessages() - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
copyWithNewLabels(Clustering) - Static method in class cc.mallet.cluster.util.ClusterUtils
corr(Factor) - Static method in class cc.mallet.grmm.types.Factors
corr(Univariate, Univariate) - Static method in class cc.mallet.util.StatFunctions
correct() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator.EntityConfidence
correct() - Method in class cc.mallet.fst.confidence.InstanceWithConfidence
correct() - Method in class cc.mallet.fst.confidence.PipedInstanceWithConfidence
correct() - Method in class cc.mallet.fst.Segment
correctLeastConfidentSegments(InstanceList, Object[], Object[]) - Method in class cc.mallet.fst.confidence.ConstrainedViterbiTransducerCorrector
correctLeastConfidentSegments(InstanceList, Object[], Object[], boolean) - Method in class cc.mallet.fst.confidence.ConstrainedViterbiTransducerCorrector
  Returns an ArrayList of corrected Sequences.
correctLeastConfidentSegments(InstanceList, Object[], Object[]) - Method in class cc.mallet.fst.confidence.IsolatedSegmentTransducerCorrector
correctLeastConfidentSegments(InstanceList, Object[], Object[]) - Method in interface cc.mallet.fst.confidence.TransducerCorrector
correctT - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
correlation() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
  Calculate pearson's R for the corellation between confidence and correct, where 1 = correct and -1 = incorrect
cosh(double) - Static method in class cc.mallet.util.Maths
cost() - Method in class cc.mallet.util.search.SearchNode.NextNodeIterator
  The cost associated to the transition from the previous state to this state.
cost() - Method in class cc.mallet.util.search.SearchState.NextStateIterator
  The cost of the transition to the current state.
count - Variable in class cc.mallet.fst.semi_supervised.GECriterion
count(int[], int) - Static method in class cc.mallet.util.ArrayUtils
  Returns the number of times a value occurs in a given array.
count(String, char) - Static method in class cc.mallet.util.Strings
CountMatches - Class in cc.mallet.pipe.tsf
CountMatches(String, Pattern, int) - Constructor for class cc.mallet.pipe.tsf.CountMatches
CountMatches(String, Pattern) - Constructor for class cc.mallet.pipe.tsf.CountMatches
CountMatchesAlignedWithOffsets - Class in cc.mallet.pipe.tsf
CountMatchesAlignedWithOffsets(String, Pattern, int[], boolean) - Constructor for class cc.mallet.pipe.tsf.CountMatchesAlignedWithOffsets
CountMatchesAlignedWithOffsets(String, Pattern, int[]) - Constructor for class cc.mallet.pipe.tsf.CountMatchesAlignedWithOffsets
CountMatchesMatching - Class in cc.mallet.pipe.tsf
CountMatchesMatching(String, Pattern, Pattern, boolean) - Constructor for class cc.mallet.pipe.tsf.CountMatchesMatching
CountMatchesMatching(String, Pattern, Pattern) - Constructor for class cc.mallet.pipe.tsf.CountMatchesMatching
cov(Univariate, Univariate) - Static method in class cc.mallet.util.StatFunctions
CPT - Class in cc.mallet.grmm.types
  $Id: CPT.java,v 1.1 2007/10/22 21:37:44 mccallum Exp $
CPT(DiscreteFactor, Variable) - Constructor for class cc.mallet.grmm.types.CPT
createAccuracyArray() - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
  Creates array of accuracy values for coverage at each step as defined by numBuckets.
createArrayList(Object[]) - Static method in class cc.mallet.util.ArrayListUtils
createBlankSubset(Variable[]) - Method in class cc.mallet.grmm.types.AbstractTableFactor
createBlankSubset(Variable[]) - Method in class cc.mallet.grmm.types.LogTableFactor
createBlankSubset(Variable[]) - Method in class cc.mallet.grmm.types.TableFactor
createBoltzmannMachine(double[][], double[]) - Static method in class cc.mallet.grmm.types.UndirectedModel
  Creates an undirected model that corresponds to a Boltzmann machine with the given weights and biases.
createEvaluator(String) - Static method in class cc.mallet.grmm.learning.extract.AcrfExtractorTui
createEvaluator(String) - Static method in class cc.mallet.grmm.learning.GenericAcrfTui
createFactorMatrix(ACRF.UnrolledVarSet) - Method in class cc.mallet.grmm.learning.ACRF.Template
  Creates an empty matrix for use in storing factor values when this template is unrolled.
createForMaxProduct() - Static method in class cc.mallet.grmm.inference.JunctionTreeInferencer
createForMaxProduct() - Static method in class cc.mallet.grmm.inference.LoopyBP
createForMaxProduct() - Static method in class cc.mallet.grmm.inference.ResidualBP
createForMaxProduct() - Static method in class cc.mallet.grmm.inference.TreeBP
createForMaxProduct() - Static method in class cc.mallet.grmm.inference.TRP
createFromRegex(Alphabet, Pattern) - Static method in class cc.mallet.types.FeatureSelection
  Creates a FeatureSelection that includes only those features whose names match a given regex.
createGainRatio(InstanceList) - Static method in class cc.mallet.types.GainRatio
  Constructs a GainRatio object.
createGainRatio(InstanceList, int[], int) - Static method in class cc.mallet.types.GainRatio
  Constructs a GainRatio object
createGrid(RandomGraphs.FactorGenerator, int) - Static method in class cc.mallet.grmm.inference.RandomGraphs
createGridWithObs(RandomGraphs.FactorGenerator, RandomGraphs.FactorGenerator, int) - Static method in class cc.mallet.grmm.inference.RandomGraphs
createMaximizable(ACRF, InstanceList) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
createPipe() - Method in class cc.mallet.pipe.tests.TestInstancePipe
createRandomChain(Randoms, int) - Static method in class cc.mallet.grmm.inference.RandomGraphs
createRandomClustering(InstanceList, Randoms) - Static method in class cc.mallet.cluster.util.ClusterUtils
createRandomGrid(int, int, int, Random) - Static method in class cc.mallet.grmm.test.TestInference
createSingletonClustering(InstanceList) - Static method in class cc.mallet.cluster.util.ClusterUtils
  Initializes Clustering to one Instance per cluster.
createSpan(Tokenization, int, int) - Method in class cc.mallet.extract.BIOTokenizationFilter
createSpan(Tokenization, int, int) - Method in class cc.mallet.extract.BIOTokenizationFilterWithTokenIndices
createTasks() - Method in class cc.mallet.fst.ThreadedOptimizable
  Creates tasks to be executed in parallel, each task looks at a batch of data.
createTestModels() - Static method in class cc.mallet.grmm.test.TestInference
createUniformChain(int) - Static method in class cc.mallet.grmm.inference.RandomGraphs
createUniformGrid(int) - Static method in class cc.mallet.grmm.inference.RandomGraphs
CRF - Class in cc.mallet.fst
  Represents a CRF model.
CRF(Pipe, Pipe) - Constructor for class cc.mallet.fst.CRF
CRF(Alphabet, Alphabet) - Constructor for class cc.mallet.fst.CRF
CRF(CRF) - Constructor for class cc.mallet.fst.CRF
  Create a CRF whose states and weights are a copy of those from another CRF.
crf - Variable in class cc.mallet.fst.CRFCacheStaleIndicator
crf - Variable in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
crf - Variable in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
crf - Variable in class cc.mallet.fst.CRFTrainerByStochasticGradient
crf - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
crf - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
CRF.Factors - Class in cc.mallet.fst
  A simple, transparent container to hold the parameters or sufficient statistics for the CRF.
CRF.Factors() - Constructor for class cc.mallet.fst.CRF.Factors
  Construct a new empty Factors with a new empty weightsAlphabet, 0-length initialWeights and finalWeights, and the other arrays null.
CRF.Factors(CRF.Factors) - Constructor for class cc.mallet.fst.CRF.Factors
  Construct new Factors by mimicking the structure of the other one, but with zero values.
CRF.Factors(CRF.Factors, boolean) - Constructor for class cc.mallet.fst.CRF.Factors
  Construct new Factors by copying the other one.
CRF.Factors(CRF) - Constructor for class cc.mallet.fst.CRF.Factors
  Construct a new Factors with the same structure as the parameters of 'crf', but with values initialized to zero.
CRF.Factors.Incrementor - Class in cc.mallet.fst
  Instances of this inner class can be passed to various inference methods, which can then gather/increment sufficient statistics counts into the containing Factor instance.
CRF.Factors.Incrementor() - Constructor for class cc.mallet.fst.CRF.Factors.Incrementor
CRF.Factors.WeightedIncrementor - Class in cc.mallet.fst
CRF.Factors.WeightedIncrementor(double) - Constructor for class cc.mallet.fst.CRF.Factors.WeightedIncrementor
CRF.State - Class in cc.mallet.fst
CRF.State() - Constructor for class cc.mallet.fst.CRF.State
CRF.State(String, int, double, double, String[], String[], String[][], CRF) - Constructor for class cc.mallet.fst.CRF.State
CRF.TransitionIterator - Class in cc.mallet.fst
CRF.TransitionIterator(CRF.State, FeatureVectorSequence, int, String, CRF) - Constructor for class cc.mallet.fst.CRF.TransitionIterator
CRF.TransitionIterator(CRF.State, FeatureVector, String, CRF) - Constructor for class cc.mallet.fst.CRF.TransitionIterator
CRFCacheStaleIndicator - Class in cc.mallet.fst
  Indicates when the value/gradient becomes stale based on updates to CRF's parameters.
CRFCacheStaleIndicator(CRF) - Constructor for class cc.mallet.fst.CRFCacheStaleIndicator
CRFExtractor - Class in cc.mallet.extract
  Created: Oct 12, 2004
CRFExtractor(CRF) - Constructor for class cc.mallet.extract.CRFExtractor
CRFExtractor(File) - Constructor for class cc.mallet.extract.CRFExtractor
CRFExtractor(CRF, Pipe) - Constructor for class cc.mallet.extract.CRFExtractor
CRFExtractor(CRF, Pipe, TokenizationFilter) - Constructor for class cc.mallet.extract.CRFExtractor
CRFExtractor(CRF, Pipe, TokenizationFilter, String) - Constructor for class cc.mallet.extract.CRFExtractor
CRFOptimizableByBatchLabelLikelihood - Class in cc.mallet.fst
  Implements label likelihood gradient computations for batches of data, can be easily parallelized.
CRFOptimizableByBatchLabelLikelihood(CRF, InstanceList, int) - Constructor for class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
CRFOptimizableByBatchLabelLikelihood.Factory - Class in cc.mallet.fst
CRFOptimizableByBatchLabelLikelihood.Factory() - Constructor for class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood.Factory
CRFOptimizableByEntropyRegularization - Class in cc.mallet.fst.semi_supervised
  A CRF objective function that is the entropy of the CRF's predictions on unlabeled data.
CRFOptimizableByEntropyRegularization(CRF, InstanceList, double) - Constructor for class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
  Initializes the structures.
CRFOptimizableByEntropyRegularization(CRF, InstanceList) - Constructor for class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
  Initializes the structures (sets the scaling factor to 1.0).
CRFOptimizableByGECriteria - Class in cc.mallet.fst.semi_supervised
  GE criteria for training a linear chain CRF.
CRFOptimizableByGECriteria(GECriteria, CRF, InstanceList, int) - Constructor for class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
  Initializes the structures.
CRFOptimizableByGradientValues - Class in cc.mallet.fst
  A CRF objective function that is the sum of multiple objective functions that implement Optimizable.ByGradientValue.
CRFOptimizableByGradientValues(CRF, Optimizable.ByGradientValue[]) - Constructor for class cc.mallet.fst.CRFOptimizableByGradientValues
CRFOptimizableByLabelLikelihood - Class in cc.mallet.fst
  An objective function for CRFs that is the label likelihood plus a Gaussian or hyperbolic prior on parameters.
CRFOptimizableByLabelLikelihood(CRF, InstanceList) - Constructor for class cc.mallet.fst.CRFOptimizableByLabelLikelihood
CRFOptimizableByLabelLikelihood.Factory - Class in cc.mallet.fst
CRFOptimizableByLabelLikelihood.Factory() - Constructor for class cc.mallet.fst.CRFOptimizableByLabelLikelihood.Factory
CRFTrainerByEntropyRegularization - Class in cc.mallet.fst.semi_supervised
  A CRF trainer that maximizes the log-likelihood plus a weighted entropy regularization term on unlabeled data.
CRFTrainerByEntropyRegularization(CRF) - Constructor for class cc.mallet.fst.semi_supervised.CRFTrainerByEntropyRegularization
CRFTrainerByGE - Class in cc.mallet.fst.semi_supervised
  Trains a CRF using Generalized Expectation constraints that considers a single label of a linear chain CRF.
CRFTrainerByGE(CRF, HashMap<Integer, GECriterion>) - Constructor for class cc.mallet.fst.semi_supervised.CRFTrainerByGE
CRFTrainerByGE(CRF, HashMap<Integer, GECriterion>, int) - Constructor for class cc.mallet.fst.semi_supervised.CRFTrainerByGE
CRFTrainerByL1LabelLikelihood - Class in cc.mallet.fst
  CRF trainer that implements L1-regularization.
CRFTrainerByL1LabelLikelihood(CRF) - Constructor for class cc.mallet.fst.CRFTrainerByL1LabelLikelihood
CRFTrainerByL1LabelLikelihood(CRF, double) - Constructor for class cc.mallet.fst.CRFTrainerByL1LabelLikelihood
  Constructor for CRF trainer.
CRFTrainerByLabelLikelihood - Class in cc.mallet.fst
  Unlike ClassifierTrainer, TransducerTrainer is not "stateless" between calls to train.
CRFTrainerByLabelLikelihood(CRF) - Constructor for class cc.mallet.fst.CRFTrainerByLabelLikelihood
CRFTrainerByStochasticGradient - Class in cc.mallet.fst
  Trains CRF by stochastic gradient.
CRFTrainerByStochasticGradient(CRF, InstanceList) - Constructor for class cc.mallet.fst.CRFTrainerByStochasticGradient
CRFTrainerByStochasticGradient(CRF, double) - Constructor for class cc.mallet.fst.CRFTrainerByStochasticGradient
CRFTrainerByThreadedLabelLikelihood - Class in cc.mallet.fst
CRFTrainerByThreadedLabelLikelihood(CRF, int) - Constructor for class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
CRFTrainerByValueGradients - Class in cc.mallet.fst
  A CRF trainer that can combine multiple objective functions, each represented by a Optmizable.ByValueGradient.
CRFTrainerByValueGradients(CRF, Optimizable.ByGradientValue[]) - Constructor for class cc.mallet.fst.CRFTrainerByValueGradients
CRFTrainerByValueGradients.OptimizableCRF - Class in cc.mallet.fst
  An optimizable CRF that contains a collection of objective functions.
CRFTrainerByValueGradients.OptimizableCRF(CRF, InstanceList) - Constructor for class cc.mallet.fst.CRFTrainerByValueGradients.OptimizableCRF
CRFWriter - Class in cc.mallet.fst
  Saves a trained model to specified filename.
CRFWriter(String) - Constructor for class cc.mallet.fst.CRFWriter
CrossTemplate1 - Class in cc.mallet.grmm.examples
  $Id: CrossTemplate1.java,v 1.1 2007/10/22 21:38:02 mccallum Exp $
CrossTemplate1(int, int) - Constructor for class cc.mallet.grmm.examples.CrossTemplate1
CrossValidationIterator - Class in cc.mallet.types
  An iterator which splits an `InstanceList` into n-folds and iterates over the folds for use in n-fold cross-validation.
CrossValidationIterator(InstanceList, int, Random) - Constructor for class cc.mallet.types.CrossValidationIterator
  Constructs a new n-fold cross-validation iterator
CrossValidationIterator(InstanceList, int) - Constructor for class cc.mallet.types.CrossValidationIterator
  Constructs a new n-fold cross-validation iterator
crossValidationIterator(int, int) - Method in class cc.mallet.types.InstanceList
crossValidationIterator(int) - Method in class cc.mallet.types.InstanceList
crossValidationIterator(int, int) - Method in class cc.mallet.types.MultiInstanceList
crossValidationIterator(int) - Method in class cc.mallet.types.MultiInstanceList
CSIntInt2ObjectMultiMap - Class in cc.mallet.grmm.util
  A map that maps (int, int) --> object, where each (int,int) key is allowed to map to multiple objects.
CSIntInt2ObjectMultiMap() - Constructor for class cc.mallet.grmm.util.CSIntInt2ObjectMultiMap
Csv2Array - Class in cc.mallet.pipe
  Converts a string of comma separated values to an array.
Csv2Array() - Constructor for class cc.mallet.pipe.Csv2Array
Csv2Array(String) - Constructor for class cc.mallet.pipe.Csv2Array
Csv2Array(CharSequenceLexer) - Constructor for class cc.mallet.pipe.Csv2Array
Csv2Classify - Class in cc.mallet.classify.tui
  Command line tool for classifying a sequence of instances directly from text input, without creating an instance list.
Csv2Classify() - Constructor for class cc.mallet.classify.tui.Csv2Classify
Csv2FeatureVector - Class in cc.mallet.pipe
  Converts a string of the form `feature_1:val_1 feature_2:val_2 ...`
Csv2FeatureVector(int) - Constructor for class cc.mallet.pipe.Csv2FeatureVector
Csv2FeatureVector() - Constructor for class cc.mallet.pipe.Csv2FeatureVector
Csv2Vectors - Class in cc.mallet.classify.tui
  Command line import tool for loading a sequence of instances from a single file, with one instance per line of the input file.
Csv2Vectors() - Constructor for class cc.mallet.classify.tui.Csv2Vectors
CsvIterator - Class in cc.mallet.pipe.iterator
  This iterator, perhaps more properly called a Line Pattern Iterator, reads through a file and returns one instance per line, based on a regular expression.
CsvIterator(Reader, Pattern, int, int, int) - Constructor for class cc.mallet.pipe.iterator.CsvIterator
CsvIterator(Reader, String, int, int, int) - Constructor for class cc.mallet.pipe.iterator.CsvIterator
CsvIterator(String, String, int, int, int) - Constructor for class cc.mallet.pipe.iterator.CsvIterator
cumulativeAccuracy() - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
  Finds the "area under the acc/cov curve" steps by one percentage point and calcs area of trapezoid
currentMessage() - Method in class cc.mallet.grmm.inference.MessageArray.ToMsgsIterator
currentToIdx() - Method in class cc.mallet.grmm.inference.MessageArray.ToMsgsIterator
curry(int) - Method in class cc.mallet.grmm.util.MIntInt2ObjectMap
  Returns an iterator over the set of (key2, value) pairs that match (key1).

## D

data - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
data - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
data - Static variable in class cc.mallet.fst.tests.TestCRF
data - Static variable in class cc.mallet.fst.tests.TestMEMM
data - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
data - Variable in class cc.mallet.topics.NPTopicModel
data - Variable in class cc.mallet.topics.ParallelTopicModel
data - Variable in class cc.mallet.topics.PolylingualTopicModel
data - Variable in class cc.mallet.topics.SimpleLDA
data - Variable in class cc.mallet.types.Instance
dataLogLikelihood(InstanceList) - Method in class cc.mallet.classify.NaiveBayes
DecisionTree - Class in cc.mallet.classify
  Decision Tree classifier.
DecisionTree(Pipe, DecisionTree.Node) - Constructor for class cc.mallet.classify.DecisionTree
DecisionTree.Node - Class in cc.mallet.classify
DecisionTree.Node(InstanceList, DecisionTree.Node, FeatureSelection) - Constructor for class cc.mallet.classify.DecisionTree.Node
DecisionTreeTrainer - Class in cc.mallet.classify
  A decision tree learner, roughly ID3, but only to a fixed given depth in all branches.
DecisionTreeTrainer(int) - Constructor for class cc.mallet.classify.DecisionTreeTrainer
DecisionTreeTrainer() - Constructor for class cc.mallet.classify.DecisionTreeTrainer
DecisionTreeTrainer.Factory - Class in cc.mallet.classify
DecisionTreeTrainer.Factory() - Constructor for class cc.mallet.classify.DecisionTreeTrainer.Factory
decompact() - Method in class cc.mallet.grmm.inference.JunctionTree
deepClone() - Method in class cc.mallet.pipe.SimpleTokenizer
deepCopy(MIntInt2ObjectMap) - Method in class cc.mallet.grmm.inference.MessageArray
DEFAULT - Static variable in class cc.mallet.grmm.types.Universe
DEFAULT_BETA - Static variable in class cc.mallet.topics.LDAHyper
  Deprecated.
DEFAULT_BETA - Static variable in class cc.mallet.topics.NPTopicModel
DEFAULT_BETA - Static variable in class cc.mallet.topics.ParallelTopicModel
DEFAULT_BETA - Static variable in class cc.mallet.topics.PolylingualTopicModel
DEFAULT_BETA - Static variable in class cc.mallet.topics.SimpleLDA
DEFAULT_BETA - Static variable in class cc.mallet.topics.WorkerRunnable
DEFAULT_COOLING_RATE - Static variable in class cc.mallet.classify.BalancedWinnowTrainer
  0.5
DEFAULT_DELTA - Static variable in class cc.mallet.classify.BalancedWinnowTrainer
  0.1
DEFAULT_EPSILON - Static variable in class cc.mallet.classify.BalancedWinnowTrainer
  0.5
DEFAULT_MAX_DEPTH - Static variable in class cc.mallet.classify.DecisionTreeTrainer
DEFAULT_MAX_ITER - Static variable in class cc.mallet.grmm.inference.LoopyBP
DEFAULT_MAX_ITER - Static variable in class cc.mallet.grmm.inference.ResidualBP
DEFAULT_MAX_ITERATIONS - Static variable in class cc.mallet.classify.BalancedWinnowTrainer
  30
DEFAULT_MAX_RESETS - Static variable in class cc.mallet.fst.CRFTrainerByValueGradients
DEFAULT_MIN_INFO_GAIN_SPLIT - Static variable in class cc.mallet.classify.DecisionTreeTrainer
DefaultAcrfTrainer - Class in cc.mallet.grmm.learning
  Class for training ACRFs.
DefaultAcrfTrainer() - Constructor for class cc.mallet.grmm.learning.DefaultAcrfTrainer
DefaultAcrfTrainer.FileEvaluator - Class in cc.mallet.grmm.learning
DefaultAcrfTrainer.FileEvaluator(File) - Constructor for class cc.mallet.grmm.learning.DefaultAcrfTrainer.FileEvaluator
DefaultAcrfTrainer.LogEvaluator - Class in cc.mallet.grmm.learning
DefaultAcrfTrainer.LogEvaluator() - Constructor for class cc.mallet.grmm.learning.DefaultAcrfTrainer.LogEvaluator
DefaultAcrfTrainer.TestResults - Class in cc.mallet.grmm.learning
defaultFeatureIndex - Variable in class cc.mallet.classify.MaxEnt
defaultIntersection(VarSet, VarSet) - Static method in class cc.mallet.grmm.inference.Utils
DefaultTokenizationFilter - Class in cc.mallet.extract
  Created: Nov 12, 2004
DefaultTokenizationFilter() - Constructor for class cc.mallet.extract.DefaultTokenizationFilter
defaultValue - Variable in class cc.mallet.util.CommandOption.Boolean
defaultValue - Variable in class cc.mallet.util.CommandOption.Double
defaultValue - Variable in class cc.mallet.util.CommandOption.DoubleArray
defaultValue - Variable in class cc.mallet.util.CommandOption.File
defaultValue - Variable in class cc.mallet.util.CommandOption.Integer
defaultValue - Variable in class cc.mallet.util.CommandOption.IntegerArray
defaultValue - Variable in class cc.mallet.util.CommandOption.Object
defaultValue - Variable in class cc.mallet.util.CommandOption.Set
defaultValue - Variable in class cc.mallet.util.CommandOption.SpacedStrings
defaultValue - Variable in class cc.mallet.util.CommandOption.String
defaultValueToString() - Method in class cc.mallet.util.CommandOption.Boolean
defaultValueToString() - Method in class cc.mallet.util.CommandOption
defaultValueToString() - Method in class cc.mallet.util.CommandOption.Double
defaultValueToString() - Method in class cc.mallet.util.CommandOption.DoubleArray
defaultValueToString() - Method in class cc.mallet.util.CommandOption.File
defaultValueToString() - Method in class cc.mallet.util.CommandOption.Integer
defaultValueToString() - Method in class cc.mallet.util.CommandOption.IntegerArray
defaultValueToString() - Method in class cc.mallet.util.CommandOption.Object
defaultValueToString() - Method in class cc.mallet.util.CommandOption.ObjectFromBean
defaultValueToString() - Method in class cc.mallet.util.CommandOption.Set
defaultValueToString() - Method in class cc.mallet.util.CommandOption.SpacedStrings
defaultValueToString() - Method in class cc.mallet.util.CommandOption.String
defaultWeights - Variable in class cc.mallet.fst.CRF.Factors
deletionMark - Static variable in class cc.mallet.types.FeatureSequenceWithBigrams
delogify() - Method in class cc.mallet.grmm.types.AbstractFactor
DenseMatrix - Class in cc.mallet.types
DenseMatrix() - Constructor for class cc.mallet.types.DenseMatrix
DenseVector - Class in cc.mallet.types
DenseVector(double[], boolean) - Constructor for class cc.mallet.types.DenseVector
DenseVector(double[]) - Constructor for class cc.mallet.types.DenseVector
DenseVector(int) - Constructor for class cc.mallet.types.DenseVector
depth() - Method in class cc.mallet.classify.C45.Node
  The root has depth zero.
depth() - Method in class cc.mallet.classify.DecisionTree.Node
  The root has depth zero.
describeTransition(double) - Method in class cc.mallet.fst.CRF.TransitionIterator
describeTransition(double) - Method in class cc.mallet.fst.MEMM.TransitionIterator
describeTransition(double) - Method in class cc.mallet.fst.Transducer.TransitionIterator
diag(int[], double) - Static method in class cc.mallet.grmm.util.Matrices
diagonalToString(double[], int) - Static method in class cc.mallet.util.MVNormal
digamma(double) - Static method in class cc.mallet.types.Dirichlet
  Calculate digamma using an asymptotic expansion involving Bernoulli numbers.
DIGAMMA_COEF_1 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_COEF_10 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_COEF_2 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_COEF_3 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_COEF_4 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_COEF_5 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_COEF_6 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_COEF_7 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_COEF_8 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_COEF_9 - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_LARGE - Static variable in class cc.mallet.types.Dirichlet
DIGAMMA_SMALL - Static variable in class cc.mallet.types.Dirichlet
digammaDifference(double, int) - Static method in class cc.mallet.types.Dirichlet
DirectedModel - Class in cc.mallet.grmm.types
  Class for directed graphical models.
DirectedModel() - Constructor for class cc.mallet.grmm.types.DirectedModel
DirectedModel(Variable[]) - Constructor for class cc.mallet.grmm.types.DirectedModel
DirectedModel(int) - Constructor for class cc.mallet.grmm.types.DirectedModel
Directory2FileIterator - Class in cc.mallet.pipe
  Convert a File object representing a directory into a FileIterator which iterates over files in the directory matching a pattern and which extracts a label from each file path to become the target field of the instance.
Directory2FileIterator(FileFilter, Pattern) - Constructor for class cc.mallet.pipe.Directory2FileIterator
Directory2FileIterator(Pattern, Pattern, Pattern) - Constructor for class cc.mallet.pipe.Directory2FileIterator
Directory2FileIterator(String) - Constructor for class cc.mallet.pipe.Directory2FileIterator
Directory2FileIterator() - Constructor for class cc.mallet.pipe.Directory2FileIterator
DirectoryFilter - Class in cc.mallet.util
DirectoryFilter() - Constructor for class cc.mallet.util.DirectoryFilter
Dirichlet - Class in cc.mallet.types
  Various useful functions related to Dirichlet distributions.
Dirichlet(double, double[]) - Constructor for class cc.mallet.types.Dirichlet
  A dirichlet parameterized by a distribution and a magnitude
Dirichlet(double[]) - Constructor for class cc.mallet.types.Dirichlet
  A dirichlet parameterized with a single vector of positive reals
Dirichlet(double[], Alphabet) - Constructor for class cc.mallet.types.Dirichlet
  Constructor that takes an alphabet representing the meaning of each dimension
Dirichlet(Alphabet) - Constructor for class cc.mallet.types.Dirichlet
  A symmetric Dirichlet with alpha_i = 1.0 and the number of dimensions of the given alphabet.
Dirichlet(Alphabet, double) - Constructor for class cc.mallet.types.Dirichlet
  A symmetric Dirichlet with alpha_i = `alpha` and the number of dimensions of the given alphabet.
Dirichlet(int) - Constructor for class cc.mallet.types.Dirichlet
  A symmetric Dirichlet with alpha_i = 1.0 and `size` dimensions
Dirichlet(int, double) - Constructor for class cc.mallet.types.Dirichlet
  A symmetric dirichlet: E(X_i) = E(X_j) for all i, j
Dirichlet.Estimator - Class in cc.mallet.types
Dirichlet.Estimator() - Constructor for class cc.mallet.types.Dirichlet.Estimator
Dirichlet.Estimator(Collection<Multinomial>) - Constructor for class cc.mallet.types.Dirichlet.Estimator
Dirichlet.MethodOfMomentsEstimator - Class in cc.mallet.types
Dirichlet.MethodOfMomentsEstimator() - Constructor for class cc.mallet.types.Dirichlet.MethodOfMomentsEstimator
dirichletMultinomialLikelihoodRatio(TIntIntHashMap, TIntIntHashMap, double, double) - Static method in class cc.mallet.types.Dirichlet
  What is the probability that these two observations were drawn from the same multinomial with symmetric Dirichlet prior alpha, relative to the probability that they were drawn from different multinomials both drawn from this Dirichlet?
dirichletMultinomialLikelihoodRatio(int[], int[], double, double) - Static method in class cc.mallet.types.Dirichlet
  What is the probability that these two observations were drawn from the same multinomial with symmetric Dirichlet prior alpha, relative to the probability that they were drawn from different multinomials both drawn from this Dirichlet?
dirichletMultinomialLikelihoodRatio(int[], int[]) - Method in class cc.mallet.types.Dirichlet
  This version uses a non-symmetric Dirichlet prior
disableDoubleBuffering(Component) - Static method in class cc.mallet.util.PrintUtilities
  The speed and quality of printing suffers dramatically if any of the containers have double buffering turned on.
disabledtestAddOrderNStates() - Method in class cc.mallet.fst.tests.TestMEMM
disabledtestCost(int) - Method in class cc.mallet.fst.tests.TestMEMM
disabledtestDenseSerialization() - Method in class cc.mallet.fst.tests.TestMEMM
disabledtestDenseTrain() - Method in class cc.mallet.fst.tests.TestMEMM
disabledtestPrint() - Method in class cc.mallet.fst.tests.TestMEMM
disabledtestSerialization() - Method in class cc.mallet.fst.tests.TestMEMM
disabledtestTrain() - Method in class cc.mallet.fst.tests.TestMEMM
disabledtestValueGradient() - Method in class cc.mallet.fst.tests.TestMEMM
DiscreteFactor - Interface in cc.mallet.grmm.types
  $Id: DiscreteFactor.java,v 1.1 2007/10/22 21:37:44 mccallum Exp $
discreteVarsOf(Factor) - Static method in class cc.mallet.grmm.types.Factors
displayGraph() - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
  Displays the accuracy v.
displayTopWords(int, boolean) - Method in class cc.mallet.topics.ParallelTopicModel
distance(SparseVector, int, SparseVector, int) - Method in interface cc.mallet.types.CachedMetric
distance(SparseVector, SparseVector) - Method in interface cc.mallet.types.Metric
distance(SparseVector, SparseVector) - Method in class cc.mallet.types.Minkowski
  Gives the Minkowski distance between two vectors.
distance(SparseVector, SparseVector) - Method in class cc.mallet.types.NormalizedDotProductMetric
distance(SparseVector, int, SparseVector, int) - Method in class cc.mallet.types.NormalizedDotProductMetric
distLinf(AbstractTableFactor, AbstractTableFactor) - Static method in class cc.mallet.grmm.types.Factors
distributionToString(double, double[]) - Static method in class cc.mallet.types.Dirichlet
  Create a printable list of alpha_i parameters
distValueLinf(AbstractTableFactor, AbstractTableFactor) - Static method in class cc.mallet.grmm.types.Factors
div() - Static method in class cc.mallet.grmm.util.Flops
divideBy(Factor) - Method in class cc.mallet.grmm.types.AbstractFactor
divideBy(Factor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Does the conceptual equivalent of this /= pot.
divideBy(double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
divideBy(Factor) - Method in class cc.mallet.grmm.types.BetaFactor
divideBy(Factor) - Method in class cc.mallet.grmm.types.CPT
divideBy(Factor) - Method in interface cc.mallet.grmm.types.Factor
  Computes this /= pot
divideBy(Factor) - Method in class cc.mallet.grmm.types.FactorGraph
divideBy(Factor) - Method in class cc.mallet.grmm.types.NormalFactor
divideBy(Factor) - Method in class cc.mallet.grmm.types.UniformFactor
divideBy(Factor) - Method in class cc.mallet.grmm.types.UniNormalFactor
divideByInternal(DiscreteFactor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
divideByInternal(DiscreteFactor) - Method in class cc.mallet.grmm.types.LogTableFactor
divideByInternal(DiscreteFactor) - Method in class cc.mallet.grmm.types.TableFactor
divideEquals(double) - Method in class cc.mallet.types.DenseMatrix
divideEquals(double) - Method in interface cc.mallet.types.Matrix
divideEquals(double) - Method in class cc.mallet.types.SparseMatrixn
DMRLoader - Class in cc.mallet.topics.tui
  This class loads data into the format for the MALLET Dirichlet-multinomial regression (DMR).
DMRLoader() - Constructor for class cc.mallet.topics.tui.DMRLoader
DMROptimizable - Class in cc.mallet.topics
DMROptimizable() - Constructor for class cc.mallet.topics.DMROptimizable
DMROptimizable(InstanceList, MaxEnt) - Constructor for class cc.mallet.topics.DMROptimizable
DMRTopicModel - Class in cc.mallet.topics
DMRTopicModel(int) - Constructor for class cc.mallet.topics.DMRTopicModel
docLengthCounts - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
docLengthCounts - Variable in class cc.mallet.topics.ParallelTopicModel
docLengthCounts - Variable in class cc.mallet.topics.PolylingualTopicModel
docLengthCounts - Variable in class cc.mallet.topics.WorkerRunnable
docsPerTopic - Variable in class cc.mallet.topics.NPTopicModel
DocumentClassifier - Class in cc.mallet.classify.examples
DocumentClassifier() - Constructor for class cc.mallet.classify.examples.DocumentClassifier
DocumentExtraction - Class in cc.mallet.extract
  Created: Oct 12, 2004
DocumentExtraction(String, LabelAlphabet, Tokenization, Sequence, String) - Constructor for class cc.mallet.extract.DocumentExtraction
DocumentExtraction(String, LabelAlphabet, Tokenization, Sequence, Sequence, String) - Constructor for class cc.mallet.extract.DocumentExtraction
DocumentExtraction(String, LabelAlphabet, Tokenization, Sequence, Sequence, String, TokenizationFilter) - Constructor for class cc.mallet.extract.DocumentExtraction
DocumentExtraction(String, LabelAlphabet, Tokenization, LabeledSpans, LabeledSpans, String) - Constructor for class cc.mallet.extract.DocumentExtraction
DocumentViewer - Class in cc.mallet.extract
  Diagnosis class that outputs HTML pages that allows you to view errors on a more global per-instance basis.
DocumentViewer() - Constructor for class cc.mallet.extract.DocumentViewer
doneWithGraph(FactorGraph) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
doProcessOptions(Class, String[]) - Static method in class cc.mallet.grmm.learning.extract.AcrfExtractorTui
doProcessOptions(Class, String[]) - Static method in class cc.mallet.grmm.learning.GenericAcrfTui
dot(double[], double[]) - Static method in class cc.mallet.types.MatrixOps
  Deprecated. Use dotProduct()
doTestCost(boolean) - Method in class cc.mallet.fst.tests.TestCRF
doTestSpacePrediction(boolean) - Method in class cc.mallet.fst.tests.TestCRF
doTestSpacePrediction(boolean, boolean, boolean) - Method in class cc.mallet.fst.tests.TestCRF
doTestSpacePrediction(boolean) - Method in class cc.mallet.fst.tests.TestMEMM
doTestSpacePrediction(boolean, boolean, boolean) - Method in class cc.mallet.fst.tests.TestMEMM
dotProduct(DenseVector) - Method in class cc.mallet.types.AugmentableFeatureVector
dotProduct(SparseVector) - Method in class cc.mallet.types.AugmentableFeatureVector
dotProduct(AugmentableFeatureVector) - Method in class cc.mallet.types.AugmentableFeatureVector
dotProduct(ConstantMatrix) - Method in interface cc.mallet.types.ConstantMatrix
dotProduct(ConstantMatrix) - Method in class cc.mallet.types.DenseMatrix
dotProduct(int, Matrix2, int) - Method in class cc.mallet.types.FeatureVectorSequence
dotProduct(int, Vector) - Method in class cc.mallet.types.FeatureVectorSequence
dotProduct(DenseVector) - Method in class cc.mallet.types.HashedSparseVector
dotProduct(SparseVector) - Method in class cc.mallet.types.HashedSparseVector
dotProduct(DenseVector) - Method in class cc.mallet.types.IndexedSparseVector
dotProduct(SparseVector) - Method in class cc.mallet.types.IndexedSparseVector
dotProduct(double[], double[]) - Static method in class cc.mallet.types.MatrixOps
dotProduct(ConstantMatrix) - Method in class cc.mallet.types.SparseMatrixn
dotProduct(double[]) - Method in class cc.mallet.types.SparseVector
  VECTOR OPERATIONS
dotProduct(ConstantMatrix) - Method in class cc.mallet.types.SparseVector
dotProduct(DenseVector) - Method in class cc.mallet.types.SparseVector
dotProduct(SparseVector) - Method in class cc.mallet.types.SparseVector
doubleArrayToString(double[], int) - Static method in class cc.mallet.util.MVNormal
  Create a string representation of a square matrix in one-dimensional array format
DoubleList - Class in cc.mallet.util
DoubleList() - Constructor for class cc.mallet.util.DoubleList
DoubleList(int) - Constructor for class cc.mallet.util.DoubleList
DoubleList(int, double) - Constructor for class cc.mallet.util.DoubleList
DoubleList(double[], int) - Constructor for class cc.mallet.util.DoubleList
DoubleList(double[]) - Constructor for class cc.mallet.util.DoubleList
drawObservation(int) - Method in class cc.mallet.types.Dirichlet
  Dirichlet-multinomial: draw a distribution from the dirichlet, then draw n samples from that multinomial.
drawObservation(int, double[]) - Method in class cc.mallet.types.Dirichlet
  Draw a count vector from the probability distribution provided.
drawObservations(int, int) - Method in class cc.mallet.types.Dirichlet
  Create a set of d draws from a dirichlet-multinomial, each with an average of n observations.
dualLattice2html(PrintWriter, String, LatticeViewer.ExtorInfo, LatticeViewer.ExtorInfo) - Static method in class cc.mallet.extract.LatticeViewer
dump() - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
dump(PrintWriter) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
dump() - Method in class cc.mallet.grmm.inference.AbstractInferencer
dump() - Method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
dump() - Method in interface cc.mallet.grmm.inference.Inferencer
dump() - Method in class cc.mallet.grmm.inference.JunctionTree
dump() - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
dump() - Method in class cc.mallet.grmm.inference.MessageArray
dump(PrintWriter) - Method in class cc.mallet.grmm.inference.MessageArray
dump() - Method in class cc.mallet.grmm.types.Assignment
dump(PrintWriter) - Method in class cc.mallet.grmm.types.Assignment
dump() - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
dump(PrintStream) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
dump(PrintWriter) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
dump() - Method in class cc.mallet.grmm.types.FactorGraph
  Dumps all the variables and factors of the model to `System.out` in human-readable text.
dump(PrintWriter) - Method in class cc.mallet.grmm.types.FactorGraph
dump() - Method in class cc.mallet.types.Alphabet
dump(PrintStream) - Method in class cc.mallet.types.Alphabet
dump(PrintWriter) - Method in class cc.mallet.types.Alphabet
dumpLogJoint(Assignment) - Method in class cc.mallet.grmm.inference.JunctionTree
dumpLogJoint(Assignment) - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
dumpNumeric() - Method in class cc.mallet.grmm.types.Assignment
dumpToString() - Method in class cc.mallet.grmm.types.AbstractTableFactor
dumpToString() - Method in class cc.mallet.grmm.types.Assignment
dumpToString() - Method in class cc.mallet.grmm.types.BetaFactor
dumpToString() - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
dumpToString() - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
dumpToString() - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
dumpToString() - Method in class cc.mallet.grmm.types.ConstantFactor
dumpToString() - Method in class cc.mallet.grmm.types.CPT
dumpToString() - Method in interface cc.mallet.grmm.types.Factor
dumpToString() - Method in class cc.mallet.grmm.types.FactorGraph
dumpToString() - Method in class cc.mallet.grmm.types.NormalFactor
dumpToString() - Method in class cc.mallet.grmm.types.PottsTableFactor
dumpToString() - Method in class cc.mallet.grmm.types.SkeletonFactor
dumpToString() - Method in class cc.mallet.grmm.types.Tree
dumpToString() - Method in class cc.mallet.grmm.types.UniformFactor
dumpToString() - Method in class cc.mallet.grmm.types.UniNormalFactor
dumpToString(Collection, String) - Static method in class cc.mallet.util.CollectionUtils
dumpToString(Collection) - Static method in class cc.mallet.util.CollectionUtils
dumpUnrolledGraphs(InstanceList) - Method in class cc.mallet.grmm.learning.ACRF
duplicate() - Method in class cc.mallet.grmm.inference.AbstractInferencer
duplicate() - Method in interface cc.mallet.grmm.inference.Inferencer
duplicate() - Method in class cc.mallet.grmm.inference.MessageArray
duplicate() - Method in class cc.mallet.grmm.types.AbstractTableFactor
duplicate() - Method in class cc.mallet.grmm.types.Assignment
duplicate() - Method in class cc.mallet.grmm.types.BetaFactor
duplicate() - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
duplicate() - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
duplicate() - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
duplicate() - Method in class cc.mallet.grmm.types.ConstantFactor
duplicate() - Method in class cc.mallet.grmm.types.CPT
duplicate() - Method in interface cc.mallet.grmm.types.Factor
duplicate() - Method in class cc.mallet.grmm.types.FactorGraph
  Returns a copy of this model.
duplicate() - Method in class cc.mallet.grmm.types.LogTableFactor
duplicate() - Method in class cc.mallet.grmm.types.NormalFactor
duplicate() - Method in class cc.mallet.grmm.types.PottsTableFactor
duplicate() - Method in class cc.mallet.grmm.types.SkeletonFactor
duplicate() - Method in class cc.mallet.grmm.types.TableFactor
duplicate() - Method in class cc.mallet.grmm.types.UniformFactor
duplicate() - Method in class cc.mallet.grmm.types.UniNormalFactor

## E

elapsedTime() - Method in class cc.mallet.util.Timing
  Returns how much time as passed since Object creation, or the most recent call to tick().
elementAt(int) - Method in class cc.mallet.util.Univariate
elementwiseAccuracy(Sequence) - Method in interface cc.mallet.fst.MaxLattice
elementwiseAccuracy(Sequence) - Method in class cc.mallet.fst.MaxLatticeDefault
elementwiseAccuracy(Sequence, Sequence) - Static method in class cc.mallet.util.Sequences
elementwiseDivideEquals(ConstantMatrix) - Method in class cc.mallet.types.DenseMatrix
elementwiseDivideEquals(ConstantMatrix, double) - Method in class cc.mallet.types.DenseMatrix
elementwiseDivideEquals(ConstantMatrix) - Method in interface cc.mallet.types.Matrix
elementwiseDivideEquals(ConstantMatrix, double) - Method in interface cc.mallet.types.Matrix
elementwiseDivideEquals(ConstantMatrix) - Method in class cc.mallet.types.SparseMatrixn
elementwiseDivideEquals(ConstantMatrix, double) - Method in class cc.mallet.types.SparseMatrixn
elementwiseTimesEquals(ConstantMatrix) - Method in class cc.mallet.types.DenseMatrix
elementwiseTimesEquals(ConstantMatrix, double) - Method in class cc.mallet.types.DenseMatrix
elementwiseTimesEquals(ConstantMatrix) - Method in interface cc.mallet.types.Matrix
elementwiseTimesEquals(ConstantMatrix, double) - Method in interface cc.mallet.types.Matrix
elementwiseTimesEquals(ConstantMatrix) - Method in class cc.mallet.types.SparseMatrixn
elementwiseTimesEquals(ConstantMatrix, double) - Method in class cc.mallet.types.SparseMatrixn
empiricalLikelihood(int, InstanceList) - Method in class cc.mallet.topics.HierarchicalLDA
  For use with empirical likelihood evaluation: sample a path through the tree, then sample a multinomial over topics in that path, then return a weighted sum of words.
empiricalLikelihood(int, InstanceList) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
EMPTY_DROP - Static variable in class cc.mallet.cluster.KMeans
  Drop an empty cluster
EMPTY_ERROR - Static variable in class cc.mallet.cluster.KMeans
  Treat an empty cluster as an error condition.
EMPTY_SINGLE - Static variable in class cc.mallet.cluster.KMeans
  Place the single instance furthest from the previous cluster mean
EmptyInstanceIterator - Class in cc.mallet.pipe.iterator
EmptyInstanceIterator() - Constructor for class cc.mallet.pipe.iterator.EmptyInstanceIterator
enableDoubleBuffering(Component) - Static method in class cc.mallet.util.PrintUtilities
  Re-enables double buffering globally.
endsPrematurely() - Method in class cc.mallet.fst.Segment
EnronMessage2TokenSequence - Class in cc.mallet.share.weili.ner.enron
EnronMessage2TokenSequence() - Constructor for class cc.mallet.share.weili.ner.enron.EnronMessage2TokenSequence
ensureCapacity(int) - Method in class cc.mallet.types.MultiInstanceList
ensureCapacity(int) - Method in class cc.mallet.types.Multinomial.Estimator
ensureOperandCompatible(DiscreteFactor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Ensures that `this.inLogSpace == ptl.inLogSpace`.
entropy - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice
entropy() - Method in class cc.mallet.grmm.inference.JunctionTree
entropy() - Method in class cc.mallet.grmm.types.AbstractFactor
entropy() - Method in class cc.mallet.grmm.types.AbstractTableFactor
entropy() - Method in class cc.mallet.grmm.types.CPT
entropy() - Method in interface cc.mallet.grmm.types.Factor
  Returns the expected log factor value, i.e., `sum_x factor.value(x) * Math.log (factor.value (x))` where the summation is taken over all passible assignments.
entropy() - Method in class cc.mallet.grmm.types.FactorGraph
entropy(FactorGraph) - Static method in class cc.mallet.grmm.util.Models
  Computes the exact entropy of a factor graph distribution using the junction tree algorithm.
EntropyLattice - Class in cc.mallet.fst.semi_supervised
  Runs subsequence constrained forward-backward to compute the entropy of label sequences.
EntropyLattice(FeatureVectorSequence, double[][], double[][][], Transducer, Transducer.Incrementor, double) - Constructor for class cc.mallet.fst.semi_supervised.EntropyLattice
  Runs constrained forward-backward.
EntropyLattice.LatticeNode - Class in cc.mallet.fst.semi_supervised
  Contains alpha, beta values at a particular input position and state pair.
entryClass() - Method in class cc.mallet.types.Alphabet
entrySet() - Method in class cc.mallet.grmm.util.THashMultiMap
EPSILON - Static variable in class cc.mallet.util.Maths
  Numbers that are closer than this are considered equal by almostEquals.
equals(Object) - Method in class cc.mallet.cluster.Clustering
equals(Object) - Method in class cc.mallet.fst.Segment
equals(Object) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
equals(Object) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
equals(Object) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
equals(Object) - Method in class cc.mallet.grmm.types.HashVarSet
equals(Object) - Method in class cc.mallet.grmm.types.ListVarSet
equals(Object) - Method in class cc.mallet.grmm.types.PottsTableFactor
equals(Object) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
equals(Object) - Method in class cc.mallet.types.Label
equals(Object) - Method in class cc.mallet.types.Matrixn
equals(Object) - Method in class cc.mallet.types.MultiInstanceList
equals(Object) - Method in class cc.mallet.types.SparseMatrixn
equals(boolean[][], boolean[][]) - Static method in class cc.mallet.util.ArrayUtils
equalsPlus(double, ConstantMatrix) - Method in class cc.mallet.types.DenseMatrix
equalsPlus(double, ConstantMatrix) - Method in interface cc.mallet.types.Matrix
equalsPlus(double, ConstantMatrix) - Method in class cc.mallet.types.SparseMatrixn
estimate() - Method in class cc.mallet.fst.FeatureTransducer
estimate() - Method in class cc.mallet.fst.HMM
estimate(int) - Method in class cc.mallet.topics.DMRTopicModel
estimate(int) - Method in class cc.mallet.topics.HierarchicalLDA
estimate(InstanceList, InstanceList, int, int, int, int, String, Randoms) - Method in class cc.mallet.topics.HierarchicalPAM
estimate(InstanceList, int, int, int, String, Randoms) - Method in class cc.mallet.topics.LDA
  Deprecated.
estimate(int, int, int, int, int, String, Randoms) - Method in class cc.mallet.topics.LDA
  Deprecated.
estimate() - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
estimate(int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
estimate(InstanceList, int, int, int, int, String, Randoms) - Method in class cc.mallet.topics.PAM4L
estimate() - Method in class cc.mallet.topics.ParallelTopicModel
estimate() - Method in class cc.mallet.topics.PolylingualTopicModel
estimate(int) - Method in class cc.mallet.topics.PolylingualTopicModel
estimate(InstanceList, int, int, int, String, Randoms) - Method in class cc.mallet.topics.TopicalNGrams
estimate() - Method in class cc.mallet.types.Dirichlet.Estimator
estimate() - Method in class cc.mallet.types.Dirichlet.MethodOfMomentsEstimator
estimate() - Method in class cc.mallet.types.Multinomial.Estimator
estimate() - Method in class cc.mallet.types.Multinomial.MAPEstimator
estimate() - Method in class cc.mallet.types.Multinomial.MEstimator
estimateAll(int) - Method in class cc.mallet.topics.LDAStream
estimateConfidence(Extraction) - Method in class cc.mallet.extract.ExtractionConfidenceEstimator
estimateConfidence(DocumentExtraction) - Method in class cc.mallet.extract.ExtractionConfidenceEstimator
estimateConfidence(DocumentExtraction) - Method in class cc.mallet.extract.TransducerExtractionConfidenceEstimator
estimateConfidenceFor(Segment, SumLatticeDefault) - Method in class cc.mallet.fst.confidence.ConstrainedForwardBackwardConfidenceEstimator
  Calculates the confidence in the tagging of a `Segment`.
estimateConfidenceFor(Segment, SumLatticeDefault) - Method in class cc.mallet.fst.confidence.GammaAverageConfidenceEstimator
  Calculates the confidence in the tagging of a `Segment`.
estimateConfidenceFor(Segment, SumLatticeDefault) - Method in class cc.mallet.fst.confidence.GammaProductConfidenceEstimator
  Calculates the confidence in the tagging of a `Segment`.
estimateConfidenceFor(Segment, SumLatticeDefault) - Method in class cc.mallet.fst.confidence.MaxEntConfidenceEstimator
  Calculates the confidence in the tagging of a `Segment`.
estimateConfidenceFor(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.MaxEntSequenceConfidenceEstimator
  Calculates the confidence in the tagging of an `Instance`.
estimateConfidenceFor(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.MinSegmentConfidenceEstimator
  Calculates the confidence in the tagging of a `Instance`.
estimateConfidenceFor(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.NBestViterbiConfidenceEstimator
  Calculates the confidence in the tagging of a `Instance`.
estimateConfidenceFor(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.QBCSequenceConfidenceEstimator
  Calculates the confidence in the tagging of a `Instance`.
estimateConfidenceFor(Segment, SumLatticeDefault) - Method in class cc.mallet.fst.confidence.RandomConfidenceEstimator
  Randomly generate the confidence in the tagging of a `Segment`.
estimateConfidenceFor(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.RandomSequenceConfidenceEstimator
  Calculates the confidence in the tagging of an `Instance`.
estimateConfidenceFor(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.SegmentProductConfidenceEstimator
  Calculates the confidence in the tagging of a `Instance`.
estimateConfidenceFor(Segment) - Method in class cc.mallet.fst.confidence.TransducerConfidenceEstimator
  Calculates the confidence in the tagging of a `Segment`.
estimateConfidenceFor(Segment, SumLatticeDefault) - Method in class cc.mallet.fst.confidence.TransducerConfidenceEstimator
estimateConfidenceFor(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.TransducerSequenceConfidenceEstimator
  Calculates the confidence in the tagging of a `Sequence`.
estimateConfidenceFor(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.ViterbiConfidenceEstimator
  Calculates the confidence in the tagging of a `Instance`.
estimateConfidenceFor(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.ViterbiRatioConfidenceEstimator
  Calculates the confidence in the tagging of an `Instance`.
euclideanDistance(AbstractTableFactor, AbstractTableFactor) - Static method in class cc.mallet.grmm.types.Factors
euclideanDistance(SparseVector, SparseVector) - Method in class cc.mallet.types.Minkowski
EULER_MASCHERONI - Static variable in class cc.mallet.types.Dirichlet
  Actually the negative Euler-Mascheroni constant
evaluate(ClassifierTrainer) - Method in class cc.mallet.classify.ClassifierEvaluator
  Evaluates a ClassifierTrainer and its Classifier on the instance lists specified in the constructor.
evaluate(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.AccuracyEvaluator
evaluate(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.BCubedEvaluator
evaluate(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.ClusteringEvaluator
evaluate(Clustering[], Clustering[]) - Method in class cc.mallet.cluster.evaluate.ClusteringEvaluator
evaluate(Clustering[], Clusterer) - Method in class cc.mallet.cluster.evaluate.ClusteringEvaluator
evaluate(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.ClusteringEvaluators
evaluate(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.MUCEvaluator
evaluate(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.PairF1Evaluator
evaluate(Neighbor) - Method in class cc.mallet.cluster.neighbor_evaluator.ClassifyingNeighborEvaluator
evaluate(Neighbor[]) - Method in class cc.mallet.cluster.neighbor_evaluator.ClassifyingNeighborEvaluator
evaluate(Neighbor[]) - Method in class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator
evaluate(Neighbor) - Method in class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator
evaluate(Neighbor) - Method in interface cc.mallet.cluster.neighbor_evaluator.NeighborEvaluator
evaluate(Neighbor[]) - Method in interface cc.mallet.cluster.neighbor_evaluator.NeighborEvaluator
evaluate(Neighbor[]) - Method in class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator
evaluate(Neighbor) - Method in class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator
evaluate(Neighbor) - Method in class cc.mallet.cluster.neighbor_evaluator.RandomEvaluator
evaluate(Neighbor[]) - Method in class cc.mallet.cluster.neighbor_evaluator.RandomEvaluator
evaluate(Neighbor) - Method in class cc.mallet.cluster.neighbor_evaluator.RankingNeighborEvaluator
evaluate(Neighbor[]) - Method in class cc.mallet.cluster.neighbor_evaluator.RankingNeighborEvaluator
evaluate(Extraction) - Method in class cc.mallet.extract.AccuracyCoverageEvaluator
evaluate(String, Extraction, PrintStream) - Method in class cc.mallet.extract.AccuracyCoverageEvaluator
evaluate(Extraction) - Method in interface cc.mallet.extract.ExtractionEvaluator
evaluate(Extraction) - Method in class cc.mallet.extract.PerDocumentF1Evaluator
evaluate(Extraction, PrintStream) - Method in class cc.mallet.extract.PerDocumentF1Evaluator
evaluate(Extraction, PrintWriter) - Method in class cc.mallet.extract.PerDocumentF1Evaluator
evaluate(String, Extraction, PrintWriter) - Method in class cc.mallet.extract.PerDocumentF1Evaluator
evaluate(Extraction) - Method in class cc.mallet.extract.PerFieldF1Evaluator
evaluate(String, Extraction, PrintStream) - Method in class cc.mallet.extract.PerFieldF1Evaluator
evaluate(Transducer, ArrayList, InstanceList, ArrayList, String, PrintStream, boolean) - Method in class cc.mallet.fst.confidence.ConfidenceCorrectorEvaluator
  Only evaluates over sequences which contain errors.
evaluate(TransducerEvaluator, InstanceList) - Method in class cc.mallet.fst.CRF
  Deprecated.
evaluate(TransducerTrainer) - Method in class cc.mallet.fst.TransducerEvaluator
  Evaluates a TransducerTrainer and its Transducer on the instance lists specified in the constructor.
evaluate(ACRF, int, InstanceList, InstanceList, InstanceList) - Method in class cc.mallet.grmm.learning.ACRFEvaluator
  Evalutes the model in the middle of training.
evaluate(ACRF, int, InstanceList, InstanceList, InstanceList) - Method in class cc.mallet.grmm.learning.AcrfSerialEvaluator
evaluate(ACRF, int, InstanceList, InstanceList, InstanceList) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.FileEvaluator
evaluate(ACRF, int, InstanceList, InstanceList, InstanceList) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.LogEvaluator
evaluate(ACRF, int, InstanceList, InstanceList, InstanceList) - Method in class cc.mallet.grmm.learning.MultiSegmentationEvaluatorACRF
evaluate(Optimizable.ByBatchGradient, int, int, int, int[]) - Method in interface cc.mallet.optimize.OptimizerEvaluator.ByBatchGradient
  Performs some operation at the end of every batch.
evaluate(Optimizable.ByGradientValue, int) - Method in interface cc.mallet.optimize.OptimizerEvaluator.ByGradient
  Performs some operation at the end of each iteration of a maximizer.
evaluateInstanceList(ClassifierTrainer, InstanceList, String) - Method in class cc.mallet.classify.ClassifierAccuracyEvaluator
evaluateInstanceList(ClassifierTrainer, InstanceList, String) - Method in class cc.mallet.classify.ClassifierEvaluator
evaluateInstanceList(TransducerTrainer, InstanceList, String) - Method in class cc.mallet.fst.CRFWriter
evaluateInstanceList(TransducerTrainer, InstanceList, String) - Method in class cc.mallet.fst.InstanceAccuracyEvaluator
evaluateInstanceList(TransducerTrainer, InstanceList, String) - Method in class cc.mallet.fst.LabelDistributionEvaluator
evaluateInstanceList(TransducerTrainer, InstanceList, String) - Method in class cc.mallet.fst.MultiSegmentationEvaluator
evaluateInstanceList(TransducerTrainer, InstanceList, String) - Method in class cc.mallet.fst.PerClassAccuracyEvaluator
evaluateInstanceList(TransducerTrainer, InstanceList, String) - Method in class cc.mallet.fst.SegmentationEvaluator
evaluateInstanceList(TransducerTrainer, InstanceList, String) - Method in class cc.mallet.fst.TokenAccuracyEvaluator
evaluateInstanceList(TransducerTrainer, InstanceList, String) - Method in class cc.mallet.fst.TransducerEvaluator
evaluateInstanceList(TransducerTrainer, InstanceList, String) - Method in class cc.mallet.fst.ViterbiWriter
evaluateLeftToRight(InstanceList, int, boolean, PrintStream) - Method in class cc.mallet.topics.MarginalProbEstimator
EvaluateTopics - Class in cc.mallet.topics.tui
EvaluateTopics() - Constructor for class cc.mallet.topics.tui.EvaluateTopics
evaluateTotals() - Method in class cc.mallet.cluster.evaluate.AccuracyEvaluator
evaluateTotals() - Method in class cc.mallet.cluster.evaluate.BCubedEvaluator
evaluateTotals() - Method in class cc.mallet.cluster.evaluate.ClusteringEvaluator
evaluateTotals() - Method in class cc.mallet.cluster.evaluate.ClusteringEvaluators
evaluateTotals() - Method in class cc.mallet.cluster.evaluate.MUCEvaluator
evaluateTotals() - Method in class cc.mallet.cluster.evaluate.PairF1Evaluator
evaluator - Variable in class cc.mallet.cluster.HillClimbingClusterer
evaluator - Variable in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
ewensLikelihoodRatio(int[], int[], double) - Static method in class cc.mallet.types.Dirichlet
  Similar to the Dirichlet-multinomial test,s this is a likelihood ratio based on the Ewens Sampling Formula, which can be considered the distribution of partitions of integers generated by the Chinese restaurant process.
ExactMatchComparator - Class in cc.mallet.extract
  Created: Nov 23, 2004
ExactMatchComparator() - Constructor for class cc.mallet.extract.ExactMatchComparator
ExactSampler - Class in cc.mallet.grmm.inference
  Computes an exact sample from the distribution of a given factor graph by forming a junction tree.
ExactSampler() - Constructor for class cc.mallet.grmm.inference.ExactSampler
ExactSampler(Randoms) - Constructor for class cc.mallet.grmm.inference.ExactSampler
Examples - Class in cc.mallet.util.resources.wn
  A class to demonstrate the functionality of the JWNL package.
Examples() - Constructor for class cc.mallet.util.resources.wn.Examples
exp() - Static method in class cc.mallet.grmm.util.Flops
exp(int) - Static method in class cc.mallet.grmm.util.Flops
EXP_GAIN - Static variable in class cc.mallet.classify.MaxEntTrainer
EXP_GAIN - Static variable in class cc.mallet.classify.MCMaxEntTrainer
expectation - Variable in class cc.mallet.fst.semi_supervised.GECriterion
expectations - Variable in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
expectations - Variable in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
expectations - Variable in class cc.mallet.fst.CRFTrainerByStochasticGradient
expectations - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
ExpGain - Class in cc.mallet.types
ExpGain(InstanceList, LabelVector[], double) - Constructor for class cc.mallet.types.ExpGain
ExpGain(InstanceList, Classification[], double) - Constructor for class cc.mallet.types.ExpGain
ExpGain.Factory - Class in cc.mallet.types
ExpGain.Factory(LabelVector[]) - Constructor for class cc.mallet.types.ExpGain.Factory
ExpGain.Factory(LabelVector[], double) - Constructor for class cc.mallet.types.ExpGain.Factory
exponentiate(double) - Method in class cc.mallet.grmm.types.AbstractFactor
exponentiate(double) - Method in class cc.mallet.grmm.types.CPT
exponentiate(double) - Method in interface cc.mallet.grmm.types.Factor
exponentiate(double) - Method in class cc.mallet.grmm.types.FactorGraph
exponentiate(double) - Method in class cc.mallet.grmm.types.LogTableFactor
exponentiate(double) - Method in class cc.mallet.grmm.types.TableFactor
extend(int[], int) - Static method in class cc.mallet.util.ArrayUtils
  Returns a new array containing all of a, with additional extra space added (zero initialized).
extend(double[], int) - Static method in class cc.mallet.util.ArrayUtils
  Returns a new array containing all of a, with additional extra space added (zero initialized).
extendedDotProduct(DenseVector) - Method in class cc.mallet.types.SparseVector
extendedDotProduct(SparseVector) - Method in class cc.mallet.types.SparseVector
extract(Object) - Method in class cc.mallet.extract.CRFExtractor
extract(Tokenization) - Method in class cc.mallet.extract.CRFExtractor
extract(InstanceList) - Method in class cc.mallet.extract.CRFExtractor
  Assumes Instance.source contains the Tokenization object.
extract(Iterator<Instance>) - Method in class cc.mallet.extract.CRFExtractor
extract(Object) - Method in interface cc.mallet.extract.Extractor
  Performs extraction given a raw object.
extract(Tokenization) - Method in interface cc.mallet.extract.Extractor
  Performs extraction from an object that has been already been tokenized.
extract(Iterator<Instance>) - Method in interface cc.mallet.extract.Extractor
  Performs extraction on a a set of raw documents.
extract(Object) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
extract(Tokenization) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
extract(Iterator<Instance>) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
extract(InstanceList) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
Extraction - Class in cc.mallet.extract
  The results of doing information extraction.
Extraction(Extractor, LabelAlphabet) - Constructor for class cc.mallet.extract.Extraction
  Creates an empty Extraction option.
Extraction(Extractor, LabelAlphabet, String, Tokenization, Sequence, String) - Constructor for class cc.mallet.extract.Extraction
  Creates an extration given a sequence output by some kind of per-sequece labeler, like an HMM or a CRF.
extraction2html(Extraction, CRFExtractor, PrintStream) - Static method in class cc.mallet.extract.LatticeViewer
extraction2html(Extraction, CRFExtractor, PrintWriter) - Static method in class cc.mallet.extract.LatticeViewer
extraction2html(Extraction, CRFExtractor, PrintStream, boolean) - Static method in class cc.mallet.extract.LatticeViewer
extraction2html(Extraction, CRFExtractor, PrintWriter, boolean) - Static method in class cc.mallet.extract.LatticeViewer
ExtractionConfidenceEstimator - Class in cc.mallet.extract
  Estimates the confidence in the labeling of a LabeledSpan.
ExtractionConfidenceEstimator() - Constructor for class cc.mallet.extract.ExtractionConfidenceEstimator
ExtractionEvaluator - Interface in cc.mallet.extract
  Created: Oct 8, 2004
extractMax(Variable[]) - Method in class cc.mallet.grmm.types.AbstractFactor
extractMax(Collection) - Method in class cc.mallet.grmm.types.AbstractFactor
extractMax(Variable) - Method in class cc.mallet.grmm.types.AbstractFactor
extractMax(Variable) - Method in class cc.mallet.grmm.types.AbstractTableFactor
extractMax(Variable[]) - Method in class cc.mallet.grmm.types.AbstractTableFactor
extractMax(Collection) - Method in class cc.mallet.grmm.types.AbstractTableFactor
extractMax(Collection) - Method in class cc.mallet.grmm.types.CPT
extractMax(Variable) - Method in class cc.mallet.grmm.types.CPT
extractMax(Variable[]) - Method in class cc.mallet.grmm.types.CPT
extractMax(Collection) - Method in interface cc.mallet.grmm.types.Factor
  Returns a potential phi over the given variables obtained by taking phi (x) = max_[all v that contain x] this.prob (x)
extractMax(Variable) - Method in interface cc.mallet.grmm.types.Factor
  Returns a potential phi over the given variables obtained by taking phi (x) = max_[all v that contain x] this.prob (x)
extractMax(Variable[]) - Method in interface cc.mallet.grmm.types.Factor
  Returns a potential phi over the given variables obtained by taking phi (x) = max_[all v that contain x] this.prob (x)
extractMax(Collection) - Method in class cc.mallet.grmm.types.FactorGraph
extractMax(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
extractMax(Variable[]) - Method in class cc.mallet.grmm.types.FactorGraph
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.AbstractFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.Assignment
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.BetaFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.ConstantFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.NormalFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.PottsTableFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.SkeletonFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.UniformFactor
extractMaxInternal(VarSet) - Method in class cc.mallet.grmm.types.UniNormalFactor
extractMin() - Method in class cc.mallet.util.search.MinHeap
extractMin() - Method in interface cc.mallet.util.search.PriorityQueue
  Remove the top element of the queue.
extractOnTestData(ACRFExtractor) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
Extractor - Interface in cc.mallet.extract
  Generic interface for objects that do information extraction.

## F

f(Object) - Method in interface cc.mallet.util.CollectionUtils.Fn
f1 - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
Factor - Interface in cc.mallet.grmm.types
  Interface for multivariate discrete probability distributions.
FactorGraph - Class in cc.mallet.grmm.types
  Class for undirected graphical models.
FactorGraph() - Constructor for class cc.mallet.grmm.types.FactorGraph
FactorGraph(Variable[]) - Constructor for class cc.mallet.grmm.types.FactorGraph
  Create a model with the variables given.
FactorGraph(Factor[]) - Constructor for class cc.mallet.grmm.types.FactorGraph
FactorGraph(Collection) - Constructor for class cc.mallet.grmm.types.FactorGraph
FactorGraph(int) - Constructor for class cc.mallet.grmm.types.FactorGraph
  Create a model with the given capacity (i.e., capacityin terms of number of variable nodes).
factorial(int) - Static method in class cc.mallet.util.Maths
FactorizedRegion - Class in cc.mallet.grmm.inference.gbp
  A more space-efficient Region class that doesn't maintain a global factor over all assignments to the region.
FactorizedRegion(List) - Constructor for class cc.mallet.grmm.inference.gbp.FactorizedRegion
factorOf(VarSet) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns the factor in this graph, if any, whose domain is a given clique.
factorOf(Variable, Variable) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns the factor defined over a given pair of variables.
factorOf(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns the factor for a given node.
factorOf(Collection) - Method in class cc.mallet.grmm.types.FactorGraph
  Searches the graphical model for a factor over the given collection of variables.
factorProduct(Assignment) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns the unnormalized probability for an assignment to the model.
factors - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
factors() - Method in class cc.mallet.grmm.types.FactorGraph
  Returns collection that contains factors in this model.
Factors - Class in cc.mallet.grmm.types
  A static utility class containing utility methods for dealing with factors, especially TableFactor objects.
Factors() - Constructor for class cc.mallet.grmm.types.Factors
factorsIterator() - Method in class cc.mallet.grmm.types.FactorGraph
  Returns an iterator of all the factors in the graph.
FALSE_NEGATIVE - Static variable in class cc.mallet.types.ROCData
FALSE_POSITIVE - Static variable in class cc.mallet.types.ROCData
FeatureConjunction - Class in cc.mallet.types
FeatureConjunction(String, Alphabet, int[], boolean[], boolean, boolean, boolean) - Constructor for class cc.mallet.types.FeatureConjunction
  If negations[i] is true, insist that the feature has non-zero value; if false, insist that it has zero value.
FeatureConjunction(String, Alphabet, int[], boolean[], boolean) - Constructor for class cc.mallet.types.FeatureConjunction
FeatureConjunction(String, Alphabet, int[], boolean[]) - Constructor for class cc.mallet.types.FeatureConjunction
FeatureConjunction(Alphabet, int[], boolean[]) - Constructor for class cc.mallet.types.FeatureConjunction
FeatureConjunction(Alphabet, int[]) - Constructor for class cc.mallet.types.FeatureConjunction
FeatureConjunction.List - Class in cc.mallet.types
FeatureConjunction.List() - Constructor for class cc.mallet.types.FeatureConjunction.List
FeatureConstraintUtil - Class in cc.mallet.classify
  Utility functions for creating feature constraints that can be used with GE training.
FeatureConstraintUtil() - Constructor for class cc.mallet.classify.FeatureConstraintUtil
FeatureCounter - Class in cc.mallet.types
  Efficient, compact, incremental counting of features in an alphabet.
FeatureCounter(Alphabet) - Constructor for class cc.mallet.types.FeatureCounter
FeatureCountPipe - Class in cc.mallet.pipe
  Pruning low-count features can be a good way to save memory and computation.
FeatureCountPipe() - Constructor for class cc.mallet.pipe.FeatureCountPipe
FeatureCountPipe(Alphabet, Alphabet) - Constructor for class cc.mallet.pipe.FeatureCountPipe
FeatureCounts - Class in cc.mallet.types
FeatureCounts(InstanceList) - Constructor for class cc.mallet.types.FeatureCounts
FeatureCounts(Alphabet, double[]) - Constructor for class cc.mallet.types.FeatureCounts
FeatureCounts.Factory - Class in cc.mallet.types
FeatureCounts.Factory() - Constructor for class cc.mallet.types.FeatureCounts.Factory
FeatureInducer - Class in cc.mallet.types
FeatureInducer(RankedFeatureVector.Factory, InstanceList, int, int, int) - Constructor for class cc.mallet.types.FeatureInducer
FeatureInducer(RankedFeatureVector.Factory, InstanceList, int) - Constructor for class cc.mallet.types.FeatureInducer
featureInducers - Variable in class cc.mallet.fst.CRF
featurePipe - Variable in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
FeatureSelectingClassifierTrainer - Class in cc.mallet.classify
  Adaptor for adding feature selection to a classifier trainer.
FeatureSelectingClassifierTrainer(ClassifierTrainer, FeatureSelector) - Constructor for class cc.mallet.classify.FeatureSelectingClassifierTrainer
featureSelection - Variable in class cc.mallet.classify.MaxEnt
featureSelection - Static variable in class cc.mallet.classify.tui.Vectors2FeatureConstraints
FeatureSelection - Class in cc.mallet.types
FeatureSelection(Alphabet, BitSet) - Constructor for class cc.mallet.types.FeatureSelection
FeatureSelection(Alphabet) - Constructor for class cc.mallet.types.FeatureSelection
FeatureSelection(RankedFeatureVector, int) - Constructor for class cc.mallet.types.FeatureSelection
featureSelections - Variable in class cc.mallet.fst.CRF
FeatureSelector - Class in cc.mallet.types
FeatureSelector(RankedFeatureVector.Factory, int) - Constructor for class cc.mallet.types.FeatureSelector
FeatureSelector(RankedFeatureVector.Factory, double) - Constructor for class cc.mallet.types.FeatureSelector
FeatureSelector(RankedFeatureVector.PerLabelFactory, int) - Constructor for class cc.mallet.types.FeatureSelector
FeatureSelector(RankedFeatureVector.PerLabelFactory, double) - Constructor for class cc.mallet.types.FeatureSelector
FeatureSequence - Class in cc.mallet.types
  An implementation of `Sequence` that ensures that every Object in the sequence has the same class.
FeatureSequence(Alphabet, int[]) - Constructor for class cc.mallet.types.FeatureSequence
  Creates a FeatureSequence given all of the objects in the sequence.
FeatureSequence(Alphabet, int[], int) - Constructor for class cc.mallet.types.FeatureSequence
FeatureSequence(Alphabet, int) - Constructor for class cc.mallet.types.FeatureSequence
FeatureSequence(Alphabet) - Constructor for class cc.mallet.types.FeatureSequence
FeatureSequence2AugmentableFeatureVector - Class in cc.mallet.pipe
  Convert the data field from a feature sequence to an augmentable feature vector.
FeatureSequence2AugmentableFeatureVector(boolean) - Constructor for class cc.mallet.pipe.FeatureSequence2AugmentableFeatureVector
FeatureSequence2AugmentableFeatureVector() - Constructor for class cc.mallet.pipe.FeatureSequence2AugmentableFeatureVector
FeatureSequence2FeatureVector - Class in cc.mallet.pipe
  Convert the data field from a feature sequence to a feature vector.
FeatureSequence2FeatureVector(boolean) - Constructor for class cc.mallet.pipe.FeatureSequence2FeatureVector
FeatureSequence2FeatureVector() - Constructor for class cc.mallet.pipe.FeatureSequence2FeatureVector
FeatureSequenceConvolution - Class in cc.mallet.pipe
FeatureSequenceConvolution() - Constructor for class cc.mallet.pipe.FeatureSequenceConvolution
FeatureSequenceWithBigrams - Class in cc.mallet.types
  A FeatureSequence with a parallel record of bigrams, kept in a separate dictionary
FeatureSequenceWithBigrams(Alphabet, Alphabet, TokenSequence) - Constructor for class cc.mallet.types.FeatureSequenceWithBigrams
featuresFile - Static variable in class cc.mallet.classify.tui.Vectors2FeatureConstraints
FeaturesInWindow - Class in cc.mallet.pipe.tsf
FeaturesInWindow(String, int, int, Pattern, boolean) - Constructor for class cc.mallet.pipe.tsf.FeaturesInWindow
FeaturesInWindow(String, int, int) - Constructor for class cc.mallet.pipe.tsf.FeaturesInWindow
  equivalent to
  `FeaturesInWindow((namePrefix, leftBoundaryOffset, rightBoundaryOffset, null, true);`
FeaturesOfFirstMention - Class in cc.mallet.pipe.tsf
FeaturesOfFirstMention(String, String, Pattern) - Constructor for class cc.mallet.pipe.tsf.FeaturesOfFirstMention
FeaturesOfFirstMention(String, Pattern, Pattern, boolean) - Constructor for class cc.mallet.pipe.tsf.FeaturesOfFirstMention
FeaturesOfFirstMention(String, Pattern) - Constructor for class cc.mallet.pipe.tsf.FeaturesOfFirstMention
FeaturesOfFirstMention(String) - Constructor for class cc.mallet.pipe.tsf.FeaturesOfFirstMention
featuresOverlap(Alphabet, int, int) - Static method in class cc.mallet.types.FeatureConjunction
FeatureTransducer - Class in cc.mallet.fst
FeatureTransducer(Alphabet, Alphabet) - Constructor for class cc.mallet.fst.FeatureTransducer
FeatureTransducer(Alphabet) - Constructor for class cc.mallet.fst.FeatureTransducer
FeatureTransducer() - Constructor for class cc.mallet.fst.FeatureTransducer
FeatureTransducer.State - Class in cc.mallet.fst
FeatureTransducer.State(String, int, double, double, int[], int[], double[], String[], FeatureTransducer) - Constructor for class cc.mallet.fst.FeatureTransducer.State
FeatureTransducer.Transition - Class in cc.mallet.fst
FeatureTransducer.Transition(int, int, double, FeatureTransducer.State, String) - Constructor for class cc.mallet.fst.FeatureTransducer.Transition
FeatureTransducer.TransitionIterator - Class in cc.mallet.fst
FeatureTransducer.TransitionIterator(FeatureTransducer.State) - Constructor for class cc.mallet.fst.FeatureTransducer.TransitionIterator
FeatureTransducer.TransitionIterator(FeatureTransducer.State, int) - Constructor for class cc.mallet.fst.FeatureTransducer.TransitionIterator
FeatureValueString2FeatureVector - Class in cc.mallet.pipe
FeatureValueString2FeatureVector(Alphabet) - Constructor for class cc.mallet.pipe.FeatureValueString2FeatureVector
FeatureValueString2FeatureVector() - Constructor for class cc.mallet.pipe.FeatureValueString2FeatureVector
FeatureVector - Class in cc.mallet.types
  A subset of an `Alphabet` in which each element of the subset has an associated value.
FeatureVector(Alphabet, int[], double[], int, int, boolean, boolean, boolean) - Constructor for class cc.mallet.types.FeatureVector
FeatureVector(Alphabet, double[]) - Constructor for class cc.mallet.types.FeatureVector
  Create a dense vector
FeatureVector(Alphabet, int[], double[]) - Constructor for class cc.mallet.types.FeatureVector
  Create non-binary vector, possibly dense if "featureIndices" or possibly sparse, if not
FeatureVector(Alphabet, int[]) - Constructor for class cc.mallet.types.FeatureVector
  Create binary vector
FeatureVector(Alphabet, Object[], double[]) - Constructor for class cc.mallet.types.FeatureVector
FeatureVector(FeatureSequence, boolean) - Constructor for class cc.mallet.types.FeatureVector
FeatureVector(FeatureSequence) - Constructor for class cc.mallet.types.FeatureVector
FeatureVector(Alphabet, PropertyList, boolean, boolean) - Constructor for class cc.mallet.types.FeatureVector
FeatureVector(Alphabet, PropertyList, boolean) - Constructor for class cc.mallet.types.FeatureVector
FeatureVector(FeatureVector, Alphabet, int[]) - Constructor for class cc.mallet.types.FeatureVector
  New feature vector containing all the features of "fv", plus new features created by making conjunctions between the features in "conjunctions" and all the other features.
FeatureVector(FeatureVector, Alphabet, FeatureSelection, FeatureSelection) - Constructor for class cc.mallet.types.FeatureVector
FeatureVectorConjunctions - Class in cc.mallet.pipe
  Include in the FeatureVector conjunctions of all its features.
FeatureVectorConjunctions() - Constructor for class cc.mallet.pipe.FeatureVectorConjunctions
FeatureVectorSequence - Class in cc.mallet.types
FeatureVectorSequence(FeatureVector[]) - Constructor for class cc.mallet.types.FeatureVectorSequence
FeatureVectorSequence(Alphabet, TokenSequence, boolean, boolean, boolean) - Constructor for class cc.mallet.types.FeatureVectorSequence
FeatureVectorSequence(Alphabet, TokenSequence, boolean, boolean) - Constructor for class cc.mallet.types.FeatureVectorSequence
FeatureVectorSequence(Alphabet, TokenSequence) - Constructor for class cc.mallet.types.FeatureVectorSequence
FeatureVectorSequence.Iterator - Class in cc.mallet.types
  An iterator over the FeatureVectors in the sequence.
FeatureVectorSequence.Iterator() - Constructor for class cc.mallet.types.FeatureVectorSequence.Iterator
FeatureVectorSequence2FeatureVectors - Class in cc.mallet.pipe
  Given instances with a FeatureVectorSequence in the data field, break up the sequence into the individual FeatureVectors, producing one FeatureVector per Instance.
FeatureVectorSequence2FeatureVectors() - Constructor for class cc.mallet.pipe.FeatureVectorSequence2FeatureVectors
FeatureWindow - Class in cc.mallet.share.upenn.ner
  Adds all features of tokens in the window to the center token.
FeatureWindow(int, int) - Constructor for class cc.mallet.share.upenn.ner.FeatureWindow
Field - Class in cc.mallet.extract
  Created: Oct 12, 2004
Field(LabeledSpan) - Constructor for class cc.mallet.extract.Field
fieldAlphabet() - Method in class cc.mallet.cluster.Record
FieldCleaner - Interface in cc.mallet.extract
  Interface for functions that are used to clean up field values after extraction has been performed.
FieldComparator - Interface in cc.mallet.extract
  Interface for functions that compares extracted values of a field to see if they match.
fields() - Method in class cc.mallet.cluster.Record
fieldsIterator() - Method in class cc.mallet.extract.Record
FileIterator - Class in cc.mallet.pipe.iterator
  An iterator that generates instances from an initial directory or set of directories.
FileIterator(File[], FileFilter, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileIterator
  Construct a FileIterator that will supply filenames within initial directories as instances
FileIterator(File[], FileFilter, Pattern) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(File[], Pattern) - Constructor for class cc.mallet.pipe.iterator.FileIterator
  Iterate over Files that pass the fileFilter test, setting...
FileIterator(File[], Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(String[], FileFilter) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(String[], String) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(String[], Pattern) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(String[], Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(File, FileFilter, Pattern) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(File, FileFilter, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(File, FileFilter) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(File, Pattern) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(File, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(String, Pattern) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(String, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(File) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(String) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileIterator(String, FileFilter) - Constructor for class cc.mallet.pipe.iterator.FileIterator
FileListIterator - Class in cc.mallet.pipe.iterator
  An iterator that generates instances for a pipe from a list of filenames.
FileListIterator(File[], FileFilter, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileListIterator
  Construct an iterator over the given arry of Files The instances constructed from the files are returned in the same order as they appear in the given array
FileListIterator(String[], FileFilter, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileListIterator
FileListIterator(File, FileFilter, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileListIterator
  Construct a FileListIterator with the file containing the list of files, which contains one filename per line.
FileListIterator(File, File, FileFilter, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileListIterator
  Construct a FileListIterator with the file containing the list of files of RELATIVE pathnames, one filename per line.
FileListIterator(String, FileFilter, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.FileListIterator
FileListIterator(String, Pattern) - Constructor for class cc.mallet.pipe.iterator.FileListIterator
Filename2CharSequence - Class in cc.mallet.pipe
  Given a filename contained in a string, read in contents of file into a CharSequence.
Filename2CharSequence() - Constructor for class cc.mallet.pipe.Filename2CharSequence
filenameToUriString(String) - Static method in class cc.mallet.util.UriUtils
FileUriIterator - Class in cc.mallet.pipe.iterator
FileUriIterator(File[], FileFilter, Pattern) - Constructor for class cc.mallet.pipe.iterator.FileUriIterator
FileUriIterator(File, FileFilter, Pattern) - Constructor for class cc.mallet.pipe.iterator.FileUriIterator
FileUriIterator(File[], Pattern) - Constructor for class cc.mallet.pipe.iterator.FileUriIterator
FileUriIterator(File, Pattern) - Constructor for class cc.mallet.pipe.iterator.FileUriIterator
FileUtils - Class in cc.mallet.util
  Contains static utilities for manipulating files.
FilterEmptyFeatureVectors - Class in cc.mallet.pipe
FilterEmptyFeatureVectors() - Constructor for class cc.mallet.pipe.FilterEmptyFeatureVectors
finalWeights - Variable in class cc.mallet.fst.CRF.Factors
findCluster(Variable[]) - Method in class cc.mallet.grmm.inference.JunctionTree
  Returns a cluster in the tree that contains exactly the given variables, or null if no such cluster exists.
findParentCluster(Variable) - Method in class cc.mallet.grmm.inference.JunctionTree
  Returns a cluster in the tree that contains var.
findParentCluster(Collection) - Method in class cc.mallet.grmm.inference.JunctionTree
  Returns a cluster in the tree that contains all the vars in a collection.
findVariable(String) - Method in class cc.mallet.grmm.types.AbstractTableFactor
findVariable(String) - Method in class cc.mallet.grmm.types.FactorGraph
  Searches this model for a variable with a given name.
finishedTraining - Variable in class cc.mallet.classify.ClassifierTrainer
FIRST_DIRECTORY - Static variable in class cc.mallet.pipe.iterator.FileIterator
  Use as label names the first directory in the filename.
FIRST_DIRECTORY - Static variable in class cc.mallet.pipe.iterator.FileListIterator
  Use as label names the first directory in the filename.
FIRST_DIRECTORY - Static variable in class cc.mallet.pipe.iterator.UnlabeledFileIterator
  Use as label names the first directory in the filename.
FirstOrderClusterExample - Class in cc.mallet.cluster.examples
  Illustrates use of a supervised clustering method that uses features over clusters.
FirstOrderClusterExample() - Constructor for class cc.mallet.cluster.examples.FirstOrderClusterExample
five - Variable in class cc.mallet.util.Univariate
Flops - Class in cc.mallet.grmm.util
  Utilities for flop (floating-point operation) counting.
Flops() - Constructor for class cc.mallet.grmm.util.Flops
Flops.Watch - Class in cc.mallet.grmm.util
Flops.Watch() - Constructor for class cc.mallet.grmm.util.Flops.Watch
forceStale() - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
forEach(TObjectProcedure, Object[]) - Static method in class cc.mallet.util.ArrayUtils
forEach(TObjectProcedure, Object[][]) - Static method in class cc.mallet.util.ArrayUtils
format(LogRecord) - Method in class cc.mallet.util.PlainLogFormatter
format(LogRecord) - Method in class cc.mallet.util.ProgressMessageLogFormatter
formatString() - Method in class cc.mallet.types.StringEditVector
formatter - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
formatter - Variable in class cc.mallet.topics.NPTopicModel
formatter - Variable in class cc.mallet.topics.ParallelTopicModel
formatter - Variable in class cc.mallet.topics.PolylingualTopicModel
formatter - Variable in class cc.mallet.topics.SimpleLDA
forwardLattice(double[][], double[][][]) - Method in class cc.mallet.fst.semi_supervised.EntropyLattice
  Computes the forward entropies (H^alpha).
freezeWeights(int) - Method in class cc.mallet.fst.CRF
  Freezes a set of weights to their current values.
freezeWeights(String) - Method in class cc.mallet.fst.CRF
  Freezes a set of weights to their current values.
from() - Method in class cc.mallet.grmm.inference.MessageArray.Iterator
FullMessageStrategy - Class in cc.mallet.grmm.inference.gbp
  A first implementation of MessageStrategy that assumes that a BP region graph is being used.
FullMessageStrategy() - Constructor for class cc.mallet.grmm.inference.gbp.FullMessageStrategy

## G

GainRatio - Class in cc.mallet.types
  List of features along with their thresholds sorted in descending order of the ratio of (1) information gained by splitting instances on the feature at its associated threshold value, to (2) the split information.
GainRatio(Alphabet, double[], double[], double, LabelVector, int, int) - Constructor for class cc.mallet.types.GainRatio
gamma - Static variable in class cc.mallet.classify.tests.TestStaticParameters.Factory
gamma - Variable in class cc.mallet.topics.NPTopicModel
gamma(double) - Static method in class cc.mallet.util.Maths
GammaAverageConfidenceEstimator - Class in cc.mallet.fst.confidence
  Calculates the confidence in an extracted segment by taking the average of P(s_i|o) for each state in the segment.
GammaAverageConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.GammaAverageConfidenceEstimator
GammaProductConfidenceEstimator - Class in cc.mallet.fst.confidence
  Calculates the confidence in an extracted segment by taking the product of eP(s_i|o) for each state in the segment.
GammaProductConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.GammaProductConfidenceEstimator
gatherConstraints(InstanceList) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
  Set the constraints by running forward-backward with the output label sequence provided, thus restricting it to only those paths that agree with the label sequence.
gatherConstraints(InstanceList) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
gatherExpectationsOrConstraints(boolean) - Method in class cc.mallet.fst.MEMMTrainer.MEMMOptimizableByLabelLikelihood
gaussianPrior(double) - Method in class cc.mallet.fst.CRF.Factors
  Return the log(p(parameters)) according to a zero-mean Gaussian with given variance.
geCriteria - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
GECriteria - Class in cc.mallet.fst.semi_supervised
  Represents GE criteria specified in the form of feature-label associations.
GECriteria(int, StateLabelMap, Map<Integer, GECriterion>) - Constructor for class cc.mallet.fst.semi_supervised.GECriteria
  Initializes the feature-label association constraints.
GECriterion - Class in cc.mallet.fst.semi_supervised
GECriterion(String, double[], double) - Constructor for class cc.mallet.fst.semi_supervised.GECriterion
GEKLCriteria - Class in cc.mallet.fst.semi_supervised
GEKLCriteria(int, StateLabelMap, Map<Integer, GECriterion>) - Constructor for class cc.mallet.fst.semi_supervised.GEKLCriteria
GEKLCriterion - Class in cc.mallet.fst.semi_supervised
GEKLCriterion(String, double[], double) - Constructor for class cc.mallet.fst.semi_supervised.GEKLCriterion
GEL2Criteria - Class in cc.mallet.fst.semi_supervised
GEL2Criteria(int, StateLabelMap, Map<Integer, GECriterion>) - Constructor for class cc.mallet.fst.semi_supervised.GEL2Criteria
GEL2Criterion - Class in cc.mallet.fst.semi_supervised
GEL2Criterion(String, double[], double) - Constructor for class cc.mallet.fst.semi_supervised.GEL2Criterion
GELattice - Class in cc.mallet.fst.semi_supervised
  Runs the dynamic programming algorithm of [Mann and McCallum 08] for computing the gradient of a Generalized Expectation constraint that considers a single label of a linear chain CRF.
GELattice(FeatureVectorSequence, double[][], double[][][], Transducer, Transducer.Incrementor, GECriteria, boolean) - Constructor for class cc.mallet.fst.semi_supervised.GELattice
GELattice.LatticeNode - Class in cc.mallet.fst.semi_supervised
  Contains forward-backward vectors correspoding to an input position and a state index.
GELattice.LatticeNode() - Constructor for class cc.mallet.fst.semi_supervised.GELattice.LatticeNode
geLatticeExecutor - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
GeneralUtils - Class in cc.mallet.grmm.util
  Static utility methods that didn't seem to belong anywhere else.
generateAttractivePotentialValues(Random, double) - Static method in class cc.mallet.grmm.inference.RandomGraphs
generateMixedPotentialValues(Random, double) - Static method in class cc.mallet.grmm.inference.RandomGraphs
generatePath() - Method in class cc.mallet.fst.Transducer
generateStoplist(SimpleTokenizer) - Static method in class cc.mallet.util.BulkLoader
  Read the data from inputFile, then write all the words that do not occur `pruneCount.value` times or more to the pruned word file.
GenericAcrfData2TokenSequence - Class in cc.mallet.grmm.learning
  Generic pipe that takes a linegroup of the form:
GenericAcrfData2TokenSequence() - Constructor for class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
GenericAcrfData2TokenSequence(int) - Constructor for class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
GenericAcrfTui - Class in cc.mallet.grmm.learning
GenericAcrfTui() - Constructor for class cc.mallet.grmm.learning.GenericAcrfTui
get(int) - Method in class cc.mallet.cluster.Clusterings
get(int, int) - Method in class cc.mallet.cluster.util.PairwiseMatrix
get(Object, Object) - Method in class cc.mallet.grmm.inference.MessageArray
get(Variable, Factor) - Method in class cc.mallet.grmm.inference.MessageArray
get(Factor, Variable) - Method in class cc.mallet.grmm.inference.MessageArray
get(int) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
get(Variable) - Method in class cc.mallet.grmm.types.Assignment
get(int, Variable) - Method in class cc.mallet.grmm.types.Assignment
  Returns the value of var in this assigment.
get(int) - Method in class cc.mallet.grmm.types.BitVarSet
get(int) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns a variable from this model with a given index.
get(int) - Method in class cc.mallet.grmm.types.HashVarSet
get(int) - Method in class cc.mallet.grmm.types.ListVarSet
get(int, int) - Method in class cc.mallet.grmm.types.UndirectedGrid
get(int) - Method in class cc.mallet.grmm.types.Universe
get(int) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
get(int) - Method in interface cc.mallet.grmm.types.VarSet
  Returns the variable in this clique at index idx.
get(int, int) - Method in class cc.mallet.grmm.util.CSIntInt2ObjectMultiMap
get(int, int) - Method in class cc.mallet.grmm.util.MIntInt2ObjectMap
get(Object) - Method in class cc.mallet.grmm.util.THashMultiMap
get(int) - Method in class cc.mallet.types.ArraySequence
get(int) - Method in class cc.mallet.types.FeatureConjunction.List
get(int) - Method in class cc.mallet.types.FeatureCounter
get(Object) - Method in class cc.mallet.types.FeatureCounter
  Unlike increment(Object), this method does not add the entry to the Alphabet if it is not there already.
get(int) - Method in class cc.mallet.types.FeatureSequence
get(int) - Method in class cc.mallet.types.FeatureVectorSequence
get(int) - Method in class cc.mallet.types.Labels
get(int) - Method in class cc.mallet.types.LabelsSequence
get(int) - Method in class cc.mallet.types.MultiInstanceList
get(int) - Method in class cc.mallet.types.PagedInstanceList
  Returns the `Instance` at the specified index.
get(int) - Method in interface cc.mallet.types.Sequence
get(int) - Method in class cc.mallet.util.DoubleList
getAccuracy(InstanceList) - Method in class cc.mallet.classify.Classifier
getAccuracy() - Method in class cc.mallet.classify.Trial
  Return the fraction of instances that have the correct label as their best predicted label.
getAccuracy(String) - Method in class cc.mallet.fst.InstanceAccuracyEvaluator
getAccuracy(String) - Method in class cc.mallet.fst.TokenAccuracyEvaluator
  Returns the accuracy from the last time test() or evaluate() was called
getAccuracyCoverageValues() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
  get accuracy at coverage for each bin of values
getAccuracyRecallValues(int) - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
  get accuracy at recall for each bin of values
getAcrf() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
getAdjacentVertices(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns all variables that are adjacent to a given variable in this graph---that is, the set of all variables that share a factor with this one.
getAlpha(int, Transducer.State) - Method in interface cc.mallet.fst.SumLattice
getAlpha(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeBeam
getAlpha(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeDefault
getAlpha(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeScaling
getAlphabet() - Method in class cc.mallet.classify.Classifier
getAlphabet() - Method in class cc.mallet.classify.NaiveBayesTrainer
getAlphabet() - Method in class cc.mallet.pipe.iterator.RandomFeatureVectorIterator
getAlphabet() - Method in class cc.mallet.pipe.iterator.RandomTokenSequenceIterator
getAlphabet() - Method in class cc.mallet.pipe.Pipe
getAlphabet() - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
getAlphabet() - Method in class cc.mallet.topics.ParallelTopicModel
getAlphabet() - Method in class cc.mallet.topics.SimpleLDA
getAlphabet() - Method in interface cc.mallet.types.AlphabetCarrying
getAlphabet() - Method in class cc.mallet.types.Dirichlet
getAlphabet() - Method in class cc.mallet.types.FeatureSelection
getAlphabet() - Method in class cc.mallet.types.FeatureSequence
getAlphabet() - Method in class cc.mallet.types.FeatureVector
getAlphabet() - Method in class cc.mallet.types.FeatureVectorSequence
getAlphabet() - Method in class cc.mallet.types.Instance
getAlphabet() - Method in class cc.mallet.types.InstanceList
getAlphabet() - Method in class cc.mallet.types.Label
getAlphabet() - Method in class cc.mallet.types.Labelings
getAlphabet() - Method in class cc.mallet.types.Labels
getAlphabet() - Method in class cc.mallet.types.LabelsSequence
getAlphabet() - Method in class cc.mallet.types.Multinomial
getAlphabet() - Method in class cc.mallet.types.ROCData
getAlphabets() - Method in class cc.mallet.classify.Classifier
getAlphabets() - Method in class cc.mallet.classify.NaiveBayesTrainer
getAlphabets() - Method in class cc.mallet.pipe.Pipe
getAlphabets() - Method in interface cc.mallet.types.AlphabetCarrying
getAlphabets() - Method in class cc.mallet.types.FeatureSelection
getAlphabets() - Method in class cc.mallet.types.FeatureSequence
getAlphabets() - Method in class cc.mallet.types.FeatureVector
getAlphabets() - Method in class cc.mallet.types.FeatureVectorSequence
getAlphabets() - Method in class cc.mallet.types.Instance
getAlphabets() - Method in class cc.mallet.types.InstanceList
getAlphabets() - Method in class cc.mallet.types.Label
getAlphabets() - Method in class cc.mallet.types.Labelings
getAlphabets() - Method in class cc.mallet.types.Labels
getAlphabets() - Method in class cc.mallet.types.LabelsSequence
getAlphabets() - Method in class cc.mallet.types.ROCData
getAssignment() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
  Returns an Assignment object that corresponds to the LabelSequence for which this graph was unrolled.
getAssignmentsPresent() - Method in class cc.mallet.grmm.learning.ACRF.Template
getAverageAccuracy() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
getAverageCorrectConfidence() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
  Average confidence score for the incorrect entities
getAverageIncorrectConfidence() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
  Average confidence score for the incorrect entities
getAveragePrecision() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
  IR Average precision measure.
getAverageRank(InstanceList) - Method in class cc.mallet.classify.Classifier
getAverageRank() - Method in class cc.mallet.classify.Trial
  Return the average rank of the correct class label as returned by Labeling.getRank(correctLabel) on the predicted Labeling.
getBackgroundTag() - Method in class cc.mallet.extract.CRFExtractor
getBackgroundTag() - Method in class cc.mallet.extract.DocumentExtraction
getBaseEntropy() - Method in class cc.mallet.types.GainRatio
getBaseEntropy() - Method in class cc.mallet.types.InfoGain
getBaseLabelDistribution() - Method in class cc.mallet.types.GainRatio
getBaseLabelDistribution() - Method in class cc.mallet.types.InfoGain
getBatchValue(int, int[]) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
  Returns the log probability of a batch of training sequence labels and the prior over parameters, if last batch then incorporate the prior on parameters as well.
getBatchValue(int, int[]) - Method in interface cc.mallet.optimize.Optimizable.ByBatchGradient
getBatchValue(int, int[]) - Method in interface cc.mallet.optimize.Optimizable.ByCombiningBatchGradient
getBatchValueGradient(double[], int, int[]) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
getBatchValueGradient(double[], int, int[]) - Method in interface cc.mallet.optimize.Optimizable.ByBatchGradient
getBatchValueGradient(double[], int, int[]) - Method in interface cc.mallet.optimize.Optimizable.ByCombiningBatchGradient
getBeamWidth() - Method in class cc.mallet.fst.SumLatticeBeam
getBestIndex() - Method in class cc.mallet.types.Label
getBestIndex() - Method in interface cc.mallet.types.Labeling
getBestIndex() - Method in class cc.mallet.types.LabelVector
getBestLabel() - Method in class cc.mallet.types.Label
getBestLabel() - Method in interface cc.mallet.types.Labeling
getBestLabel() - Method in class cc.mallet.types.LabelVector
getBestLabels(InstanceList) - Method in class cc.mallet.grmm.learning.ACRF
getBestLabels(Instance) - Method in class cc.mallet.grmm.learning.ACRF
getBestValue() - Method in class cc.mallet.types.Label
getBestValue() - Method in interface cc.mallet.types.Labeling
getBestValue() - Method in class cc.mallet.types.LabelVector
getBeta(int, Transducer.State) - Method in interface cc.mallet.fst.SumLattice
getBeta(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeBeam
getBeta(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeDefault
getBeta(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeScaling
getBiAlphabet() - Method in class cc.mallet.types.FeatureSequenceWithBigrams
getBigramAlphabet() - Method in class cc.mallet.pipe.TokenSequence2FeatureSequenceWithBigrams
getBiIndexAtPosition(int) - Method in class cc.mallet.types.FeatureSequenceWithBigrams
getBitSet() - Method in class cc.mallet.types.FeatureSelection
getCharSequence() - Method in class cc.mallet.util.CharSequenceLexer
getChild() - Method in class cc.mallet.grmm.types.CPT
getChildren(Object) - Method in class cc.mallet.grmm.types.Tree
getClassificationScores(Instance, double[]) - Method in class cc.mallet.classify.MaxEnt
getClassificationScores(Instance, double[]) - Method in class cc.mallet.classify.MCMaxEnt
getClassificationScores(Instance, double[]) - Method in class cc.mallet.classify.RankMaxEnt
getClassificationScoresForTies(Instance, double[], int[]) - Method in class cc.mallet.classify.RankMaxEnt
  Used by RankMaxEntTrainer to calculate the value when the labeling contains ties.
getClassificationScoresWithTemperature(Instance, double, double[]) - Method in class cc.mallet.classify.MaxEnt
getClassifier() - Method in class cc.mallet.classify.AdaBoostM2Trainer
getClassifier() - Method in class cc.mallet.classify.AdaBoostTrainer
getClassifier() - Method in class cc.mallet.classify.BaggingTrainer
getClassifier() - Method in class cc.mallet.classify.BalancedWinnowTrainer
getClassifier() - Method in class cc.mallet.classify.C45Trainer
getClassifier() - Method in class cc.mallet.classify.Classification
getClassifier() - Method in class cc.mallet.classify.ClassifierEnsembleTrainer
getClassifier() - Method in class cc.mallet.classify.ClassifierTrainer
getClassifier() - Method in class cc.mallet.classify.ConfidencePredictingClassifierTrainer
getClassifier() - Method in class cc.mallet.classify.DecisionTreeTrainer
getClassifier() - Method in class cc.mallet.classify.FeatureSelectingClassifierTrainer
getClassifier() - Method in class cc.mallet.classify.MaxEntGETrainer
getClassifier() - Method in class cc.mallet.classify.MaxEntOptimizableByGE
getClassifier() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
getClassifier() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
getClassifier() - Method in class cc.mallet.classify.MaxEntTrainer
getClassifier() - Method in class cc.mallet.classify.MCMaxEntTrainer
getClassifier() - Method in class cc.mallet.classify.NaiveBayesEMTrainer
getClassifier() - Method in class cc.mallet.classify.NaiveBayesTrainer
getClassifier() - Method in class cc.mallet.classify.Trial
getClassifier() - Method in class cc.mallet.classify.WinnowTrainer
getClassifier() - Method in class cc.mallet.cluster.neighbor_evaluator.ClassifyingNeighborEvaluator
getClassifier() - Method in class cc.mallet.fst.confidence.MaxEntSequenceConfidenceEstimator
getClassifier() - Method in class cc.mallet.topics.DMROptimizable
getClassPrior(int) - Method in class cc.mallet.classify.evaluate.ConfusionMatrix
  Returns the percentage of instances with true label = classIndex
getCluster(int) - Method in class cc.mallet.cluster.Clustering
  Return an list of instances with a particular label.
getClustering() - Method in class cc.mallet.cluster.iterator.NeighborIterator
getClusterMeans() - Method in class cc.mallet.cluster.KMeans
  Return the ArrayList of cluster means after a run of the algorithm.
getClusters() - Method in class cc.mallet.cluster.Clustering
  Returns an array of instance lists corresponding to clusters.
getCollectGarbage() - Method in class cc.mallet.types.PagedInstanceList
getColumnInt(Variable) - Method in class cc.mallet.grmm.types.Assignment
getCombinedInstances(Clustering, int, int) - Static method in class cc.mallet.cluster.util.ClusterUtils
getCommandOption(int) - Method in class cc.mallet.util.CommandOption.List
getCommandOptionList() - Static method in class cc.mallet.classify.MCMaxEntTrainer
getCommandOptionList() - Method in interface cc.mallet.util.CommandOption.ListProviding
getComparator() - Method in class cc.mallet.extract.AccuracyCoverageEvaluator
getComparator() - Method in class cc.mallet.extract.PerDocumentF1Evaluator
getComparator() - Method in class cc.mallet.extract.PerFieldF1Evaluator
getConfidence() - Method in class cc.mallet.extract.LabeledSpan
getConfidence() - Method in class cc.mallet.fst.confidence.InstanceWithConfidence
getConfidence() - Method in class cc.mallet.fst.confidence.PipedInstanceWithConfidence
getConfidence() - Method in class cc.mallet.fst.Segment
getConfidenceMean() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
getConfidenceStandardDeviation() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
  Standard deviation of confidence scores
getConfidenceSum() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
getConfusionBetween(int, int) - Method in class cc.mallet.classify.evaluate.ConfusionMatrix
  Returns percent of time that class2 is true class when class1 is predicted class
getConstraint(int) - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Returns the `FeatureInfo` object mapped to the feature index.
getConstraintBits() - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Returns bits for all instances, each set if instance has at least one feature constraint.
getConstraintBitsForInstance(FeatureVectorSequence) - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Returns bits for an instance, each bit corresponds to a feature index and is set if the feature is present in the instance.
getConstraints(int) - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
getCost() - Method in class cc.mallet.util.search.SearchNode
  Get the cost for this node.
getCount() - Method in class cc.mallet.fst.semi_supervised.GECriterion
  Returns the count of the feature.
getCount(int) - Method in class cc.mallet.types.Multinomial.Estimator
getCountFeatureTopic(int, int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
getCounts(Label) - Method in class cc.mallet.types.ROCData
  Gets the raw counts for a specified label.
getCounts(Label, double) - Method in class cc.mallet.types.ROCData
  Gets the raw counts for a specified label and threshold.
getCountTokensPerTopic(int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
getCountWithFeature(int) - Method in class cc.mallet.types.InvertedIndex
getCountWithFeature(Object) - Method in class cc.mallet.types.InvertedIndex
getCPF(VarSet) - Method in class cc.mallet.grmm.inference.JunctionTree
getCptofVar(Variable) - Method in class cc.mallet.grmm.types.DirectedModel
  Returns the conditional distribution `P ( node | Parents (node) )`
getCrf() - Method in class cc.mallet.extract.CRFExtractor
getCRF() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getCRF() - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
getCRF() - Method in class cc.mallet.fst.CRFTrainerByValueGradients
getData() - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
getData() - Method in class cc.mallet.topics.ParallelTopicModel
getData() - Method in class cc.mallet.topics.PolylingualTopicModel
getData() - Method in class cc.mallet.topics.SimpleLDA
getData() - Method in class cc.mallet.types.Instance
getData() - Method in class cc.mallet.util.Univariate
getDataAlphabet() - Method in class cc.mallet.pipe.AddClassifierTokenPredictions
getDataAlphabet() - Method in class cc.mallet.pipe.Pipe
getDataAlphabet() - Method in class cc.mallet.types.Instance
getDataAlphabet() - Method in class cc.mallet.types.InstanceList
  Returns the `Alphabet` mapping features of the data to integers.
getDataClass() - Method in class cc.mallet.types.InstanceList
  Returns the Java Class 'data' field of Instances in this list.
getDefaultFeatureIndex() - Method in class cc.mallet.classify.MaxEnt
getDefaultFeatureIndex() - Method in class cc.mallet.grmm.learning.ACRF
getDefaultWeight(int) - Method in class cc.mallet.grmm.learning.ACRF.Template
getDefaultWeights() - Method in class cc.mallet.fst.CRF
getDefaultWeights() - Method in class cc.mallet.grmm.learning.ACRF.FixedFactorTemplate
getDefaultWeights() - Method in class cc.mallet.grmm.learning.ACRF.Template
getDegree(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns the degree of a given variable in this factor graph, that is, the number of factors in which the variable is an argument.
getDelta(int, int) - Method in interface cc.mallet.fst.MaxLattice
getDelta(int, int) - Method in class cc.mallet.fst.MaxLatticeDefault
getDepthLimited() - Method in class cc.mallet.classify.C45Trainer
getDestinationState(int) - Method in class cc.mallet.fst.CRF.State
getDestinationState() - Method in class cc.mallet.fst.CRF.TransitionIterator
getDestinationState() - Method in class cc.mallet.fst.FeatureTransducer.Transition
getDestinationState() - Method in class cc.mallet.fst.FeatureTransducer.TransitionIterator
getDestinationState(int) - Method in class cc.mallet.fst.HMM.State
getDestinationState() - Method in class cc.mallet.fst.HMM.TransitionIterator
getDestinationState() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  The state we are in after taking this transition.
getDimensions(int[]) - Method in interface cc.mallet.types.ConstantMatrix
getDimensions(int[]) - Method in class cc.mallet.types.DenseMatrix
getDimensions(int[]) - Method in class cc.mallet.types.DenseVector
getDimensions(int[]) - Method in class cc.mallet.types.Matrix2
  Deprecated.
getDimensions(int[]) - Method in class cc.mallet.types.Matrixn
getDimensions(int[]) - Method in class cc.mallet.types.SparseMatrixn
getDimensions(int[]) - Method in class cc.mallet.types.SparseVector
getDocLengthCounts() - Method in class cc.mallet.topics.WorkerRunnable
getDocLengthNormalization() - Method in class cc.mallet.classify.NaiveBayesEMTrainer
getDocLengthNormalization() - Method in class cc.mallet.classify.NaiveBayesTrainer
getDocTopicCounts() - Method in class cc.mallet.topics.LDA
  Deprecated.
getDocument() - Method in class cc.mallet.extract.DocumentExtraction
getDocument() - Method in class cc.mallet.extract.LabeledSpan
getDocument() - Method in class cc.mallet.extract.LabeledSpans
getDocument() - Method in interface cc.mallet.extract.Span
getDocument() - Method in class cc.mallet.extract.StringSpan
getDocument() - Method in class cc.mallet.extract.StringTokenization
getDocument() - Method in interface cc.mallet.extract.Tokenization
  Returns the document of which this is a tokenization.
getDocumentExtraction(int) - Method in class cc.mallet.extract.Extraction
getDoPruning() - Method in class cc.mallet.classify.C45Trainer
getDouble(Variable) - Method in class cc.mallet.grmm.types.Assignment
getDouble(int, Variable) - Method in class cc.mallet.grmm.types.Assignment
  Returns the value of var in this assigment.
getEdgeSet() - Method in class cc.mallet.grmm.types.UndirectedModel
getEnd() - Method in class cc.mallet.fst.Segment
getEndIdx() - Method in class cc.mallet.extract.LabeledSpan
getEndIdx() - Method in interface cc.mallet.extract.Span
  Returns an integer index identifying the end of this span.
getEndIdx() - Method in class cc.mallet.extract.StringSpan
getEndOffset() - Method in class cc.mallet.util.CharSequenceLexer
getEndOffset() - Method in interface cc.mallet.util.Lexer
getEntropy() - Method in class cc.mallet.fst.semi_supervised.EntropyLattice
getEntropy(double[]) - Static method in class cc.mallet.util.Maths
getEntry() - Method in class cc.mallet.types.Label
getErrorOutputStream() - Method in class cc.mallet.extract.AccuracyCoverageEvaluator
getErrorOutputStream() - Method in class cc.mallet.extract.PerDocumentF1Evaluator
getErrorOutputStream() - Method in class cc.mallet.extract.PerFieldF1Evaluator
getEvaluationScores(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.AccuracyEvaluator
getEvaluationScores(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.BCubedEvaluator
getEvaluationScores(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.ClusteringEvaluator
getEvaluationScores(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.ClusteringEvaluators
getEvaluationScores(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.MUCEvaluator
getEvaluationScores(Clustering, Clustering) - Method in class cc.mallet.cluster.evaluate.PairF1Evaluator
getEvaluator() - Method in class cc.mallet.cluster.HillClimbingClusterer
getExpectation() - Method in class cc.mallet.fst.semi_supervised.GECriterion
  Returns the model expectation of the feature.
getExpectation(int) - Method in class cc.mallet.fst.semi_supervised.GECriterion
  Returns the model expectation for the feature and label li.
getExpectationForInstance(int, FeatureVectorSequence, double[][], double[]) - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Returns the number of times the feature occurred in the sequence (an instance).
getExpectationForInstance(int, FeatureVectorSequence, double[][]) - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Returns the expectation of a feature in one instance.
getExpectations(int) - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
getExpectationValue(int, int[]) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
  Computes log probability of a batch of training data, fill in corresponding expectations as well
getExpectationValue() - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
getExpectationValue() - Method in class cc.mallet.fst.MEMMTrainer.MEMMOptimizableByLabelLikelihood
getExtractedSpans() - Method in class cc.mallet.extract.DocumentExtraction
getExtractor() - Method in class cc.mallet.extract.Extraction
getF1(InstanceList, int) - Method in class cc.mallet.classify.Classifier
getF1(InstanceList, Labeling) - Method in class cc.mallet.classify.Classifier
getF1(InstanceList, Object) - Method in class cc.mallet.classify.Classifier
getF1(Object) - Method in class cc.mallet.classify.Trial
  Calculate the F1-measure of the classifier on an instance list for a particular target entry
getF1(Labeling) - Method in class cc.mallet.classify.Trial
getF1(int) - Method in class cc.mallet.classify.Trial
  Calculate the F1-measure for a particular target index from an array list of classifications
getFactor() - Method in class cc.mallet.grmm.learning.ACRF.BigramTemplate
getFactor() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledVarSet
getFactor(int) - Method in class cc.mallet.grmm.types.FactorGraph
getFeatureAbsentChild() - Method in class cc.mallet.classify.DecisionTree.Node
getFeatureIndexIterator() - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Returns an iterator to the indices of the feature constraints.
getFeatureIndices(Alphabet, String) - Static method in class cc.mallet.types.FeatureConjunction
getFeatureMultinomialEstimator() - Method in class cc.mallet.classify.NaiveBayesEMTrainer
getFeatureMultinomialEstimator() - Method in class cc.mallet.classify.NaiveBayesTrainer
  Get the MultinomialEstimator instance used to specify the type of estimator for features.
getFeatureName() - Method in class cc.mallet.pipe.tsf.OffsetFeatureConjunction
getFeaturePatterns() - Method in class cc.mallet.pipe.tsf.OffsetFeatureConjunction
getFeaturePipe() - Method in class cc.mallet.extract.CRFExtractor
getFeaturePipe() - Method in interface cc.mallet.extract.Extractor
  Returns the pipe used by this extractor for.
getFeaturePipe() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
getFeaturePresentChild() - Method in class cc.mallet.classify.DecisionTree.Node
getFeatures() - Method in class cc.mallet.fst.confidence.SequenceConfidenceInstance
getFeatures() - Method in class cc.mallet.types.FeatureSequence
getFeatures() - Method in interface cc.mallet.types.PropertyHolder
getFeatures() - Method in class cc.mallet.types.Token
getFeatureSelection() - Method in class cc.mallet.classify.Classifier
getFeatureSelection() - Method in class cc.mallet.classify.MaxEnt
getFeatureSelection() - Method in class cc.mallet.types.InstanceList
getFeaturesIncludeToken() - Method in class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
getFeatureValue(String) - Method in class cc.mallet.fst.confidence.SequenceConfidenceInstance
getFeatureValue(String) - Method in interface cc.mallet.types.PropertyHolder
getFeatureValue(String) - Method in class cc.mallet.types.Token
getFeatureVector(int) - Method in class cc.mallet.types.FeatureVectorSequence
getField(Label) - Method in class cc.mallet.extract.Record
getFileArray() - Method in class cc.mallet.pipe.iterator.FileIterator
getFileArray() - Method in class cc.mallet.pipe.iterator.FileListIterator
getFileArray() - Method in class cc.mallet.pipe.iterator.UnlabeledFileIterator
getFilter() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
getFinalWeight() - Method in class cc.mallet.fst.CRF.State
getFinalWeight() - Method in class cc.mallet.fst.FeatureTransducer.State
getFinalWeight() - Method in class cc.mallet.fst.HMM.State
getFinalWeight() - Method in class cc.mallet.fst.Transducer.State
getFirstString() - Method in class cc.mallet.types.StringEditVector
getFirstStringChar(int) - Method in class cc.mallet.types.StringEditVector
getFixedTemplates() - Method in class cc.mallet.grmm.learning.ACRF
getFlops() - Static method in class cc.mallet.grmm.util.Flops
getFullName() - Method in class cc.mallet.util.CommandOption
getFv() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledVarSet
getGainRatio() - Method in class cc.mallet.classify.C45.Node
getGammaProbability(int, Transducer.State) - Method in interface cc.mallet.fst.SumLattice
getGammaProbability(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeBeam
getGammaProbability(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeDefault
getGammaProbability(int, int) - Method in class cc.mallet.fst.SumLatticeDefault
getGammaProbability(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeScaling
getGammaProbability(int, int) - Method in class cc.mallet.fst.SumLatticeScaling
getGammas() - Method in interface cc.mallet.fst.SumLattice
getGammas() - Method in class cc.mallet.fst.SumLatticeBeam
getGammas() - Method in class cc.mallet.fst.SumLatticeDefault
getGammas() - Method in class cc.mallet.fst.SumLatticeScaling
getGammaWeight(int, Transducer.State) - Method in interface cc.mallet.fst.SumLattice
getGammaWeight(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeBeam
getGammaWeight(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeDefault
getGammaWeight(int, int) - Method in class cc.mallet.fst.SumLatticeDefault
getGammaWeight(int, Transducer.State) - Method in class cc.mallet.fst.SumLatticeScaling
getGammaWeight(int, int) - Method in class cc.mallet.fst.SumLatticeScaling
getGaussianPriorVariance() - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
getGaussianPriorVariance() - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
getGaussianPriorVariance() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getGaussianPriorVariance() - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
getGaussianPriorVariance() - Method in class cc.mallet.grmm.learning.ACRF
getGECriteria() - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
getGEValue() - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Computes sum of GE constraint values.
getGEValue() - Method in class cc.mallet.fst.semi_supervised.GEKLCriteria
  Computes sum of GE constraint values.
getGEValue() - Method in class cc.mallet.fst.semi_supervised.GEL2Criteria
  Computes sum of GE constraint values.
getGISUpdate(double[]) - Method in interface cc.mallet.optimize.Optimizable.ByGISUpdate
getGradientConstant(int) - Method in class cc.mallet.fst.semi_supervised.GECriterion
  Returns the constant value from the gradient, which will be different for different criteria.
getGradientConstant(int) - Method in class cc.mallet.fst.semi_supervised.GEKLCriterion
  Returns the target/expectation ratio required in lattice computations.
getGradientConstant(int) - Method in class cc.mallet.fst.semi_supervised.GEL2Criterion
getHeight() - Method in class cc.mallet.grmm.types.UndirectedGrid
getID() - Method in class cc.mallet.types.IDSorter
getIndex() - Method in class cc.mallet.fst.CRF.State
getIndex() - Method in class cc.mallet.fst.CRF.TransitionIterator
getIndex() - Method in class cc.mallet.fst.FeatureTransducer.State
getIndex() - Method in class cc.mallet.fst.FeatureTransducer.TransitionIterator
getIndex() - Method in class cc.mallet.fst.HMM.State
getIndex() - Method in class cc.mallet.fst.HMM.TransitionIterator
getIndex() - Method in class cc.mallet.fst.Transducer.State
getIndex() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  An implementation-specific index for this transition object, can be used to index into arrays of per-transition parameters.
getIndex(Factor) - Method in class cc.mallet.grmm.inference.MessageArray
getIndex(Variable) - Method in class cc.mallet.grmm.inference.MessageArray
getIndex(VarSet) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
getIndex(Variable) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
getIndex(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns a unique numeric index for a variable in this model.
getIndex(Factor) - Method in class cc.mallet.grmm.types.FactorGraph
getIndex(Variable) - Method in class cc.mallet.grmm.types.Universe
getIndex() - Method in class cc.mallet.grmm.types.Variable
  Returns the index of this variable in its universe
getIndex() - Method in class cc.mallet.types.FeatureConjunction
getIndex() - Method in class cc.mallet.types.FeatureVectorSequence.Iterator
getIndex() - Method in class cc.mallet.types.Label
getIndex() - Method in class cc.mallet.types.LabelSequence.Iterator
getIndexAtPosition(int) - Method in class cc.mallet.types.FeatureSequence
getIndexAtRank(int) - Method in class cc.mallet.types.RankedFeatureVector
getIndices() - Method in class cc.mallet.types.SparseMatrixn
  Returns an array of all the present indices.
getIndices() - Method in class cc.mallet.types.SparseVector
getIndicesWithLabel(int) - Method in class cc.mallet.cluster.Clustering
getInertiaWeight() - Method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
getInferenceCache(Class) - Method in class cc.mallet.grmm.types.FactorGraph
  Caches some information about this graph that is specific to a given type of inferencer (e.g., a junction tree).
getInferencer() - Method in class cc.mallet.grmm.learning.ACRF
getInferencer() - Method in class cc.mallet.topics.ParallelTopicModel
  Return a tool for estimating topic distributions for new documents
getInfoGain(int) - Method in class cc.mallet.types.PerLabelInfoGain
getInitialStepSize() - Method in class cc.mallet.optimize.ConjugateGradient
getInitialStepSize() - Method in class cc.mallet.optimize.GradientAscent
getInitialWeight() - Method in class cc.mallet.fst.CRF.State
getInitialWeight() - Method in class cc.mallet.fst.FeatureTransducer.State
getInitialWeight() - Method in class cc.mallet.fst.HMM.State
getInitialWeight() - Method in class cc.mallet.fst.Transducer.State
getInProduction() - Method in class cc.mallet.pipe.AddClassifierTokenPredictions
getInput() - Method in class cc.mallet.extract.DocumentExtraction
getInput() - Method in class cc.mallet.fst.CRF.TransitionIterator
getInput() - Method in class cc.mallet.fst.FeatureTransducer.TransitionIterator
getInput() - Method in class cc.mallet.fst.HMM.TransitionIterator
getInput() - Method in class cc.mallet.fst.MaxLatticeDefault
getInput() - Method in class cc.mallet.fst.Segment
getInput() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  The input symbol or object appearing on this transition.
getInputAlphabet() - Method in class cc.mallet.extract.CRFExtractor
getInputAlphabet() - Method in interface cc.mallet.extract.Extractor
  Returns an alphabet of the features used by the extractor.
getInputAlphabet() - Method in class cc.mallet.fst.CRF
getInputAlphabet() - Method in class cc.mallet.fst.FeatureTransducer
getInputAlphabet() - Method in class cc.mallet.fst.HMM
getInputAlphabet() - Method in class cc.mallet.grmm.learning.ACRF
getInputAlphabet() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
getInputPipe() - Method in class cc.mallet.fst.Transducer
getInputPipe() - Method in class cc.mallet.grmm.learning.ACRF
getInputPositionIncrement() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  The number of input positions that this transition consumes.
getInstance() - Method in class cc.mallet.classify.Classification
getInstance() - Method in class cc.mallet.fst.confidence.InstanceWithConfidence
getInstance() - Method in class cc.mallet.fst.confidence.PipedInstanceWithConfidence
getInstance() - Method in class cc.mallet.fst.confidence.SequenceConfidenceInstance
getInstanceId() - Method in class cc.mallet.pipe.Pipe
getInstanceId() - Method in class cc.mallet.types.Alphabet
getInstanceList() - Method in class cc.mallet.topics.LDA
  Deprecated.
getInstanceList() - Method in class cc.mallet.types.InvertedIndex
getInstancePipe() - Method in class cc.mallet.classify.Classifier
getInstances() - Method in class cc.mallet.classify.C45.Node
getInstances() - Method in class cc.mallet.cluster.Clustering
getInstancesWithFeature(int) - Method in class cc.mallet.types.InvertedIndex
getInstancesWithFeature(Object) - Method in class cc.mallet.types.InvertedIndex
getInstanceWeight(Instance) - Method in class cc.mallet.types.InstanceList
getInstanceWeight(int) - Method in class cc.mallet.types.InstanceList
getInTag() - Method in class cc.mallet.fst.Segment
getInterpreter() - Static method in class cc.mallet.util.CommandOption
getIteration() - Method in interface cc.mallet.classify.ClassifierTrainer.ByOptimization
getIteration() - Method in class cc.mallet.classify.MaxEntGETrainer
getIteration() - Method in class cc.mallet.classify.MaxEntTrainer
getIteration() - Method in class cc.mallet.classify.NaiveBayesEMTrainer
getIteration() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getIteration() - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
getIteration() - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
getIteration() - Method in class cc.mallet.fst.CRFTrainerByValueGradients
getIteration() - Method in class cc.mallet.fst.HMMTrainerByLikelihood
getIteration() - Method in class cc.mallet.fst.MEMMTrainer
getIteration() - Method in class cc.mallet.fst.NoopTransducerTrainer
getIteration() - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByEntropyRegularization
getIteration() - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByGE
getIteration() - Method in class cc.mallet.fst.ShallowTransducerTrainer
  Deprecated.
getIteration() - Method in class cc.mallet.fst.TransducerTrainer
getIteration() - Method in class cc.mallet.optimize.LimitedMemoryBFGS
getIteration() - Method in class cc.mallet.optimize.OrthantWiseLimitedMemoryBFGS
getJointAccuracy() - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.LogEvaluator
getJointAccuracy() - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
getKey() - Method in class cc.mallet.util.PropertyList.Iterator
getLabel(int) - Method in class cc.mallet.cluster.Clustering
  Get the cluster label for a particular instance.
getLabel() - Method in class cc.mallet.extract.LabeledSpan
getLabel(int) - Method in class cc.mallet.extract.LabeledSpans
getLabel() - Method in class cc.mallet.grmm.types.BitVarSet
getLabel() - Method in class cc.mallet.grmm.types.HashVarSet
getLabel() - Method in class cc.mallet.grmm.types.Variable
getLabelAlphabet() - Method in class cc.mallet.classify.Classifier
getLabelAlphabet() - Method in class cc.mallet.extract.Extraction
getLabelAlphabet() - Method in class cc.mallet.fst.semi_supervised.StateLabelMap
  Returns the label (target) alphabet.
getLabelAlphabet(int) - Method in class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
getLabelAlphabet() - Method in class cc.mallet.grmm.types.Variable
getLabelAlphabet() - Method in class cc.mallet.pipe.iterator.RandomFeatureVectorIterator
getLabelAlphabet() - Method in class cc.mallet.types.Label
getLabelAlphabet() - Method in interface cc.mallet.types.Labeling
getLabelAlphabet() - Method in class cc.mallet.types.LabelSequence
getLabelAlphabet() - Method in class cc.mallet.types.LabelVector
getLabelAlphabet() - Method in class cc.mallet.types.ROCData
  Gets the label alphabet
getLabelAtPosition(int) - Method in class cc.mallet.types.LabelSequence
getLabelAtRank(int) - Method in class cc.mallet.types.Label
getLabelAtRank(int) - Method in interface cc.mallet.types.Labeling
getLabelAtRank(int) - Method in class cc.mallet.types.LabelVector
getLabeledSpan(int) - Method in class cc.mallet.extract.LabeledSpans
getLabelIndex(int) - Method in class cc.mallet.fst.semi_supervised.StateLabelMap
  Returns the label index mapped to the state index.
getLabeling() - Method in class cc.mallet.classify.Classification
getLabeling() - Method in class cc.mallet.types.Instance
getLabelingAtPosition(int) - Method in interface cc.mallet.fst.SumLattice
getLabelingAtPosition(int) - Method in class cc.mallet.fst.SumLatticeBeam
getLabelingAtPosition(int) - Method in class cc.mallet.fst.SumLatticeDefault
getLabelingAtPosition(int) - Method in class cc.mallet.fst.SumLatticeScaling
getLabelName(int) - Method in class cc.mallet.fst.CRF.State
getLabels() - Method in class cc.mallet.cluster.Clustering
getLabels(int) - Method in class cc.mallet.types.LabelsSequence
getLabelsSequence() - Method in class cc.mallet.grmm.util.LabelsAssignment
getLabelVector() - Method in class cc.mallet.classify.Classification
getLastChange() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledVarSet
getLastResids() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
getLatticeNode(int, int) - Method in class cc.mallet.fst.semi_supervised.EntropyLattice
getLatticeNode(int, int) - Method in class cc.mallet.fst.SumLatticeDefault
getLatticeNode(int, int) - Method in class cc.mallet.fst.SumLatticeScaling
getLearningRate() - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
getLeastConfidentSegments() - Method in class cc.mallet.fst.confidence.ConstrainedViterbiTransducerCorrector
  Returns the least confident segments from each sequence in the previous call to `correctLeastConfidentSegments`
getLeastConfidentSegments(InstanceList, Object[], Object[]) - Method in class cc.mallet.fst.confidence.ConstrainedViterbiTransducerCorrector
  Returns the least confident segments in `ilist`
getLeftChild() - Method in class cc.mallet.classify.C45.Node
getLength() - Method in class cc.mallet.types.FeatureSequence
getLengthFirstString() - Method in class cc.mallet.types.StringEditVector
getLengthSecondString() - Method in class cc.mallet.types.StringEditVector
getLineMaximizer() - Method in class cc.mallet.optimize.GradientAscent
getList(Class) - Static method in class cc.mallet.util.CommandOption
getLogger(String) - Static method in class cc.mallet.util.MalletLogger
getLogger(String) - Static method in class cc.mallet.util.MalletProgressMessageLogger
getLogNumAssignments() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
getLogValueMatrix() - Method in class cc.mallet.grmm.types.AbstractTableFactor
getLogValueMatrix() - Method in class cc.mallet.grmm.types.LogTableFactor
getLogValueMatrix() - Method in class cc.mallet.grmm.types.TableFactor
getMatch() - Method in class cc.mallet.types.StringEditVector
getMaxDepth() - Method in class cc.mallet.classify.C45Trainer
getMaxer() - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
getMaximizable(InstanceList) - Method in class cc.mallet.grmm.learning.ACRF
getMaximizableTrainer(InstanceList) - Method in class cc.mallet.classify.MCMaxEntTrainer
getMaximizableTrainer(InstanceList) - Method in class cc.mallet.classify.RankMaxEntTrainer
getMaxLatticeFactory() - Method in class cc.mallet.fst.Transducer
getMaxValue() - Method in class cc.mallet.types.RankedFeatureVector
getMaxValuedIndex() - Method in class cc.mallet.types.RankedFeatureVector
getMaxValuedIndexIn(FeatureSelection) - Method in class cc.mallet.types.RankedFeatureVector
getMaxValuedObject() - Method in class cc.mallet.types.RankedFeatureVector
getMaxValuedObjectIn(FeatureSelection) - Method in class cc.mallet.types.RankedFeatureVector
getMaxValuedThreshold() - Method in class cc.mallet.types.GainRatio
getMaxValueIn(FeatureSelection) - Method in class cc.mallet.types.RankedFeatureVector
getMDL() - Method in class cc.mallet.classify.C45.Node
  Calculates the minimum description length of this node, i.e., the length of the binary encoding that describes the feature and the split value used at this node
getMessager() - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
getMessagesSent() - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
  Returns the total number of messages this inferencer has sent since its creation.
getMessagesUsedLastTime() - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
  Returns the number of messages sent during the last call to computeMarginals.
getMinNumInsts() - Method in class cc.mallet.classify.C45Trainer
getModified() - Method in class cc.mallet.cluster.neighbor_evaluator.Neighbor
getMultinomials() - Method in class cc.mallet.classify.NaiveBayes
getName() - Method in class cc.mallet.classify.C45.Node
getName() - Method in class cc.mallet.classify.DecisionTree.Node
getName() - Method in class cc.mallet.extract.DocumentExtraction
getName() - Method in class cc.mallet.extract.Field
getName() - Method in class cc.mallet.extract.Record
getName() - Method in class cc.mallet.fst.CRF.State
getName() - Method in class cc.mallet.fst.FeatureTransducer.State
getName() - Method in class cc.mallet.fst.HMM.State
getName() - Method in class cc.mallet.fst.semi_supervised.GECriterion
  Returns the constraint name.
getName() - Method in class cc.mallet.fst.Transducer.State
getName(Alphabet, int[], boolean[]) - Static method in class cc.mallet.types.FeatureConjunction
getName(Alphabet, int[]) - Static method in class cc.mallet.types.FeatureConjunction
getName(Alphabet, int, int) - Static method in class cc.mallet.types.FeatureConjunction
getName() - Method in class cc.mallet.types.Instance
getName() - Method in class cc.mallet.util.CommandOption
getNewCluster() - Method in class cc.mallet.cluster.neighbor_evaluator.AgglomerativeNeighbor
getNewMessages() - Method in class cc.mallet.grmm.inference.gbp.AbstractMessageStrategy
getNewMessages() - Method in interface cc.mallet.grmm.inference.gbp.MessageStrategy
getNextElement() - Method in class cc.mallet.pipe.iterator.PatternMatchIterator
getNextNodes() - Method in class cc.mallet.util.search.AStarNode
getNextNodes() - Method in class cc.mallet.util.search.SearchNode
  Get an iterator over the new search nodes reachable from this node by state transitions.
getNextStates() - Method in interface cc.mallet.util.search.SearchState
  Get an iterator over the states with transitions from this state.
getNonNegated() - Method in class cc.mallet.pipe.tsf.OffsetFeatureConjunction
getNstatesExpl() - Method in class cc.mallet.fst.SumLatticeBeam
getNumBatches() - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
getNumBatches() - Method in interface cc.mallet.optimize.Optimizable.ByCombiningBatchGradient
getNumClasses() - Method in class cc.mallet.types.PerLabelInfoGain
getNumClusters() - Method in class cc.mallet.cluster.Clustering
getNumCols() - Method in class cc.mallet.types.Matrix2
  Deprecated.
getNumDescendants() - Method in class cc.mallet.classify.C45.Node
  Count the number of non-leaf descendant nodes
getNumDimensions() - Method in interface cc.mallet.types.ConstantMatrix
getNumDimensions() - Method in class cc.mallet.types.DenseMatrix
getNumDimensions() - Method in class cc.mallet.types.DenseVector
getNumDimensions() - Method in class cc.mallet.types.Matrix2
  Deprecated.
getNumDimensions() - Method in class cc.mallet.types.Matrixn
getNumDimensions() - Method in class cc.mallet.types.SparseMatrixn
getNumDimensions() - Method in class cc.mallet.types.SparseVector
  ACCESSORS
getNumDocuments() - Method in class cc.mallet.extract.Extraction
getNumericProperty(String) - Method in class cc.mallet.grmm.types.Variable
getNumericProperty(String) - Method in class cc.mallet.types.Instance
getNumericProperty(String) - Method in interface cc.mallet.types.PropertyHolder
getNumericProperty(String) - Method in class cc.mallet.types.Token
getNumericProperty(String) - Method in class cc.mallet.types.TokenSequence
getNumericValue() - Method in class cc.mallet.util.PropertyList.Iterator
getNumFactors() - Method in class cc.mallet.fst.CRF.Factors
getNumFeaturesToDisplay() - Static method in class cc.mallet.extract.LatticeViewer
getNumInstances() - Method in class cc.mallet.cluster.Clustering
getNumInstances() - Method in interface cc.mallet.optimize.Optimizable.ByVotedPerceptron
getNumIter() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
getNumLabels() - Method in class cc.mallet.fst.semi_supervised.StateLabelMap
  Returns the number of labels in the map.
getNumOutcomes() - Method in class cc.mallet.grmm.types.Variable
getNumParameters() - Method in class cc.mallet.classify.MaxEnt
getNumParameters(Pipe) - Static method in class cc.mallet.classify.MaxEnt
getNumParameters() - Method in class cc.mallet.classify.MaxEntOptimizableByGE
getNumParameters() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
getNumParameters() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
getNumParameters() - Method in class cc.mallet.fst.CRF
getNumParameters() - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
getNumParameters() - Method in class cc.mallet.fst.CRFOptimizableByGradientValues
getNumParameters() - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
getNumParameters() - Method in class cc.mallet.fst.CRFTrainerByValueGradients.OptimizableCRF
getNumParameters() - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
getNumParameters() - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
getNumParameters() - Method in class cc.mallet.fst.ThreadedOptimizable
getNumParameters() - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
getNumParameters() - Method in interface cc.mallet.optimize.Optimizable
getNumParameters() - Method in class cc.mallet.optimize.OptimizableCollection.ByGradientValue
getNumParameters() - Method in class cc.mallet.topics.DMROptimizable
getNumRecords() - Method in class cc.mallet.extract.Extraction
getNumRows() - Method in class cc.mallet.types.Matrix2
  Deprecated.
getNumSplitPointsForBestFeature() - Method in class cc.mallet.types.GainRatio
getNumStates() - Method in class cc.mallet.fst.semi_supervised.StateLabelMap
  Returns the number of states in the map.
getNumTopics() - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
getNumTopics() - Method in class cc.mallet.topics.ParallelTopicModel
getNumTopics() - Method in class cc.mallet.topics.PolylingualTopicModel
getNumTopics() - Method in class cc.mallet.topics.SimpleLDA
getNumVars() - Method in class cc.mallet.grmm.types.AbstractTableFactor
getNumWeakClassifiers() - Method in class cc.mallet.classify.AdaBoost
  Get the number of weak classifiers in this ensemble classifier
getNumWeakClassifiers() - Method in class cc.mallet.classify.AdaBoostM2
  Get the number of weak classifiers in this ensemble classifier
getObject(Variable) - Method in class cc.mallet.grmm.types.Assignment
getObject(int, Variable) - Method in class cc.mallet.grmm.types.Assignment
getObjectAtPosition(int) - Method in class cc.mallet.types.FeatureSequence
getObjectAtPosition(int) - Method in class cc.mallet.types.FeatureSequenceWithBigrams
getObjectAtRank(int) - Method in class cc.mallet.types.RankedFeatureVector
getObjectIndices(Object[], Alphabet, boolean) - Static method in class cc.mallet.types.FeatureVector
getObjectValue() - Method in class cc.mallet.util.PropertyList.Iterator
getOffsets() - Method in class cc.mallet.pipe.tsf.OffsetFeatureConjunction
getOldClusters() - Method in class cc.mallet.cluster.neighbor_evaluator.AgglomerativeNeighbor
getOldMessages() - Method in class cc.mallet.grmm.inference.gbp.AbstractMessageStrategy
getOldMessages() - Method in interface cc.mallet.grmm.inference.gbp.MessageStrategy
getOptimizable() - Method in class cc.mallet.classify.MaxEntGETrainer
getOptimizable() - Method in class cc.mallet.classify.MaxEntTrainer
getOptimizable(InstanceList) - Method in class cc.mallet.classify.MaxEntTrainer
getOptimizable(InstanceList, MaxEnt) - Method in class cc.mallet.classify.MaxEntTrainer
getOptimizable() - Method in class cc.mallet.fst.ThreadedOptimizable
getOptimizable() - Method in class cc.mallet.optimize.AGIS
getOptimizable() - Method in class cc.mallet.optimize.ConjugateGradient
getOptimizable() - Method in class cc.mallet.optimize.GradientAscent
getOptimizable() - Method in class cc.mallet.optimize.LimitedMemoryBFGS
getOptimizable() - Method in interface cc.mallet.optimize.Optimizer
getOptimizable() - Method in class cc.mallet.optimize.OrthantWiseLimitedMemoryBFGS
getOptimizableByGradientValueObjects() - Method in class cc.mallet.fst.CRFTrainerByValueGradients
getOptimizableCRF(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getOptimizableCRF(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
getOptimizableCRF(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByValueGradients
  Returns an optimizable CRF that contains a collection of objective functions.
getOptimizableMEMM(InstanceList) - Method in class cc.mallet.fst.MEMMTrainer
getOptimizer() - Method in interface cc.mallet.classify.ClassifierTrainer.ByOptimization
getOptimizer() - Method in class cc.mallet.classify.MaxEntGETrainer
getOptimizer() - Method in class cc.mallet.classify.MaxEntL1Trainer
getOptimizer(InstanceList) - Method in class cc.mallet.classify.MaxEntL1Trainer
getOptimizer() - Method in class cc.mallet.classify.MaxEntTrainer
getOptimizer(InstanceList) - Method in class cc.mallet.classify.MaxEntTrainer
  This method is called by the train method.
getOptimizer(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByL1LabelLikelihood
getOptimizer() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getOptimizer(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getOptimizer() - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
getOptimizer(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
getOptimizer() - Method in class cc.mallet.fst.CRFTrainerByValueGradients
getOptimizer(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByValueGradients
  Returns a L-BFGS optimizer, creating if one doesn't exist.
getOptimizer() - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByEntropyRegularization
getOptimizer() - Method in interface cc.mallet.fst.TransducerTrainer.ByOptimization
getOriginal() - Method in class cc.mallet.cluster.neighbor_evaluator.Neighbor
getOutput() - Method in class cc.mallet.fst.CRF.TransitionIterator
getOutput() - Method in class cc.mallet.fst.FeatureTransducer.TransitionIterator
getOutput() - Method in class cc.mallet.fst.HMM.TransitionIterator
getOutput() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  The output symbol or object appearing on this transition.
getOutputAlphabet() - Method in class cc.mallet.fst.CRF
getOutputAlphabet() - Method in class cc.mallet.fst.FeatureTransducer
getOutputAlphabet() - Method in class cc.mallet.fst.HMM
getOutputAlphabet(int) - Method in class cc.mallet.grmm.util.LabelsAssignment
getOutputPipe() - Method in class cc.mallet.fst.Transducer
getOutputPositionIncrement() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  The number of output positions that this transition produces.
getParameter(int) - Method in class cc.mallet.classify.MaxEntOptimizableByGE
getParameter(int) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
getParameter(int) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
getParameter(int) - Method in class cc.mallet.fst.CRF.Factors
getParameter(int, int, int) - Method in class cc.mallet.fst.CRF
  Only gets the parameter from the first group of parameters.
getParameter(int, int, int, int) - Method in class cc.mallet.fst.CRF
getParameter(int) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
getParameter(int) - Method in class cc.mallet.fst.CRFOptimizableByGradientValues
getParameter(int) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
getParameter(int) - Method in class cc.mallet.fst.CRFTrainerByValueGradients.OptimizableCRF
getParameter(int) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
getParameter(int) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
getParameter(int) - Method in class cc.mallet.fst.ThreadedOptimizable
getParameter(int) - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
getParameter(int) - Method in interface cc.mallet.optimize.Optimizable
getParameter(int) - Method in class cc.mallet.optimize.OptimizableCollection.ByGradientValue
getParameter(int) - Method in class cc.mallet.topics.DMROptimizable
getParameters() - Method in class cc.mallet.classify.MaxEnt
getParameters(double[]) - Method in class cc.mallet.classify.MaxEntOptimizableByGE
getParameters(double[]) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
getParameters(double[]) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
getParameters() - Method in class cc.mallet.classify.MCMaxEnt
getParameters(double[]) - Method in class cc.mallet.fst.CRF.Factors
getParameters() - Method in class cc.mallet.fst.CRF
getParameters(double[]) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
getParameters(double[]) - Method in class cc.mallet.fst.CRFOptimizableByGradientValues
getParameters(double[]) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
getParameters(double[]) - Method in class cc.mallet.fst.CRFTrainerByValueGradients.OptimizableCRF
getParameters(double[]) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
getParameters(double[]) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
getParameters(double[]) - Method in class cc.mallet.fst.ThreadedOptimizable
getParameters(double[]) - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
getParameters(double[]) - Method in interface cc.mallet.optimize.Optimizable
getParameters(double[]) - Method in class cc.mallet.optimize.OptimizableCollection.ByGradientValue
getParameters(double[]) - Method in class cc.mallet.topics.DMROptimizable
getParametersAbsNorm() - Method in class cc.mallet.fst.CRF.Factors
getParametersAbsNorm() - Method in class cc.mallet.fst.CRF
getParent() - Method in class cc.mallet.classify.C45.Node
getParent(Object) - Method in class cc.mallet.grmm.types.Tree
getParent() - Method in class cc.mallet.util.search.SearchNode
  The node that generated this node.
getParents() - Method in class cc.mallet.grmm.types.CPT
getPattern() - Method in class cc.mallet.util.CharSequenceLexer
getPerClassFeatureSelection() - Method in class cc.mallet.classify.Classifier
getPerClassFeatureSelection() - Method in class cc.mallet.classify.MaxEnt
getPerLabelFeatureSelection() - Method in class cc.mallet.types.InstanceList
getPipe() - Method in class cc.mallet.cluster.Clusterer
getPipe(int) - Method in class cc.mallet.pipe.SerialPipes
getPipe() - Method in class cc.mallet.types.InstanceList
  Returns the pipe through which each added `Instance` is passed, which may be `null`.
getPosition() - Method in interface cc.mallet.util.search.QueueElement
  Get the queue position of this element.
getPosition() - Method in class cc.mallet.util.search.SearchNode
getPositivePercent(Label, double) - Method in class cc.mallet.types.ROCData
  Gets the estimated percentage of training events that exceed the threshold.
getPrecision(InstanceList, int) - Method in class cc.mallet.classify.Classifier
getPrecision(InstanceList, Labeling) - Method in class cc.mallet.classify.Classifier
getPrecision(InstanceList, Object) - Method in class cc.mallet.classify.Classifier
getPrecision(int) - Method in class cc.mallet.classify.evaluate.ConfusionMatrix
  Returns the precision of this predicted class
getPrecision(Object) - Method in class cc.mallet.classify.Trial
  Calculate the precision of the classifier on an instance list for a particular target entry
getPrecision(Labeling) - Method in class cc.mallet.classify.Trial
getPrecision(int) - Method in class cc.mallet.classify.Trial
  Calculate the precision for a particular target index from an array list of classifications
getPrecision(Label, double) - Method in class cc.mallet.types.ROCData
  Gets the precision for a specified label and threshold.
getPrecisionForScore(Label, double) - Method in class cc.mallet.types.ROCData
  Gets the precision for a specified label and score.
getPredicted(int) - Method in class cc.mallet.fst.Segment
getPredicted() - Method in class cc.mallet.fst.Segment
getPredictedLabels() - Method in class cc.mallet.extract.DocumentExtraction
getPreferredSize() - Method in class cc.mallet.classify.evaluate.Graph
getPriority() - Method in interface cc.mallet.util.search.QueueElement
  Get this element's priority.
getPriority() - Method in class cc.mallet.util.search.SearchNode
getPriorMultinomialEstimator() - Method in class cc.mallet.classify.NaiveBayesEMTrainer
getPriorMultinomialEstimator() - Method in class cc.mallet.classify.NaiveBayesTrainer
  Get the MultinomialEstimator instance used to specify the type of estimator for priors.
getPriors() - Method in class cc.mallet.classify.NaiveBayes
getProbEstimator() - Method in class cc.mallet.topics.ParallelTopicModel
  Return a tool for evaluating the marginal probability of new documents under this model
getProperties() - Method in class cc.mallet.types.Instance
  Deprecated.
getProperties() - Method in interface cc.mallet.types.PropertyHolder
getProperties() - Method in class cc.mallet.types.Token
getProperties() - Method in class cc.mallet.types.TokenSequence
getProperty(String) - Method in class cc.mallet.types.Instance
getProperty(String) - Method in interface cc.mallet.types.PropertyHolder
getProperty(String) - Method in class cc.mallet.types.Token
getProperty(String) - Method in class cc.mallet.types.TokenSequence
getProvidedOutput() - Method in class cc.mallet.fst.MaxLatticeDefault
getPrunedAlphabet(int) - Method in class cc.mallet.pipe.FeatureCountPipe
  Returns a new alphabet that contains only features at or above the specified limit.
getRandom() - Static method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
getRank(Label) - Method in class cc.mallet.types.Label
getRank(int) - Method in class cc.mallet.types.Label
getRank(Label) - Method in interface cc.mallet.types.Labeling
getRank(int) - Method in interface cc.mallet.types.Labeling
getRank(Label) - Method in class cc.mallet.types.LabelVector
getRank(int) - Method in class cc.mallet.types.LabelVector
getRank(Object) - Method in class cc.mallet.types.RankedFeatureVector
getRank(int) - Method in class cc.mallet.types.RankedFeatureVector
getRecall(InstanceList, int) - Method in class cc.mallet.classify.Classifier
getRecall(InstanceList, Labeling) - Method in class cc.mallet.classify.Classifier
getRecall(InstanceList, Object) - Method in class cc.mallet.classify.Classifier
getRecall(Object) - Method in class cc.mallet.classify.Trial
  Calculate the recall of the classifier on an instance list for a particular target entry
getRecall(Labeling) - Method in class cc.mallet.classify.Trial
getRecall(int) - Method in class cc.mallet.classify.Trial
  Calculate the recall for a particular target index from an array list of classifications
getRecall(Label, double) - Method in class cc.mallet.types.ROCData
  Gets the recall rate for a specified label and threshold.
getRecord(int) - Method in class cc.mallet.extract.Extraction
getRightChild() - Method in class cc.mallet.classify.C45.Node
getRoot() - Method in class cc.mallet.classify.C45
getRoot() - Method in class cc.mallet.classify.DecisionTree
getRoot() - Method in class cc.mallet.grmm.types.Tree
getRootLogger() - Method in class cc.mallet.util.MalletLogger
  Convenience method for finding the root logger.
getRow(int) - Method in class cc.mallet.grmm.types.Assignment
getSampledDistribution(Instance, int, int, int) - Method in class cc.mallet.topics.TopicInferencer
  Use Gibbs sampling to infer a topic distribution.
getScalingFactor() - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
getScatterMatrix(double[][]) - Static method in class cc.mallet.util.MVNormal
getScore(Clustering, int, int) - Method in class cc.mallet.cluster.GreedyAgglomerative
getSecondString() - Method in class cc.mallet.types.StringEditVector
getSecondStringChar(int) - Method in class cc.mallet.types.StringEditVector
getSegmentConfidences() - Method in class cc.mallet.fst.confidence.ConstrainedViterbiTransducerCorrector
getSegmentConfidences() - Method in class cc.mallet.fst.confidence.TransducerConfidenceEstimator
getSegmentInputSequence() - Method in class cc.mallet.fst.Segment
getSepset(VarSet, VarSet) - Method in class cc.mallet.grmm.inference.JunctionTree
getSepsetPot(VarSet, VarSet) - Method in class cc.mallet.grmm.inference.JunctionTree
getSize() - Method in class cc.mallet.classify.C45
getSize() - Method in class cc.mallet.classify.C45.Node
getSortedTopicWords(int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
getSortedWords() - Method in class cc.mallet.topics.ParallelTopicModel
  Return an array of sorted sets (one set per topic).
getSource() - Method in class cc.mallet.types.Instance
getSourceState() - Method in class cc.mallet.fst.CRF.TransitionIterator
getSourceState() - Method in class cc.mallet.fst.FeatureTransducer.TransitionIterator
getSourceState() - Method in class cc.mallet.fst.HMM.TransitionIterator
getSourceState() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  The state we were in before taking this transition.
getSpan() - Method in class cc.mallet.extract.LabeledSpan
getSpan(int) - Method in class cc.mallet.extract.LabeledSpans
getSpan(int) - Method in class cc.mallet.extract.StringTokenization
getSpan(int) - Method in interface cc.mallet.extract.Tokenization
getSplitFeature() - Method in class cc.mallet.classify.C45.Node
getSplitFeature() - Method in class cc.mallet.classify.DecisionTree.Node
getSplitInfoGain() - Method in class cc.mallet.classify.DecisionTree.Node
getStart() - Method in class cc.mallet.fst.Segment
getStartIdx() - Method in class cc.mallet.extract.LabeledSpan
getStartIdx() - Method in interface cc.mallet.extract.Span
  Returns an integer index identifying the start of this span.
getStartIdx() - Method in class cc.mallet.extract.StringSpan
getStartOffset() - Method in class cc.mallet.util.CharSequenceLexer
getStartOffset() - Method in interface cc.mallet.util.Lexer
getStartTag() - Method in class cc.mallet.fst.Segment
getState(String) - Method in class cc.mallet.fst.CRF
getState(int) - Method in class cc.mallet.fst.CRF
getState(int) - Method in class cc.mallet.fst.FeatureTransducer
getState(String) - Method in class cc.mallet.fst.HMM
getState(int) - Method in class cc.mallet.fst.HMM
getState(int) - Method in class cc.mallet.fst.Transducer
getState() - Method in class cc.mallet.util.search.SearchNode
  The state for this search node.
getStateAlphabet() - Method in class cc.mallet.fst.semi_supervised.StateLabelMap
  Returns the state alphabet.
getStateIndices(int) - Method in class cc.mallet.fst.semi_supervised.StateLabelMap
  Returns the state indices that map to the label index.
getStateIter() - Method in class cc.mallet.util.search.SearchNode.NextNodeIterator
getStateLabelMap() - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Returns the state-label mapping.
getStepSize() - Method in class cc.mallet.optimize.ConjugateGradient
getStpmax() - Method in class cc.mallet.optimize.GradientAscent
getString1() - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString1BlockAtIndex(int) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString1Char(int) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString1EOBIndex(String) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString1EOBIndex(String, int) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString1IndexOf(String, int) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString1Length() - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString2() - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString2BlockAtIndex(int) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString2Char(int) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString2EOBIndex(String) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString2EOBIndex(String, int) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString2IndexOf(String, int) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getString2Length() - Method in class cc.mallet.types.StringEditFeatureVectorSequence
getStringBufferName() - Method in class cc.mallet.classify.C45.Node
getSubDirs(File) - Static method in class cc.mallet.cluster.tui.Text2Clusterings
getSumLatticeFactory() - Method in class cc.mallet.fst.Transducer
getSwapIns() - Method in class cc.mallet.types.PagedInstanceList
getSwapInTime() - Method in class cc.mallet.types.PagedInstanceList
getSwapOuts() - Method in class cc.mallet.types.PagedInstanceList
getSwapOutTime() - Method in class cc.mallet.types.PagedInstanceList
getTarget() - Method in class cc.mallet.extract.DocumentExtraction
getTarget() - Method in class cc.mallet.fst.semi_supervised.GECriterion
  Returns the target expectation for the feature.
getTarget(int) - Method in class cc.mallet.fst.semi_supervised.GECriterion
  Returns the target expectation for the feature and label li.
getTarget() - Method in class cc.mallet.types.Instance
getTargetAlphabet() - Method in class cc.mallet.extract.CRFExtractor
getTargetAlphabet() - Method in interface cc.mallet.extract.Extractor
  Returns an alphabet of the labels used by the extractor.
getTargetAlphabet() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
getTargetAlphabet() - Method in class cc.mallet.pipe.Pipe
getTargetAlphabet() - Method in class cc.mallet.types.Instance
getTargetAlphabet() - Method in class cc.mallet.types.InstanceList
  Returns the `Alphabet` mapping target output labels to integers.
getTargetClass() - Method in class cc.mallet.types.InstanceList
  Returns the Java Class 'target' field of Instances in this list.
getTargetRecord(int) - Method in class cc.mallet.extract.Extraction
getTargetSpans() - Method in class cc.mallet.extract.DocumentExtraction
getTctIter() - Method in class cc.mallet.fst.SumLatticeBeam
getTemplate() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledVarSet
getTemplates() - Method in class cc.mallet.grmm.learning.ACRF
getTest() - Method in class cc.mallet.topics.LDAStream
getTestingData() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
getText() - Method in class cc.mallet.extract.LabeledSpan
getText() - Method in interface cc.mallet.extract.Span
  Returns a textual representatio of the span, suitable for XML output, e.g.
getText() - Method in class cc.mallet.types.Token
getThresholdAtRank(int) - Method in class cc.mallet.types.GainRatio
getThresholds() - Method in class cc.mallet.types.ROCData
  Gets the thresholds being tracked
getTokenizationFilter() - Method in class cc.mallet.extract.CRFExtractor
getTokenizationPipe() - Method in class cc.mallet.extract.CRFExtractor
getTokenizationPipe() - Method in interface cc.mallet.extract.Extractor
  Returns the pipe used by this extractor to tokenize the input.
getTokenizationPipe() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
getTokensPerTopic() - Method in class cc.mallet.topics.LDA
  Deprecated.
getTokensPerTopic() - Method in class cc.mallet.topics.MarginalProbEstimator
getTokensPerTopic() - Method in class cc.mallet.topics.WorkerRunnable
getTokenString() - Method in class cc.mallet.util.CharSequenceLexer
getTokenString() - Method in interface cc.mallet.util.Lexer
getTopicAlphabet() - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
getTopicAlphabet() - Method in class cc.mallet.topics.ParallelTopicModel
getTopicAlphabet() - Method in class cc.mallet.topics.PolylingualTopicModel
getTopicAlphabet() - Method in class cc.mallet.topics.SimpleLDA
getTopicDocCounts() - Method in class cc.mallet.topics.WorkerRunnable
getTopicTotals() - Method in class cc.mallet.topics.SimpleLDA
getTopWords(int) - Method in class cc.mallet.topics.ParallelTopicModel
  Return an array (one element for each topic) of arrays of words, which are the most probable words for that topic in descending order.
getTotalMessagesSent() - Static method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
  Returns the total number of messages all BP inferencers have sent in the current Java image.
getTotalMessagesSent() - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
  Returns the total number of messages this inferencer has sent.
getTotalNodes() - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
getTotalWeight() - Method in interface cc.mallet.fst.SumLattice
getTotalWeight() - Method in class cc.mallet.fst.SumLatticeBeam
getTotalWeight() - Method in class cc.mallet.fst.SumLatticeDefault
getTotalWeight() - Method in class cc.mallet.fst.SumLatticeScaling
getTrainer() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
getTrainingData() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
getTransducer() - Method in class cc.mallet.fst.confidence.TransducerConfidenceEstimator
getTransducer() - Method in class cc.mallet.fst.CRF.State
getTransducer() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getTransducer() - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
getTransducer() - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
getTransducer() - Method in class cc.mallet.fst.CRFTrainerByValueGradients
getTransducer() - Method in class cc.mallet.fst.FeatureTransducer.State
getTransducer() - Method in class cc.mallet.fst.HMM.State
getTransducer() - Method in class cc.mallet.fst.HMMTrainerByLikelihood
getTransducer() - Method in interface cc.mallet.fst.MaxLattice
getTransducer() - Method in class cc.mallet.fst.MaxLatticeDefault
getTransducer() - Method in class cc.mallet.fst.MEMMTrainer
getTransducer() - Method in class cc.mallet.fst.NoopTransducerTrainer
getTransducer() - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByEntropyRegularization
getTransducer() - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByGE
getTransducer() - Method in class cc.mallet.fst.ShallowTransducerTrainer
  Deprecated.
getTransducer() - Method in interface cc.mallet.fst.SumLattice
getTransducer() - Method in class cc.mallet.fst.SumLatticeBeam
getTransducer() - Method in class cc.mallet.fst.SumLatticeDefault
getTransducer() - Method in class cc.mallet.fst.SumLatticeScaling
getTransducer() - Method in class cc.mallet.fst.Transducer.State
getTransducer() - Method in class cc.mallet.fst.Transducer.TransitionIterator
getTransducer() - Method in class cc.mallet.fst.TransducerTrainer
getTransitionEstimator() - Method in class cc.mallet.fst.FeatureTransducer.State
getTrimmedClassifier(int) - Method in class cc.mallet.classify.AdaBoost
  Return an AdaBoost classifier that uses only the first `numWeakClassifiersToUse` weak learners.
getTrimmedClassifier(int) - Method in class cc.mallet.classify.AdaBoostM2
  Return an AdaBoostM2 classifier that uses only the first `numWeakClassifiersToUse` weak learners.
getTruth(int) - Method in class cc.mallet.fst.Segment
getTruth() - Method in class cc.mallet.fst.Segment
getTypeTopicCounts() - Method in class cc.mallet.topics.LDA
  Deprecated.
getTypeTopicCounts() - Method in class cc.mallet.topics.MarginalProbEstimator
getTypeTopicCounts() - Method in class cc.mallet.topics.SimpleLDA
getTypeTopicCounts() - Method in class cc.mallet.topics.WorkerRunnable
getUniverse() - Method in class cc.mallet.grmm.types.Variable
getUnlabeledDataWeight() - Method in class cc.mallet.classify.NaiveBayesEMTrainer
getUnnormalizedClassificationScores(Instance, double[]) - Method in class cc.mallet.classify.MaxEnt
getUnnormalizedClassificationScores(Instance, double[]) - Method in class cc.mallet.classify.MCMaxEnt
getUnnormalizedClassificationScores(Instance, double[]) - Method in class cc.mallet.classify.RankMaxEnt
  returns unnormalized scores, corresponding to the score an element of the InstanceList being the "top" instance
getUnrolledVarSet(int) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
getUnrolledVarSet(Factor) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
getUseForwardBackwardBeam() - Method in class cc.mallet.fst.SumLatticeBeam
getUseHyperbolicPriorSharpness() - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
getUseHyperbolicPriorSharpness() - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
getUseHyperbolicPriorSharpness() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getUseHyperbolicPriorSlope() - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
getUseHyperbolicPriorSlope() - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
getUseHyperbolicPriorSlope() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getUseInertia() - Method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
getUseSparseWeights() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
getUseSparseWeights() - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
getValidationInstances() - Method in class cc.mallet.classify.ClassifierTrainer
getValue() - Method in class cc.mallet.classify.MaxEntOptimizableByGE
getValue() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
  Return the log probability of the training label distributions
getValue() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
getValue() - Method in class cc.mallet.fst.CRFOptimizableByGradientValues
  Returns the log probability of the training sequence labels and the prior over parameters.
getValue() - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
  Returns the log probability of the training sequence labels and the prior over parameters.
getValue() - Method in class cc.mallet.fst.CRFTrainerByValueGradients.OptimizableCRF
  Returns the log probability of the training sequence labels and the prior over parameters.
getValue() - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
getValue() - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
getValue() - Method in class cc.mallet.fst.ThreadedOptimizable
getValue() - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
  Returns the log probability of the training sequence labels
getValue() - Method in interface cc.mallet.optimize.Optimizable.ByGISUpdate
getValue() - Method in interface cc.mallet.optimize.Optimizable.ByGradientValue
getValue() - Method in interface cc.mallet.optimize.Optimizable.ByValue
getValue() - Method in class cc.mallet.optimize.OptimizableCollection.ByGradientValue
getValue() - Method in class cc.mallet.topics.DMROptimizable
  The log probability of the observed count vectors given the features.
getValueAtRank(int) - Method in class cc.mallet.types.Label
getValueAtRank(int) - Method in interface cc.mallet.types.Labeling
getValueAtRank(int) - Method in class cc.mallet.types.LabelVector
getValueAtRank(int) - Method in class cc.mallet.types.RankedFeatureVector
getValueCalls() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
  Counts how many times this trainer has computed the log probability of training labels.
getValueCalls() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
  Counts how many times this trainer has computed the log probability of training labels.
getValueCalls() - Method in class cc.mallet.classify.MCMaxEntTrainer
  Counts how many times this trainer has computed the log probability of training labels.
getValueGradient(double[]) - Method in class cc.mallet.classify.MaxEntOptimizableByGE
getValueGradient(double[]) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
getValueGradient(double[]) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
getValueGradient(double[]) - Method in class cc.mallet.fst.CRFOptimizableByGradientValues
getValueGradient(double[]) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
getValueGradient(double[]) - Method in class cc.mallet.fst.CRFTrainerByValueGradients.OptimizableCRF
getValueGradient(double[]) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
getValueGradient(double[]) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
getValueGradient(double[]) - Method in class cc.mallet.fst.ThreadedOptimizable
  Returns the gradient, re-computes if gradient is stale.
getValueGradient(double[]) - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
  Computes the graident of the penalized log likelihood of the ACRF, and returns it in buf[].
getValueGradient(double[]) - Method in interface cc.mallet.optimize.Optimizable.ByGradient
getValueGradient(double[]) - Method in interface cc.mallet.optimize.Optimizable.ByGradientValue
getValueGradient(double[]) - Method in class cc.mallet.optimize.OptimizableCollection.ByGradientValue
getValueGradient(double[]) - Method in class cc.mallet.topics.DMROptimizable
getValueGradientCalls() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
  Counts how many times this trainer has computed the gradient of the log probability of training labels.
getValueGradientCalls() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
  Counts how many times this trainer has computed the gradient of the log probability of training labels.
getValueGradientCalls() - Method in class cc.mallet.classify.MCMaxEntTrainer
  Counts how many times this trainer has computed the gradient of the log probability of training labels.
getValueGradientForInstance(int, double[]) - Method in interface cc.mallet.optimize.Optimizable.ByVotedPerceptron
getValueHessian(double[][]) - Method in interface cc.mallet.optimize.Optimizable.ByHessian
getValueMatrix() - Method in class cc.mallet.grmm.types.AbstractTableFactor
getValueMatrix() - Method in class cc.mallet.grmm.types.LogTableFactor
getValueMatrix() - Method in class cc.mallet.grmm.types.TableFactor
getValues() - Method in class cc.mallet.grmm.types.AbstractTableFactor
getValues() - Method in class cc.mallet.types.SparseVector
getVariable(int) - Method in class cc.mallet.grmm.types.AbstractFactor
getVariable(int) - Method in class cc.mallet.grmm.types.AbstractTableFactor
getVariable(int) - Method in class cc.mallet.grmm.types.Assignment
getVariable(int) - Method in class cc.mallet.grmm.types.CPT
getVariable(int) - Method in interface cc.mallet.grmm.types.Factor
getVariable(int) - Method in class cc.mallet.grmm.types.FactorGraph
getVars() - Method in class cc.mallet.grmm.types.Assignment
  Returns all variables which are assigned to.
getVerticesIterator() - Method in class cc.mallet.grmm.types.Tree
getViterbiInferencer() - Method in class cc.mallet.grmm.learning.ACRF
getViterbiNode(int, int) - Method in class cc.mallet.fst.MaxLatticeDefault
getWeight() - Method in class cc.mallet.fst.CRF.TransitionIterator
getWeight() - Method in class cc.mallet.fst.FeatureTransducer.TransitionIterator
getWeight() - Method in class cc.mallet.fst.HMM.TransitionIterator
getWeight() - Method in class cc.mallet.fst.semi_supervised.GECriterion
  Returns the weight (gamma) for the constraint.
getWeight() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  The weight (between infinity and -infinity) associated with taking this transition with this input/output.
getWeight() - Method in class cc.mallet.pipe.iterator.PipeInputIterator
  Deprecated.
getWeight() - Method in class cc.mallet.types.IDSorter
getWeight() - Method in class cc.mallet.types.SequencePairAlignment
getWeightNames(int) - Method in class cc.mallet.fst.CRF.State
getWeights() - Method in class cc.mallet.classify.BalancedWinnow
getWeights(String) - Method in class cc.mallet.fst.CRF
getWeights(int) - Method in class cc.mallet.fst.CRF
getWeights() - Method in class cc.mallet.fst.CRF
getWeights() - Method in class cc.mallet.grmm.learning.ACRF.FixedFactorTemplate
getWeights() - Method in class cc.mallet.grmm.learning.ACRF.Template
  Returns the weights for this clique template.
getWeightsIndex(String) - Method in class cc.mallet.fst.CRF
getWeightsName(int) - Method in class cc.mallet.fst.CRF
getWeightsStructureChangeStamp() - Method in class cc.mallet.fst.CRF
getWeightsValueChangeStamp() - Method in class cc.mallet.fst.CRF
getWidth() - Method in class cc.mallet.grmm.types.UndirectedGrid
getWorstAveragePrecision() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
  For comparison, rank segments as badly as possible (all "incorrect" before "correct").
getXiProbability(int, Transducer.State, Transducer.State) - Method in interface cc.mallet.fst.SumLattice
getXiProbability(int, Transducer.State, Transducer.State) - Method in class cc.mallet.fst.SumLatticeBeam
getXiProbability(int, Transducer.State, Transducer.State) - Method in class cc.mallet.fst.SumLatticeDefault
getXiProbability(int, Transducer.State, Transducer.State) - Method in class cc.mallet.fst.SumLatticeScaling
getXis() - Method in interface cc.mallet.fst.SumLattice
getXis() - Method in class cc.mallet.fst.SumLatticeBeam
getXis() - Method in class cc.mallet.fst.SumLatticeDefault
getXis() - Method in class cc.mallet.fst.SumLatticeScaling
getXiWeight(int, Transducer.State, Transducer.State) - Method in interface cc.mallet.fst.SumLattice
getXiWeight(int, Transducer.State, Transducer.State) - Method in class cc.mallet.fst.SumLatticeBeam
getXiWeight(int, Transducer.State, Transducer.State) - Method in class cc.mallet.fst.SumLatticeDefault
getXiWeight(int, Transducer.State, Transducer.State) - Method in class cc.mallet.fst.SumLatticeScaling
GibbsSampler - Class in cc.mallet.grmm.inference
  Created: Mar 28, 2005
GibbsSampler() - Constructor for class cc.mallet.grmm.inference.GibbsSampler
GibbsSampler(int) - Constructor for class cc.mallet.grmm.inference.GibbsSampler
GibbsSampler(Randoms, int) - Constructor for class cc.mallet.grmm.inference.GibbsSampler
globalFeatureSelection - Variable in class cc.mallet.fst.CRF
go() - Method in class cc.mallet.util.resources.wn.Examples
gradient - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
GRADIENT_GAIN - Static variable in class cc.mallet.classify.MaxEntTrainer
GRADIENT_GAIN - Static variable in class cc.mallet.classify.MCMaxEntTrainer
GradientAscent - Class in cc.mallet.optimize
GradientAscent(Optimizable.ByGradientValue) - Constructor for class cc.mallet.optimize.GradientAscent
GradientBracketLineOptimizer - Class in cc.mallet.optimize
GradientBracketLineOptimizer(Optimizable.ByGradientValue) - Constructor for class cc.mallet.optimize.GradientBracketLineOptimizer
GradientGain - Class in cc.mallet.types
GradientGain(InstanceList, LabelVector[]) - Constructor for class cc.mallet.types.GradientGain
GradientGain(InstanceList, Classification[]) - Constructor for class cc.mallet.types.GradientGain
GradientGain.Factory - Class in cc.mallet.types
GradientGain.Factory(LabelVector[]) - Constructor for class cc.mallet.types.GradientGain.Factory
Graph - Class in cc.mallet.classify.evaluate
  Framework for standard graph.
Graph(String, int, int, String, String) - Constructor for class cc.mallet.classify.evaluate.Graph
  Creates a Graph object
Graph.Legend - Class in cc.mallet.classify.evaluate
Graph.Legend() - Constructor for class cc.mallet.classify.evaluate.Graph.Legend
Graph2 - Class in cc.mallet.classify.evaluate
  Methods for a 2-D graph
Graph2(String, int, int, String, String) - Constructor for class cc.mallet.classify.evaluate.Graph2
GraphItem - Class in cc.mallet.classify.evaluate
  Holds data for a point on a graph
GraphItem(String, int, Color) - Constructor for class cc.mallet.classify.evaluate.GraphItem
Graphs - Class in cc.mallet.grmm.util
  Created: Dec 21, 2005
Graphs() - Constructor for class cc.mallet.grmm.util.Graphs
GreedyAgglomerative - Class in cc.mallet.cluster
  Greedily merges Instances until convergence.
GreedyAgglomerative(Pipe, NeighborEvaluator, double) - Constructor for class cc.mallet.cluster.GreedyAgglomerative
GreedyAgglomerativeByDensity - Class in cc.mallet.cluster
  Greedily merges Instances until convergence.
GreedyAgglomerativeByDensity(Pipe, NeighborEvaluator, double, boolean, Random) - Constructor for class cc.mallet.cluster.GreedyAgglomerativeByDensity
growIfNecessary() - Method in class cc.mallet.types.FeatureSequence
growthStopped() - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
growthStopped() - Method in class cc.mallet.types.Alphabet

## H

HALF_LOG_TWO_PI - Static variable in class cc.mallet.types.Dirichlet
hasConverged() - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
hasConverged(double) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
hasFeature(String) - Method in class cc.mallet.fst.confidence.SequenceConfidenceInstance
hashCode() - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
hashCode() - Method in class cc.mallet.grmm.types.BitVarSet
hashCode() - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
hashCode() - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
hashCode() - Method in class cc.mallet.grmm.types.HashVarSet
hashCode() - Method in class cc.mallet.grmm.types.ListVarSet
hashCode() - Method in class cc.mallet.grmm.types.PottsTableFactor
hashCode() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
hashCode() - Method in class cc.mallet.types.MultiInstanceList
HashedSparseVector - Class in cc.mallet.types
HashedSparseVector(int[], double[], int, int, boolean, boolean, boolean) - Constructor for class cc.mallet.types.HashedSparseVector
HashedSparseVector() - Constructor for class cc.mallet.types.HashedSparseVector
  Create an empty vector
HashedSparseVector(int[], double[]) - Constructor for class cc.mallet.types.HashedSparseVector
  Create non-binary vector, possibly dense if "featureIndices" or possibly sparse, if not
HashedSparseVector(int[]) - Constructor for class cc.mallet.types.HashedSparseVector
  Create binary vector
HashVarSet - Class in cc.mallet.grmm.types
  A clique is a collection of nodes in a graph that are all adjacent.
HashVarSet() - Constructor for class cc.mallet.grmm.types.HashVarSet
  Create an empty clique.
HashVarSet(Collection) - Constructor for class cc.mallet.grmm.types.HashVarSet
  Create a Clique given a Collection of nodes.
HashVarSet(Variable[]) - Constructor for class cc.mallet.grmm.types.HashVarSet
hasInfinite - Variable in class cc.mallet.types.DenseMatrix
hasInfinite - Variable in class cc.mallet.types.SparseVector
hasLabel() - Method in class cc.mallet.grmm.types.BitVarSet
hasNext() - Method in class cc.mallet.cluster.iterator.AllPairsIterator
hasNext() - Method in class cc.mallet.cluster.iterator.PairSampleIterator
hasNext() - Method in class cc.mallet.fst.CRF.TransitionIterator
hasNext() - Method in class cc.mallet.fst.FeatureTransducer.TransitionIterator
hasNext() - Method in class cc.mallet.fst.HMM.TransitionIterator
hasNext() - Method in class cc.mallet.fst.Transducer.TransitionIterator
hasNext() - Method in class cc.mallet.grmm.inference.MessageArray.Iterator
hasNext() - Method in class cc.mallet.grmm.inference.MessageArray.ToMsgsIterator
hasNext() - Method in class cc.mallet.grmm.util.PipedIterator
  Deprecated.
hasNext() - Method in class cc.mallet.pipe.iterator.ArrayDataAndTargetIterator
hasNext() - Method in class cc.mallet.pipe.iterator.ArrayIterator
hasNext() - Method in class cc.mallet.pipe.iterator.ConcatenatedInstanceIterator
hasNext() - Method in class cc.mallet.pipe.iterator.CsvIterator
hasNext() - Method in class cc.mallet.pipe.iterator.EmptyInstanceIterator
hasNext() - Method in class cc.mallet.pipe.iterator.FileIterator
hasNext() - Method in class cc.mallet.pipe.iterator.FileListIterator
hasNext() - Method in class cc.mallet.pipe.iterator.LineGroupIterator
hasNext() - Method in class cc.mallet.pipe.iterator.LineIterator
hasNext() - Method in class cc.mallet.pipe.iterator.ParenGroupIterator
hasNext() - Method in class cc.mallet.pipe.iterator.PatternMatchIterator
hasNext() - Method in class cc.mallet.pipe.iterator.PipeExtendedIterator
  Deprecated.
hasNext() - Method in class cc.mallet.pipe.iterator.PipeInputIterator
  Deprecated.
hasNext() - Method in class cc.mallet.pipe.iterator.RandomFeatureVectorIterator
hasNext() - Method in class cc.mallet.pipe.iterator.RandomTokenSequenceIterator
hasNext() - Method in class cc.mallet.pipe.iterator.SegmentIterator
hasNext() - Method in class cc.mallet.pipe.iterator.SelectiveFileLineIterator
hasNext() - Method in class cc.mallet.pipe.iterator.SimpleFileLineIterator
hasNext() - Method in class cc.mallet.pipe.iterator.StringArrayIterator
hasNext() - Method in class cc.mallet.pipe.iterator.UnlabeledFileIterator
hasNext() - Method in class cc.mallet.types.ChainedInstanceIterator
  Deprecated.
hasNext() - Method in class cc.mallet.types.CrossValidationIterator
hasNext() - Method in class cc.mallet.types.FeatureVectorSequence.Iterator
hasNext() - Method in class cc.mallet.types.InstanceList.CrossValidationIterator
hasNext() - Method in class cc.mallet.types.LabelSequence.Iterator
hasNext() - Method in class cc.mallet.types.SingleInstanceIterator
hasNext() - Method in class cc.mallet.util.CharSequenceLexer
hasNext() - Method in interface cc.mallet.util.Lexer
hasNext() - Method in class cc.mallet.util.PropertyList.Iterator
hasNext() - Method in class cc.mallet.util.search.AStar
hasNext() - Method in class cc.mallet.util.search.SearchNode.NextNodeIterator
hasNext() - Method in class cc.mallet.util.search.SearchState.NextStateIterator
hasProperty(String) - Method in class cc.mallet.types.Instance
hasProperty(String) - Method in interface cc.mallet.types.PropertyHolder
hasProperty(String) - Method in class cc.mallet.types.Token
hasProperty(String) - Method in class cc.mallet.types.TokenSequence
hasProperty(String) - Method in class cc.mallet.util.PropertyList
hideSomeLabels(double, Randoms) - Method in class cc.mallet.types.InstanceList
hideSomeLabels(BitSet) - Method in class cc.mallet.types.InstanceList
HierarchicalLDA - Class in cc.mallet.topics
HierarchicalLDA() - Constructor for class cc.mallet.topics.HierarchicalLDA
HierarchicalLDATUI - Class in cc.mallet.topics.tui
HierarchicalLDATUI() - Constructor for class cc.mallet.topics.tui.HierarchicalLDATUI
HierarchicalPAM - Class in cc.mallet.topics
  Hierarchical PAM, where each node in the DAG has a distribution over all topics on the next level and one additional "node-specific" topic.
HierarchicalPAM(int, int, double, double) - Constructor for class cc.mallet.topics.HierarchicalPAM
HierarchicalTokenizationFilter - Class in cc.mallet.extract
  Tokenization filter that will create nested spans based on a hierarchical labeling of the data.
HierarchicalTokenizationFilter() - Constructor for class cc.mallet.extract.HierarchicalTokenizationFilter
HierarchicalTokenizationFilter(Pattern) - Constructor for class cc.mallet.extract.HierarchicalTokenizationFilter
HillClimbingClusterer - Class in cc.mallet.cluster
  A Clusterer that iteratively improves a predicted Clustering using a `NeighborEvaluator`.
HillClimbingClusterer(Pipe, NeighborEvaluator) - Constructor for class cc.mallet.cluster.HillClimbingClusterer
HMM - Class in cc.mallet.fst
  A Hidden Markov Model.
HMM(Pipe, Pipe) - Constructor for class cc.mallet.fst.HMM
HMM(Alphabet, Alphabet) - Constructor for class cc.mallet.fst.HMM
HMM.Incrementor - Class in cc.mallet.fst
HMM.Incrementor() - Constructor for class cc.mallet.fst.HMM.Incrementor
HMM.State - Class in cc.mallet.fst
HMM.State() - Constructor for class cc.mallet.fst.HMM.State
HMM.State(String, int, double, double, String[], String[], HMM) - Constructor for class cc.mallet.fst.HMM.State
HMM.TransitionIterator - Class in cc.mallet.fst
HMM.TransitionIterator(HMM.State, FeatureSequence, int, String, HMM) - Constructor for class cc.mallet.fst.HMM.TransitionIterator
HMM.WeightedIncrementor - Class in cc.mallet.fst
HMM.WeightedIncrementor(double) - Constructor for class cc.mallet.fst.HMM.WeightedIncrementor
HMMTrainerByLikelihood - Class in cc.mallet.fst
HMMTrainerByLikelihood(HMM) - Constructor for class cc.mallet.fst.HMMTrainerByLikelihood
hyberbolicPrior(double, double) - Method in class cc.mallet.fst.CRF.Factors
  Return the log(p(parameters)) according to a a hyperbolic curve that is a smooth approximation to an L1 prior.

## I

IDSorter - Class in cc.mallet.types
  This class is contains a comparator for use in sorting integers that have associated floating point values.
IDSorter(int, double) - Constructor for class cc.mallet.types.IDSorter
IDSorter(int, int) - Constructor for class cc.mallet.types.IDSorter
idx2obj(int) - Method in class cc.mallet.grmm.inference.MessageArray
ignoreTestNumMessages() - Method in class cc.mallet.grmm.test.TestInference
ignoreTestSerialization() - Method in class cc.mallet.grmm.test.TestLogTableFactor
ignoreTestSerialization() - Method in class cc.mallet.grmm.test.TestTableFactor
IMPOSSIBLE_WEIGHT - Static variable in class cc.mallet.fst.Transducer
improveClustering(Clustering) - Method in class cc.mallet.cluster.GreedyAgglomerative
  For each pair of clusters, calculate the score of the `Neighbor` that would result from merging the two clusters.
improveClustering(Clustering) - Method in class cc.mallet.cluster.GreedyAgglomerativeByDensity
improveClustering(Clustering) - Method in class cc.mallet.cluster.HillClimbingClusterer
incIter() - Method in class cc.mallet.fst.SumLatticeBeam
increment(int) - Static method in class cc.mallet.grmm.util.Flops
increment(Object) - Method in class cc.mallet.types.FeatureCounter
increment(Object, int) - Method in class cc.mallet.types.FeatureCounter
increment(int) - Method in class cc.mallet.types.FeatureCounter
increment(int, int) - Method in class cc.mallet.types.FeatureCounter
increment(int, double) - Method in class cc.mallet.types.Multinomial.Estimator
increment(String, double) - Method in class cc.mallet.types.Multinomial.Estimator
increment(FeatureSequence, double) - Method in class cc.mallet.types.Multinomial.Estimator
increment(FeatureSequence) - Method in class cc.mallet.types.Multinomial.Estimator
increment(FeatureVector, double) - Method in class cc.mallet.types.Multinomial.Estimator
increment(FeatureVector) - Method in class cc.mallet.types.Multinomial.Estimator
incrementalTrain(ACRF, InstanceList, InstanceList, InstanceList, int) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
incrementalTrain(ACRF, InstanceList, InstanceList, InstanceList, ACRFEvaluator, int) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
incrementCount(double) - Method in class cc.mallet.fst.FeatureTransducer.TransitionIterator
incrementCounts(Sequence, Sequence) - Method in class cc.mallet.grmm.learning.MultiSegmentationEvaluatorACRF.TestResults
incrementFinalCount(double) - Method in class cc.mallet.fst.FeatureTransducer.State
incrementFinalCount(double) - Method in class cc.mallet.fst.HMM.State
incrementFinalState(Transducer.State, double) - Method in class cc.mallet.fst.CRF.Factors.Incrementor
incrementFinalState(Transducer.State, double) - Method in class cc.mallet.fst.CRF.Factors.WeightedIncrementor
incrementFinalState(Transducer.State, double) - Method in class cc.mallet.fst.HMM.Incrementor
incrementFinalState(Transducer.State, double) - Method in class cc.mallet.fst.HMM.WeightedIncrementor
incrementFinalState(Transducer.State, double) - Method in interface cc.mallet.fst.Transducer.Incrementor
incrementInitialCount(double) - Method in class cc.mallet.fst.FeatureTransducer.State
incrementInitialCount(double) - Method in class cc.mallet.fst.HMM.State
incrementInitialState(Transducer.State, double) - Method in class cc.mallet.fst.CRF.Factors.Incrementor
incrementInitialState(Transducer.State, double) - Method in class cc.mallet.fst.CRF.Factors.WeightedIncrementor
incrementInitialState(Transducer.State, double) - Method in class cc.mallet.fst.HMM.Incrementor
incrementInitialState(Transducer.State, double) - Method in class cc.mallet.fst.HMM.WeightedIncrementor
incrementInitialState(Transducer.State, double) - Method in interface cc.mallet.fst.Transducer.Incrementor
incrementor - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
incrementor - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
incrementSingleValue(int, double) - Method in class cc.mallet.types.DenseMatrix
incrementSingleValue(int, double) - Method in interface cc.mallet.types.Matrix
incrementSingleValue(int, double) - Method in class cc.mallet.types.SparseMatrixn
incrementTransducer(Transducer.Incrementor) - Method in class cc.mallet.fst.MaxLatticeDefault
  Increment states and transitions with a count of 1.0 along the best state sequence.
incrementTransition(Transducer.TransitionIterator, double) - Method in class cc.mallet.fst.CRF.Factors.Incrementor
incrementTransition(Transducer.TransitionIterator, double) - Method in class cc.mallet.fst.CRF.Factors.WeightedIncrementor
incrementTransition(Transducer.TransitionIterator, double) - Method in class cc.mallet.fst.HMM.Incrementor
incrementTransition(Transducer.TransitionIterator, double) - Method in class cc.mallet.fst.HMM.WeightedIncrementor
incrementTransition(Transducer.TransitionIterator, double) - Method in interface cc.mallet.fst.Transducer.Incrementor
incrementValue(int, double) - Method in class cc.mallet.types.SparseVector
  Increments this[index] by value.
index - Variable in class cc.mallet.grmm.learning.ACRF.Template
indexAtLocation(int) - Method in class cc.mallet.grmm.types.AbstractTableFactor
indexAtLocation(int) - Method in class cc.mallet.grmm.types.CPT
indexAtLocation(int) - Method in interface cc.mallet.grmm.types.DiscreteFactor
indexAtLocation(int) - Method in class cc.mallet.types.AugmentableFeatureVector
indexAtLocation(int) - Method in interface cc.mallet.types.ConstantMatrix
indexAtLocation(int) - Method in class cc.mallet.types.DenseMatrix
indexAtLocation(int) - Method in class cc.mallet.types.Label
indexAtLocation(int) - Method in interface cc.mallet.types.Labeling
indexAtLocation(int) - Method in class cc.mallet.types.SparseMatrixn
indexAtLocation(int) - Method in class cc.mallet.types.SparseVector
IndexedSparseVector - Class in cc.mallet.types
IndexedSparseVector(int[], double[], int, int, boolean, boolean, boolean) - Constructor for class cc.mallet.types.IndexedSparseVector
IndexedSparseVector() - Constructor for class cc.mallet.types.IndexedSparseVector
  Create an empty vector
IndexedSparseVector(int[], double[]) - Constructor for class cc.mallet.types.IndexedSparseVector
  Create non-binary vector, possibly dense if "featureIndices" or possibly sparse, if not
IndexedSparseVector(int[]) - Constructor for class cc.mallet.types.IndexedSparseVector
  Create binary vector
indexInSegment(int) - Method in class cc.mallet.fst.Segment
indexOf(Object) - Method in class cc.mallet.types.MultiInstanceList
indexOf(Object[], Object) - Static method in class cc.mallet.util.ArrayUtils
indexOf(int[], int) - Static method in class cc.mallet.util.ArrayUtils
indexOf(double) - Method in class cc.mallet.util.Univariate
indexOfCurrentAssn() - Method in interface cc.mallet.grmm.types.AssignmentIterator
indexVector() - Method in class cc.mallet.types.HashedSparseVector
indexVector() - Method in class cc.mallet.types.IndexedSparseVector
indices - Variable in class cc.mallet.types.SparseVector
  If the vector is sparse, then both indices and values are sparse.
induceFeatures(InstanceList, boolean, boolean) - Method in class cc.mallet.classify.DecisionTree
induceFeatures(AugmentableFeatureVector, FeatureSelection, FeatureSelection[], FeatureSelection, FeatureSelection[], boolean, boolean, double) - Method in class cc.mallet.classify.DecisionTree.Node
induceFeaturesFor(InstanceList) - Method in class cc.mallet.fst.CRF
  When the CRF has done feature induction, these new feature conjunctions must be created in the test or validation data in order for them to take effect.
induceFeaturesFor(InstanceList, boolean, boolean) - Method in class cc.mallet.types.FeatureInducer
inference(int) - Method in class cc.mallet.topics.LDAStream
inferenceAll(int) - Method in class cc.mallet.topics.LDAStream
inferenceOneByOne(int) - Method in class cc.mallet.topics.LDAStream
Inferencer - Interface in cc.mallet.grmm.inference
  Interface implemented by all inferencers, which are algorithms for computing (perhaps approximately) marginal distributions over nodes in the model.
inferencer - Variable in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
inferenceWithTheta(int, InstanceList) - Method in class cc.mallet.topics.LDAStream
InferTopics - Class in cc.mallet.topics.tui
InferTopics() - Constructor for class cc.mallet.topics.tui.InferTopics
infiniteValues - Variable in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
infiniteValues - Variable in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
infinityNorm() - Method in class cc.mallet.types.AugmentableFeatureVector
infinityNorm() - Method in interface cc.mallet.types.ConstantMatrix
infinityNorm() - Method in class cc.mallet.types.DenseMatrix
infinityNorm(double[]) - Static method in class cc.mallet.types.DenseMatrix
infinityNorm(double[]) - Static method in class cc.mallet.types.MatrixOps
infinityNorm() - Method in class cc.mallet.types.SparseMatrixn
infinityNorm() - Method in class cc.mallet.types.SparseVector
infinityNormalize() - Method in class cc.mallet.types.DenseMatrix
infinityNormalize() - Method in interface cc.mallet.types.Matrix
infinityNormalize() - Method in class cc.mallet.types.SparseMatrixn
InfoGain - Class in cc.mallet.types
InfoGain(InstanceList) - Constructor for class cc.mallet.types.InfoGain
InfoGain(Alphabet, double[]) - Constructor for class cc.mallet.types.InfoGain
InfoGain.Factory - Class in cc.mallet.types
InfoGain.Factory() - Constructor for class cc.mallet.types.InfoGain.Factory
INFORMATION_GAIN - Static variable in class cc.mallet.classify.MaxEntTrainer
INFORMATION_GAIN - Static variable in class cc.mallet.classify.MCMaxEntTrainer
initEmissions(Random, double) - Method in class cc.mallet.fst.HMM
initForGraph(FactorGraph) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
initForGraph(FactorGraph) - Method in class cc.mallet.grmm.inference.TreeBP
initForGraph(FactorGraph) - Method in class cc.mallet.grmm.inference.TRP
initialize(Map<Integer, SumLattice>) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
  Initializes the gradient to zero and re-computes expectations for a new iteration.
initialize(InstanceList, InstanceList, int, Randoms) - Method in class cc.mallet.topics.HierarchicalLDA
initialize() - Method in class cc.mallet.topics.MultinomialHMM
initializeAlphaStatistics(int) - Method in class cc.mallet.topics.WorkerRunnable
initializeClustering(InstanceList) - Method in class cc.mallet.cluster.GreedyAgglomerative
initializeClustering(InstanceList) - Method in class cc.mallet.cluster.HillClimbingClusterer
initializeFromState(File) - Method in class cc.mallet.topics.ParallelTopicModel
initializeHistogramsAndCachedValues() - Method in class cc.mallet.topics.LDAHyper
  Deprecated. Gather statistics on the size of documents and create histograms for use in Dirichlet hyperparameter optimization.
initialStateIterator() - Method in class cc.mallet.fst.CRF
initialStateIterator() - Method in class cc.mallet.fst.FeatureTransducer
initialStateIterator() - Method in class cc.mallet.fst.HMM
initialStateIterator() - Method in class cc.mallet.fst.Transducer
initialStates - Variable in class cc.mallet.fst.CRF
initialWeights - Variable in class cc.mallet.fst.CRF.Factors
initTransitions(Random, double) - Method in class cc.mallet.fst.HMM
  Separate initialization of initial/transitions and emissions.
initWeights(InstanceList) - Method in class cc.mallet.grmm.learning.ACRF.FixedFactorTemplate
initWeights(InstanceList) - Method in class cc.mallet.grmm.learning.ACRF.Template
  Initializes the weight vectors to the appropriate size for a set of training data.
input - Variable in class cc.mallet.types.SequencePair
input() - Method in class cc.mallet.types.SequencePair
Input2CharSequence - Class in cc.mallet.pipe
  Pipe that can read from various kinds of text sources (either URI, File, or Reader) into a CharSequence
Input2CharSequence() - Constructor for class cc.mallet.pipe.Input2CharSequence
Input2CharSequence(String) - Constructor for class cc.mallet.pipe.Input2CharSequence
inputAlphabet - Variable in class cc.mallet.fst.CRF
inputLength - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice
inputPipe - Variable in class cc.mallet.fst.Transducer
  A pipe that should produce a Sequence in the "data" slot, (and possibly one in the "target" slot also
insert(QueueElement) - Method in class cc.mallet.util.search.MinHeap
insert(QueueElement) - Method in interface cc.mallet.util.search.PriorityQueue
  Insert element `e` into the queue.
instance - Variable in class cc.mallet.topics.LDAHyper.Topication
  Deprecated.
instance - Variable in class cc.mallet.topics.TopicAssignment
Instance - Class in cc.mallet.types
  A machine learning "example" to be used in training, testing or performance of various machine learning algorithms.
Instance(Object, Object, Object, Object) - Constructor for class cc.mallet.types.Instance
  In certain unusual circumstances, you might want to create an Instance without sending it through a pipe.
InstanceAccuracyEvaluator - Class in cc.mallet.fst
  Reports the percentage of instances for which the entire predicted sequence was correct.
InstanceAccuracyEvaluator() - Constructor for class cc.mallet.fst.InstanceAccuracyEvaluator
instanceFrom(Instance) - Method in class cc.mallet.pipe.Pipe
instanceLength(Instance) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
InstanceList - Class in cc.mallet.types
  A list of machine learning instances, typically used for training or testing of a machine learning algorithm.
InstanceList(Pipe, int) - Constructor for class cc.mallet.types.InstanceList
  Construct an InstanceList having given capacity, with given default pipe.
InstanceList(Pipe) - Constructor for class cc.mallet.types.InstanceList
  Construct an InstanceList with initial capacity of 10, with given default pipe.
InstanceList(Alphabet, Alphabet) - Constructor for class cc.mallet.types.InstanceList
  Construct an InstanceList with initial capacity of 10, with a Noop default pipe.
InstanceList() - Constructor for class cc.mallet.types.InstanceList
  Deprecated.
InstanceList(Randoms, Dirichlet, double, double, double, double, String[]) - Constructor for class cc.mallet.types.InstanceList
  Creates a list consisting of randomly-generated `FeatureVector`s.
InstanceList(Randoms, Alphabet, String[], int) - Constructor for class cc.mallet.types.InstanceList
InstanceList(Randoms, int, int) - Constructor for class cc.mallet.types.InstanceList
InstanceList.CrossValidationIterator - Class in cc.mallet.types
  `CrossValidationIterator` allows iterating over pairs of `InstanceList`, where each pair is split into training/testing based on nfolds.
InstanceList.CrossValidationIterator(int, int) - Constructor for class cc.mallet.types.InstanceList.CrossValidationIterator
InstanceList.CrossValidationIterator(int) - Constructor for class cc.mallet.types.InstanceList.CrossValidationIterator
instanceListDescriptions - Variable in class cc.mallet.fst.TransducerEvaluator
instanceLists - Variable in class cc.mallet.fst.TransducerEvaluator
InstanceListTrimFeaturesByCount - Class in cc.mallet.pipe
  Unimplemented.
InstanceListTrimFeaturesByCount(int) - Constructor for class cc.mallet.pipe.InstanceListTrimFeaturesByCount
InstanceListTUI - Class in cc.mallet.types
InstanceListTUI() - Constructor for class cc.mallet.types.InstanceListTUI
instancePipe - Variable in class cc.mallet.classify.Classifier
instances - Variable in class cc.mallet.cluster.Clustering
instances - Variable in class cc.mallet.cluster.iterator.PairSampleIterator
instances - Variable in class cc.mallet.topics.PolylingualTopicModel.TopicAssignment
instancesFrom(Iterator<Instance>) - Method in class cc.mallet.pipe.Pipe
  A convenience method that will pull all instances from source through this pipe, and return the results as an array.
instancesFrom(Instance) - Method in class cc.mallet.pipe.Pipe
InstanceWithConfidence - Class in cc.mallet.fst.confidence
  Helper class to store confidence of an Instance.
InstanceWithConfidence(Instance, double, Sequence) - Constructor for class cc.mallet.fst.confidence.InstanceWithConfidence
InstanceWithConfidence(Instance, double, boolean) - Constructor for class cc.mallet.fst.confidence.InstanceWithConfidence
INTEGER_COUNT - Static variable in class cc.mallet.pipe.tsf.CountMatches
intersection(Span) - Method in class cc.mallet.extract.LabeledSpan
intersection(Span) - Method in interface cc.mallet.extract.Span
  Returns a new span that is the intersection of this span and another.
intersection(Span) - Method in class cc.mallet.extract.StringSpan
intersection(VarSet) - Method in class cc.mallet.grmm.types.BitVarSet
intersection(VarSet) - Method in class cc.mallet.grmm.types.HashVarSet
  Returns the intersection of two cliques.
intersection(VarSet) - Method in class cc.mallet.grmm.types.ListVarSet
intersection(VarSet) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
intersection(VarSet) - Method in interface cc.mallet.grmm.types.VarSet
  Returns the intersection of two cliques.
intersection(Collection, Collection) - Static method in class cc.mallet.util.CollectionUtils
  Computes a nondestructive intersection of two collections.
intersectionSize(BitVarSet) - Method in class cc.mallet.grmm.types.BitVarSet
  Returns the number of variables in the intersection between this clique and other.
intersects(Span) - Method in class cc.mallet.extract.LabeledSpan
intersects(Span) - Method in interface cc.mallet.extract.Span
intersects(Span) - Method in class cc.mallet.extract.StringSpan
InvalidOptimizableException - Exception in cc.mallet.optimize
  Exception thrown by optimization algorithms, when the problem is usually due to a problem with the given Maximizable instance.
InvalidOptimizableException() - Constructor for exception cc.mallet.optimize.InvalidOptimizableException
InvalidOptimizableException(String) - Constructor for exception cc.mallet.optimize.InvalidOptimizableException
InvalidOptimizableException(String, Throwable) - Constructor for exception cc.mallet.optimize.InvalidOptimizableException
InvalidOptimizableException(Throwable) - Constructor for exception cc.mallet.optimize.InvalidOptimizableException
InvertedIndex - Class in cc.mallet.types
InvertedIndex(InstanceList) - Constructor for class cc.mallet.types.InvertedIndex
invertLowerTriangular(double[], int) - Static method in class cc.mallet.util.MVNormal
  This method returns the (lower-triangular) inverse of a lower triangular matrix.
invertSPD(double[], int) - Static method in class cc.mallet.util.MVNormal
IoUtils - Class in cc.mallet.util
IoUtils() - Constructor for class cc.mallet.util.IoUtils
ip - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice.LatticeNode
isAdjacent(Variable, Variable) - Method in class cc.mallet.grmm.types.FactorGraph
  Returns whether two variables are adjacent in the model's graph.
isBackground() - Method in class cc.mallet.extract.LabeledSpan
isBinary() - Method in class cc.mallet.types.SparseVector
isCacheUnrolledGraphs() - Method in class cc.mallet.grmm.learning.ACRF
isConnected(Variable, Variable) - Method in class cc.mallet.grmm.types.UndirectedModel
isContinuous() - Method in class cc.mallet.grmm.types.Variable
isConverged() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
isConverged() - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
isConverged() - Method in class cc.mallet.fst.CRFTrainerByValueGradients
  Returns true if training converged, false otherwise.
isConverged() - Method in class cc.mallet.grmm.inference.TRP
isConverged() - Method in class cc.mallet.optimize.AGIS
isConverged() - Method in class cc.mallet.optimize.ConjugateGradient
isConverged() - Method in class cc.mallet.optimize.GradientAscent
isConverged() - Method in class cc.mallet.optimize.LimitedMemoryBFGS
isConverged() - Method in interface cc.mallet.optimize.Optimizer
isConverged() - Method in class cc.mallet.optimize.OrthantWiseLimitedMemoryBFGS
isDataAlphabetSet() - Method in class cc.mallet.pipe.Pipe
isDistinguishEndpts() - Method in class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
isDoSizeScale() - Method in class cc.mallet.grmm.learning.ACRF
isEmpty() - Method in class cc.mallet.grmm.types.BitVarSet
isEmpty() - Method in class cc.mallet.grmm.types.HashVarSet
isEmpty() - Method in class cc.mallet.grmm.types.ListVarSet
isEmpty() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
isEmpty() - Method in class cc.mallet.types.MultiInstanceList
isExcludeAdjacent() - Method in class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
isFinal() - Method in class cc.mallet.util.search.SearchNode
  Is the node's state final?
isFinal() - Method in interface cc.mallet.util.search.SearchState
  Is this state final?
isFinishedTraining() - Method in class cc.mallet.classify.ClassifierTrainer
isFinishedTraining() - Method in class cc.mallet.classify.DecisionTreeTrainer
isFinishedTraining() - Method in class cc.mallet.classify.NaiveBayesEMTrainer
isFinishedTraining() - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
isFinishedTraining() - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
isFinishedTraining() - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
isFinishedTraining() - Method in class cc.mallet.fst.CRFTrainerByValueGradients
  Returns true if training converged, false otherwise.
isFinishedTraining() - Method in class cc.mallet.fst.HMMTrainerByLikelihood
isFinishedTraining() - Method in class cc.mallet.fst.MEMMTrainer
isFinishedTraining() - Method in class cc.mallet.fst.NoopTransducerTrainer
isFinishedTraining() - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByEntropyRegularization
isFinishedTraining() - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByGE
isFinishedTraining() - Method in class cc.mallet.fst.ShallowTransducerTrainer
  Deprecated.
isFinishedTraining() - Method in class cc.mallet.fst.TransducerTrainer
isGenerative() - Method in class cc.mallet.fst.Transducer
  If true, this is a "generative transducer".
isGradientStale() - Method in interface cc.mallet.fst.CacheStaleIndicator
isGradientStale() - Method in class cc.mallet.fst.CRFCacheStaleIndicator
  Returns true if the gradient is stale, also updates the cacheGradientStamp.
isInfinite(double[]) - Static method in class cc.mallet.types.MatrixOps
isInfinite() - Method in class cc.mallet.types.SparseVector
isInLexicon(String) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
isInLogSpace() - Method in class cc.mallet.grmm.inference.MessageArray
isInLogSpace() - Method in class cc.mallet.grmm.types.AbstractFactor
isLabelsAtEnd() - Method in class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
isLeaf() - Method in class cc.mallet.classify.C45.Node
isLeaf() - Method in class cc.mallet.classify.DecisionTree.Node
isLeaf(Object) - Method in class cc.mallet.grmm.types.Tree
isLocked() - Method in class cc.mallet.types.Instance
isNaN() - Method in class cc.mallet.grmm.inference.JunctionTree
isNaN() - Method in class cc.mallet.grmm.types.AbstractTableFactor
isNaN() - Method in class cc.mallet.grmm.types.Assignment
isNaN() - Method in class cc.mallet.grmm.types.BetaFactor
isNaN() - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
isNaN() - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
isNaN() - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
isNaN() - Method in class cc.mallet.grmm.types.ConstantFactor
isNaN() - Method in class cc.mallet.grmm.types.CPT
isNaN() - Method in interface cc.mallet.grmm.types.Factor
isNaN() - Method in class cc.mallet.grmm.types.FactorGraph
isNaN() - Method in class cc.mallet.grmm.types.NormalFactor
isNaN() - Method in class cc.mallet.grmm.types.PottsTableFactor
isNaN() - Method in class cc.mallet.grmm.types.SkeletonFactor
isNaN() - Method in class cc.mallet.grmm.types.UniformFactor
isNaN() - Method in class cc.mallet.grmm.types.UniNormalFactor
isNaN() - Method in interface cc.mallet.types.ConstantMatrix
isNaN() - Method in class cc.mallet.types.DenseMatrix
isNaN(double[]) - Static method in class cc.mallet.types.MatrixOps
isNaN() - Method in class cc.mallet.types.SparseMatrixn
isNaN() - Method in class cc.mallet.types.SparseVector
isNaNOrInfinite(double[]) - Static method in class cc.mallet.types.MatrixOps
isNaNOrInfinite() - Method in class cc.mallet.types.SparseVector
isNonZero(double[]) - Static method in class cc.mallet.types.MatrixOps
isNumeric() - Method in class cc.mallet.util.PropertyList.Iterator
IsolatedSegmentTransducerCorrector - Class in cc.mallet.fst.confidence
  Corrects a subset of the `Segment`s produced by a `Transducer`.
IsolatedSegmentTransducerCorrector(TransducerConfidenceEstimator, Transducer) - Constructor for class cc.mallet.fst.confidence.IsolatedSegmentTransducerCorrector
IsolatedSegmentTransducerCorrector(Transducer) - Constructor for class cc.mallet.fst.confidence.IsolatedSegmentTransducerCorrector
isOneToOneMapping() - Method in class cc.mallet.fst.semi_supervised.StateLabelMap
  Returns `true` if there is a one-to-one mapping between the states and labels and `false` otherwise.
isPresent1(String) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
isPresent2(String) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
isPresentInString1(String) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
isPresentInString2(String) - Method in class cc.mallet.types.StringEditFeatureVectorSequence
isRethrowExceptions() - Static method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
isRoot() - Method in class cc.mallet.classify.C45.Node
isRoot() - Method in class cc.mallet.classify.DecisionTree.Node
isRoot(Object) - Method in class cc.mallet.grmm.types.Tree
isSubspan(Span) - Method in class cc.mallet.extract.LabeledSpan
isSubspan(Span) - Method in interface cc.mallet.extract.Span
isSubspan(Span) - Method in class cc.mallet.extract.StringSpan
isSupportedOnly() - Method in class cc.mallet.grmm.learning.ACRF.Template
isTagAllTimesteps() - Method in class cc.mallet.pipe.tsf.OffsetFeatureConjunction
isTargetProcessing() - Method in class cc.mallet.pipe.Pipe
  Return true iff this pipe expects and processes information in the `target` slot.
isTrainable() - Method in class cc.mallet.fst.CRF
isTrainable() - Method in class cc.mallet.fst.FeatureTransducer
isTrainable() - Method in class cc.mallet.fst.HMM
isTrainable() - Method in class cc.mallet.grmm.learning.ACRF.FixedFactorTemplate
isTrainable() - Method in class cc.mallet.grmm.learning.ACRF.Template
isUnsupportedWeightsAdded() - Method in class cc.mallet.grmm.learning.ACRF.Template
isValidConjunction(int[]) - Static method in class cc.mallet.types.FeatureConjunction
isValue(String) - Method in class cc.mallet.extract.Field
  Returns true if `filler` is an exact match to one of the values of this field.
isValue(String, FieldComparator) - Method in class cc.mallet.extract.Field
isValueStale() - Method in interface cc.mallet.fst.CacheStaleIndicator
isValueStale() - Method in class cc.mallet.fst.CRFCacheStaleIndicator
  Returns true if the value is stale, also updates the cacheValueStamp.
isWeightsFrozen(int) - Method in class cc.mallet.fst.CRF
isZero(double[]) - Static method in class cc.mallet.types.MatrixOps
iterationCount - Variable in class cc.mallet.fst.CRFTrainerByStochasticGradient
iterationsSoFar - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
iterationsSoFar - Variable in class cc.mallet.topics.PolylingualTopicModel
iterationsUsed() - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
iterationsUsed() - Method in class cc.mallet.grmm.inference.ResidualBP
iterator() - Method in class cc.mallet.grmm.inference.MessageArray
iterator() - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
iterator() - Method in class cc.mallet.grmm.types.BitVarSet
iterator() - Method in class cc.mallet.grmm.types.HashVarSet
iterator() - Method in class cc.mallet.grmm.types.ListVarSet
iterator() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
iterator() - Method in class cc.mallet.types.Alphabet
iterator() - Method in class cc.mallet.types.FeatureVectorSequence
iterator() - Method in class cc.mallet.types.LabelSequence
iterator() - Method in class cc.mallet.types.MultiInstanceList
iterator() - Method in class cc.mallet.util.PropertyList
iterUsed - Variable in class cc.mallet.grmm.inference.AbstractBeliefPropagation

## J

jensenShannonDivergence(double[], double[]) - Static method in class cc.mallet.util.Maths
  Returns the Jensen-Shannon divergence.
joint(FactorGraph) - Method in class cc.mallet.grmm.inference.BruteForceInferencer
joint(JunctionTree) - Method in class cc.mallet.grmm.inference.BruteForceInferencer
jtCurrent - Variable in class cc.mallet.grmm.inference.JunctionTreeInferencer
JunctionTree - Class in cc.mallet.grmm.inference
  Datastructure for a junction tree.
JunctionTree(int) - Constructor for class cc.mallet.grmm.inference.JunctionTree
JunctionTreeInferencer - Class in cc.mallet.grmm.inference
  Does inference in general graphical models using the Hugin junction tree algorithm.
JunctionTreeInferencer() - Constructor for class cc.mallet.grmm.inference.JunctionTreeInferencer
JunctionTreeInferencer(JunctionTreePropagation) - Constructor for class cc.mallet.grmm.inference.JunctionTreeInferencer

## K

K(String, String) - Method in class cc.mallet.types.StringKernel
  Computes the normalized string kernel between two strings.
KBestClusterer - Class in cc.mallet.cluster
  Return the K best predicted Clusterings
KBestClusterer(Pipe) - Constructor for class cc.mallet.cluster.KBestClusterer
key - Variable in class cc.mallet.util.PropertyList
keys1() - Method in class cc.mallet.grmm.util.MIntInt2ObjectMap
  Returns an array of first-level keys.
keys2(int) - Method in class cc.mallet.grmm.util.MIntInt2ObjectMap
Kikuchi4SquareRegionGenerator - Class in cc.mallet.grmm.inference.gbp
  Created: May 31, 2005
Kikuchi4SquareRegionGenerator() - Constructor for class cc.mallet.grmm.inference.gbp.Kikuchi4SquareRegionGenerator
KL(AbstractTableFactor, AbstractTableFactor) - Static method in class cc.mallet.grmm.types.Factors
KL(FactorGraph, FactorGraph) - Static method in class cc.mallet.grmm.util.Models
  Computes the KL divergence `KL(mdl1||mdl2)`.
klDivergence(double[], double[]) - Static method in class cc.mallet.util.Maths
  Returns the KL divergence, K(p1 || p2).
KLGain - Class in cc.mallet.types
KLGain(InstanceList, LabelVector[]) - Constructor for class cc.mallet.types.KLGain
KLGain(InstanceList, Classification[]) - Constructor for class cc.mallet.types.KLGain
KMeans - Class in cc.mallet.cluster
  KMeans Clusterer Clusters the points into k clusters by minimizing the total intra-cluster variance.
KMeans(Pipe, int, Metric, int) - Constructor for class cc.mallet.cluster.KMeans
  Construct a KMeans object
KMeans(Pipe, int, Metric) - Constructor for class cc.mallet.cluster.KMeans
  Construct a KMeans object

## L

l1Distance(AbstractTableFactor, AbstractTableFactor) - Static method in class cc.mallet.grmm.types.Factors
label(Instance) - Method in class cc.mallet.fst.Transducer
  Take input sequence from instance.data and put the output sequence in instance.target.
Label - Class in cc.mallet.types
Label() - Constructor for class cc.mallet.types.Label
label(Instance) - Method in interface cc.mallet.types.Labeler
  Given the (presumably unlabeled) instanceToLabel, set its target field to the true label.
LabelAlphabet - Class in cc.mallet.types
  A mapping from arbitrary objects (usually String's) to integers (and corresponding Label objects) and back.
LabelAlphabet() - Constructor for class cc.mallet.types.LabelAlphabet
labelAlphabetOfSize(int) - Static method in class cc.mallet.types.AlphabetFactory
  Create a dummy label alphabet with `n` dimensions
labelAtLocation(int) - Method in class cc.mallet.types.Label
labelAtLocation(int) - Method in interface cc.mallet.types.Labeling
labelAtLocation(int) - Method in class cc.mallet.types.LabelVector
LabelDistributionEvaluator - Class in cc.mallet.fst
  Prints predicted and true label distribution.
LabelDistributionEvaluator(InstanceList[], String[]) - Constructor for class cc.mallet.fst.LabelDistributionEvaluator
LabeledSpan - Class in cc.mallet.extract
  Created: Oct 12, 2004
LabeledSpan(Span, Label, boolean) - Constructor for class cc.mallet.extract.LabeledSpan
LabeledSpan(Span, Label, boolean, double) - Constructor for class cc.mallet.extract.LabeledSpan
LabeledSpans - Class in cc.mallet.extract
  Created: Oct 31, 2004
LabeledSpans(Object) - Constructor for class cc.mallet.extract.LabeledSpans
Labeler - Interface in cc.mallet.types
labelExpExecutor - Variable in class cc.mallet.fst.semi_supervised.GECriteria
labelFeatures(InstanceList, ArrayList<Integer>) - Static method in class cc.mallet.classify.FeatureConstraintUtil
  Label features using heuristic described in "Learning from Labeled Features using Generalized Expectation Criteria" Gregory Druck, Gideon Mann, Andrew McCallum.
Labeling - Interface in cc.mallet.types
  A distribution over possible labels for an instance.
Labelings - Class in cc.mallet.types
  A collection of labelings, either for a multi-label problem (all labels are part of the same label dictionary), or a factorized labeling, (each label is part of a different dictionary).
Labelings(Labeling[]) - Constructor for class cc.mallet.types.Labelings
labelLogLikelihood(InstanceList) - Method in class cc.mallet.classify.NaiveBayes
labelOfVar(Variable) - Method in class cc.mallet.grmm.util.LabelsAssignment
labels - Variable in class cc.mallet.cluster.Clustering
labels - Static variable in class cc.mallet.share.weili.ner.enron.EnronMessage2TokenSequence
Labels - Class in cc.mallet.types
  Usually some distribution over possible labels for an instance.
Labels(Label[]) - Constructor for class cc.mallet.types.Labels
LabelsAssignment - Class in cc.mallet.grmm.util
  A special kind of assignment for Variables that can be arranged in a LabelsSequence.
LabelsAssignment(LabelsSequence) - Constructor for class cc.mallet.grmm.util.LabelsAssignment
LabelSequence - Class in cc.mallet.types
LabelSequence(LabelAlphabet, int[]) - Constructor for class cc.mallet.types.LabelSequence
LabelSequence(LabelAlphabet, int) - Constructor for class cc.mallet.types.LabelSequence
LabelSequence(Label[]) - Constructor for class cc.mallet.types.LabelSequence
LabelSequence(Alphabet) - Constructor for class cc.mallet.types.LabelSequence
LabelSequence.Iterator - Class in cc.mallet.types
LabelSequence.Iterator() - Constructor for class cc.mallet.types.LabelSequence.Iterator
LabelsSequence - Class in cc.mallet.types
  A simple `Sequence` implementation where all of the elements must be Labels.
LabelsSequence(Labels[]) - Constructor for class cc.mallet.types.LabelsSequence
  Create a LabelsSequence from an array.
LabelsSequence(LabelSequence) - Constructor for class cc.mallet.types.LabelsSequence
LabelsSequence2Assignment - Class in cc.mallet.grmm.util
  $Id: LabelsSequence2Assignment.java,v 1.1 2007/10/22 21:37:58 mccallum Exp $
LabelsSequence2Assignment() - Constructor for class cc.mallet.grmm.util.LabelsSequence2Assignment
LabelVector - Class in cc.mallet.types
LabelVector(LabelAlphabet, int[], double[]) - Constructor for class cc.mallet.types.LabelVector
LabelVector(Label[], double[]) - Constructor for class cc.mallet.types.LabelVector
LabelVector(LabelAlphabet, double[]) - Constructor for class cc.mallet.types.LabelVector
lambda - Variable in class cc.mallet.fst.CRFTrainerByStochasticGradient
languageCachedCoefficients - Variable in class cc.mallet.topics.PolylingualTopicModel
languageMaxTypeCounts - Variable in class cc.mallet.topics.PolylingualTopicModel
languageSmoothingOnlyMasses - Variable in class cc.mallet.topics.PolylingualTopicModel
languageTokensPerTopic - Variable in class cc.mallet.topics.PolylingualTopicModel
languageTypeTopicCounts - Variable in class cc.mallet.topics.PolylingualTopicModel
last() - Method in class cc.mallet.util.PropertyList
LAST_DIRECTORY - Static variable in class cc.mallet.pipe.iterator.FileIterator
  Use as label name the last directory in the filename.
LAST_DIRECTORY - Static variable in class cc.mallet.pipe.iterator.FileListIterator
  Use as label name the last directory in the filename.
LAST_DIRECTORY - Static variable in class cc.mallet.pipe.iterator.UnlabeledFileIterator
  Use as label name the last directory in the filename.
lastIndexOf(Object) - Method in class cc.mallet.types.MultiInstanceList
lattice - Variable in class cc.mallet.fst.semi_supervised.GELattice
latticeLength - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice
latticeLength - Variable in class cc.mallet.fst.semi_supervised.GELattice
LatticeViewer - Class in cc.mallet.extract
  Created: Oct 31, 2004
LatticeViewer() - Constructor for class cc.mallet.extract.LatticeViewer
LDA - Class in cc.mallet.topics
  Deprecated. Use ParallelTopicModel instead.
LDA(int) - Constructor for class cc.mallet.topics.LDA
  Deprecated.
LDA(int, double, double) - Constructor for class cc.mallet.topics.LDA
  Deprecated.
ldaFile - Static variable in class cc.mallet.classify.tui.Vectors2FeatureConstraints
LDAHyper - Class in cc.mallet.topics
  Deprecated. Use ParallelTopicModel instead, which uses substantially faster data structures even for non-parallel operation.
LDAHyper(int) - Constructor for class cc.mallet.topics.LDAHyper
  Deprecated.
LDAHyper(int, double, double) - Constructor for class cc.mallet.topics.LDAHyper
  Deprecated.
LDAHyper(int, double, double, Randoms) - Constructor for class cc.mallet.topics.LDAHyper
  Deprecated.
LDAHyper(LabelAlphabet, double, double, Randoms) - Constructor for class cc.mallet.topics.LDAHyper
  Deprecated.
LDAHyper.Topication - Class in cc.mallet.topics
  Deprecated.
LDAHyper.Topication(Instance, LDAHyper, LabelSequence) - Constructor for class cc.mallet.topics.LDAHyper.Topication
  Deprecated.
LDAStream - Class in cc.mallet.topics
LDAStream(int) - Constructor for class cc.mallet.topics.LDAStream
LDAStream(int, double, double) - Constructor for class cc.mallet.topics.LDAStream
LDAStream(int, double, double, Randoms) - Constructor for class cc.mallet.topics.LDAStream
LDAStream(LabelAlphabet, double, double, Randoms) - Constructor for class cc.mallet.topics.LDAStream
learningRate - Variable in class cc.mallet.fst.CRFTrainerByStochasticGradient
learnParameters() - Method in class cc.mallet.topics.DMRTopicModel
learnParameters(double[], int[][], int[]) - Method in class cc.mallet.topics.PAM4L
  Use the fixed point iteration described by Tom Minka.
learnParameters(double[], int[][], int[]) - Static method in class cc.mallet.types.Dirichlet
  Learn Dirichlet parameters using frequency histograms
learnParameters(double[], int[][], int[], double, double, int) - Static method in class cc.mallet.types.Dirichlet
  Learn Dirichlet parameters using frequency histograms
learnParametersWithDigamma(Object[]) - Method in class cc.mallet.types.Dirichlet
  Use the fixed point iteration described by Tom Minka.
learnParametersWithDigamma(int[][], int[]) - Method in class cc.mallet.types.Dirichlet
learnParametersWithHistogram(Object[]) - Method in class cc.mallet.types.Dirichlet
  Use the fixed point iteration described by Tom Minka.
learnParametersWithHistogram(int[][], int[]) - Method in class cc.mallet.types.Dirichlet
learnParametersWithLeaveOneOut(Object[]) - Method in class cc.mallet.types.Dirichlet
learnParametersWithLeaveOneOut(int[][], int[]) - Method in class cc.mallet.types.Dirichlet
  Learn parameters using Minka's Leave-One-Out (LOO) likelihood
learnParametersWithMoments(Object[]) - Method in class cc.mallet.types.Dirichlet
  Estimate a dirichlet with the moment matching method described by Ronning.
learnSymmetricConcentration(int[], int[], int, double) - Static method in class cc.mallet.types.Dirichlet
  Learn the concentration parameter of a symmetric Dirichlet using frequency histograms.
leftToRight(FeatureSequence, boolean) - Method in class cc.mallet.topics.MarginalProbEstimator
length(int) - Method in class cc.mallet.cluster.util.PairwiseMatrix
length() - Method in interface cc.mallet.fst.SumLattice
length() - Method in class cc.mallet.fst.SumLatticeBeam
length() - Method in class cc.mallet.fst.SumLatticeDefault
length() - Method in class cc.mallet.fst.SumLatticeScaling
LengthBins - Class in cc.mallet.share.upenn.ner
  A feature approximating string length.
LengthBins(String, int[]) - Constructor for class cc.mallet.share.upenn.ner.LengthBins
  bins contains the maximum sizes of elements in each bin.
less_efficient_sumLogProb(double, double) - Static method in class cc.mallet.fst.Transducer
levenshteinDistance(String, String) - Static method in class cc.mallet.util.Strings
LEX_ALPHA - Static variable in class cc.mallet.util.CharSequenceLexer
LEX_NONWHITESPACE_CLASSES - Static variable in class cc.mallet.util.CharSequenceLexer
LEX_NONWHITESPACE_TOGETHER - Static variable in class cc.mallet.util.CharSequenceLexer
LEX_WORD_CLASSES - Static variable in class cc.mallet.util.CharSequenceLexer
LEX_WORDS - Static variable in class cc.mallet.util.CharSequenceLexer
Lexer - Interface in cc.mallet.util
LexiconMembership - Class in cc.mallet.pipe.tsf
LexiconMembership(String, Reader, boolean) - Constructor for class cc.mallet.pipe.tsf.LexiconMembership
LexiconMembership(String, File, boolean) - Constructor for class cc.mallet.pipe.tsf.LexiconMembership
LexiconMembership(File, boolean) - Constructor for class cc.mallet.pipe.tsf.LexiconMembership
LexiconMembership(File) - Constructor for class cc.mallet.pipe.tsf.LexiconMembership
LimitedMemoryBFGS - Class in cc.mallet.optimize
LimitedMemoryBFGS(Optimizable.ByGradientValue) - Constructor for class cc.mallet.optimize.LimitedMemoryBFGS
LineGroupIterator - Class in cc.mallet.pipe.iterator
  Iterate over groups of lines of text, separated by lines that match a regular expression.
LineGroupIterator(Reader, Pattern, boolean) - Constructor for class cc.mallet.pipe.iterator.LineGroupIterator
LineGroupString2TokenSequence - Class in cc.mallet.pipe
LineGroupString2TokenSequence() - Constructor for class cc.mallet.pipe.LineGroupString2TokenSequence
LineIterator - Class in cc.mallet.pipe.iterator
LineIterator(Reader, Pattern, int, int, int) - Constructor for class cc.mallet.pipe.iterator.LineIterator
LineIterator(Reader, String, int, int, int) - Constructor for class cc.mallet.pipe.iterator.LineIterator
LineIterator(String, String, int, int, int) - Constructor for class cc.mallet.pipe.iterator.LineIterator
LineOptimizer - Interface in cc.mallet.optimize
  Optimize, constrained to move parameters along the direction of a specified line.
LineOptimizer.ByGradient - Interface in cc.mallet.optimize
listIterator() - Method in class cc.mallet.types.MultiInstanceList
listIterator(int) - Method in class cc.mallet.types.MultiInstanceList
ListMember - Class in cc.mallet.share.upenn.ner
  Checks membership in a lexicon in a text file.
ListMember(String, File, boolean) - Constructor for class cc.mallet.share.upenn.ner.ListMember
ListVarSet - Class in cc.mallet.grmm.types
  A clique that uses very little time and memory based on the flyweight pattern, in the same way as BitVarSet.
ListVarSet(Universe, Collection) - Constructor for class cc.mallet.grmm.types.ListVarSet
ListVarSet(VarSet) - Constructor for class cc.mallet.grmm.types.ListVarSet
load(File) - Static method in class cc.mallet.share.upenn.MaxEntShell
  Load a classifier from a file.
load(File, File, File) - Method in class cc.mallet.topics.tui.DMRLoader
load(File) - Static method in class cc.mallet.types.InstanceList
  Constructs a new `InstanceList`, deserialized from `file`.
load(File) - Static method in class cc.mallet.types.PagedInstanceList
  Constructs a new `InstanceList`, deserialized from `file`.
loadAlphaFromFile(String) - Method in class cc.mallet.topics.MultinomialHMM
loadFromFile(File) - Static method in class cc.mallet.types.AlphabetFactory
  Load an alphabet from a file, one item per line
loadSequenceIDsFromFile(String) - Method in class cc.mallet.topics.MultinomialHMM
loadTestingIDs(File) - Method in class cc.mallet.topics.PolylingualTopicModel
loadTopicsFromFile(String) - Method in class cc.mallet.topics.MultinomialHMM
localMagnetization(Inferencer, Variable) - Static method in class cc.mallet.grmm.inference.Utils
location(int) - Method in class cc.mallet.types.AugmentableFeatureVector
location(int) - Method in interface cc.mallet.types.ConstantMatrix
location(int) - Method in class cc.mallet.types.DenseMatrix
location(Object) - Method in class cc.mallet.types.FeatureVector
location(int) - Method in class cc.mallet.types.IndexedSparseVector
location(int) - Method in class cc.mallet.types.SparseMatrixn
location(int) - Method in class cc.mallet.types.SparseVector
lock() - Method in class cc.mallet.types.Instance
log() - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
log(String) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
log() - Method in class cc.mallet.grmm.types.AbstractFactor
log() - Static method in class cc.mallet.grmm.util.Flops
log(int) - Static method in class cc.mallet.grmm.util.Flops
log(double[]) - Static method in class cc.mallet.types.MatrixOps
log(LogRecord) - Method in class cc.mallet.util.MalletProgressMessageLogger
log2 - Static variable in class cc.mallet.types.GainRatio
log2 - Static variable in class cc.mallet.util.Maths
logBeta(double, double) - Static method in class cc.mallet.util.Maths
logBinom(int, int, double) - Static method in class cc.mallet.util.Maths
  Computes p(x;n,p) where x~B(n,p)
logErrorRange(AbstractTableFactor, AbstractTableFactor) - Static method in class cc.mallet.grmm.types.Factors
  Implements the error range measure from Ihler et al.
logFactorial(int) - Static method in class cc.mallet.util.Maths
logGamma(double) - Static method in class cc.mallet.types.Dirichlet
  Currently aliased to `logGammaStirling`
logGamma(double) - Static method in class cc.mallet.util.Maths
logGammaDefinition(double) - Static method in class cc.mallet.types.Dirichlet
  This calculates a log gamma function exactly.
logGammaDifference(double, int) - Static method in class cc.mallet.types.Dirichlet
  This directly calculates the difference between two log gamma functions using a recursive formula.
logGammaNemes(double) - Static method in class cc.mallet.types.Dirichlet
  Gergo Nemes' approximation
logGammaStirling(double) - Static method in class cc.mallet.types.Dirichlet
  Use a fifth order Stirling's approximation.
logger - Static variable in class cc.mallet.grmm.inference.AbstractBeliefPropagation
logger - Static variable in class cc.mallet.topics.HierarchicalPAM
logger - Static variable in class cc.mallet.topics.ParallelTopicModel
LoggingLevels - Static variable in class cc.mallet.util.MalletLogger
logify() - Method in class cc.mallet.grmm.types.AbstractFactor
logify() - Method in class cc.mallet.grmm.types.FactorGraph
logit(double) - Static method in class cc.mallet.util.Maths
logOptions(Logger) - Method in class cc.mallet.util.CommandOption.List
logProbability(int) - Method in class cc.mallet.types.Multinomial.Logged
logProbability(int) - Method in class cc.mallet.types.Multinomial
logProbability(Object) - Method in class cc.mallet.types.Multinomial
logResults(String) - Method in class cc.mallet.grmm.learning.MultiSegmentationEvaluatorACRF.TestResults
logsum() - Method in class cc.mallet.grmm.types.AbstractTableFactor
logsum() - Method in class cc.mallet.grmm.types.LogTableFactor
LogTableFactor - Class in cc.mallet.grmm.types
  Created: Jan 4, 2006
LogTableFactor(AbstractTableFactor) - Constructor for class cc.mallet.grmm.types.LogTableFactor
LogTableFactor(Variable) - Constructor for class cc.mallet.grmm.types.LogTableFactor
LogTableFactor(Variable[]) - Constructor for class cc.mallet.grmm.types.LogTableFactor
LogTableFactor(Collection) - Constructor for class cc.mallet.grmm.types.LogTableFactor
logValue(Assignment) - Method in class cc.mallet.grmm.types.AbstractFactor
logValue(AssignmentIterator) - Method in class cc.mallet.grmm.types.AbstractFactor
logValue(int) - Method in class cc.mallet.grmm.types.AbstractFactor
logValue(AssignmentIterator) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
logValue(AssignmentIterator) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
logValue(AssignmentIterator) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
logValue(AssignmentIterator) - Method in class cc.mallet.grmm.types.CPT
logValue(Assignment) - Method in class cc.mallet.grmm.types.CPT
logValue(int) - Method in class cc.mallet.grmm.types.CPT
logValue(AssignmentIterator) - Method in interface cc.mallet.grmm.types.Factor
logValue(Assignment) - Method in interface cc.mallet.grmm.types.Factor
logValue(int) - Method in interface cc.mallet.grmm.types.Factor
logValue(AssignmentIterator) - Method in class cc.mallet.grmm.types.FactorGraph
logValue(int) - Method in class cc.mallet.grmm.types.FactorGraph
logValue(Assignment) - Method in class cc.mallet.grmm.types.FactorGraph
logValue(AssignmentIterator) - Method in class cc.mallet.grmm.types.LogTableFactor
logValue(int) - Method in class cc.mallet.grmm.types.LogTableFactor
logValue(Assignment) - Method in class cc.mallet.grmm.types.LogTableFactor
logValue(AssignmentIterator) - Method in class cc.mallet.grmm.types.PottsTableFactor
logValue(AssignmentIterator) - Method in class cc.mallet.grmm.types.TableFactor
logValue(Assignment) - Method in class cc.mallet.grmm.types.TableFactor
logValue(int) - Method in class cc.mallet.grmm.types.TableFactor
logValueOfIndicatorFeature(FeatureVectorSequence, int, int) - Static method in class cc.mallet.fst.semi_supervised.GELattice
  Returns indicator value of feature at specified position in logspace.
longestString() - Method in class cc.mallet.classify.evaluate.Graph.Legend
LongRegexMatches - Class in cc.mallet.share.upenn.ner
  Matches a regular expression which spans several tokens.
LongRegexMatches(String, Pattern, int, int) - Constructor for class cc.mallet.share.upenn.ner.LongRegexMatches
lookupAssignment() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledVarSet
lookupAssignmentNumber() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledVarSet
lookupIndex(Object, boolean) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
  Return -1 if entry isn't present.
lookupIndex(Object) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
lookupIndex(Object) - Method in class cc.mallet.grmm.types.Tree
lookupIndex(Object, boolean) - Method in class cc.mallet.types.Alphabet
  Return -1 if entry isn't present.
lookupIndex(Object) - Method in class cc.mallet.types.Alphabet
lookupIndex(Object, boolean) - Method in class cc.mallet.types.LabelAlphabet
lookupIndices(Object[], boolean) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
lookupIndices(Object[], boolean) - Method in class cc.mallet.types.Alphabet
lookupJoint(Assignment) - Method in class cc.mallet.grmm.inference.AbstractInferencer
lookupJoint(Assignment) - Method in class cc.mallet.grmm.inference.BruteForceInferencer
lookupJoint(Assignment) - Method in interface cc.mallet.grmm.inference.Inferencer
  Returns the joint probability of a given assignment, computed in some factorized fashion.
lookupJunctionTree() - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
  Returns the JunctionTree computed from the last call to `JunctionTreeInferencer.computeMarginals(cc.mallet.grmm.types.FactorGraph)`.
lookupLabel(Object, boolean) - Method in class cc.mallet.types.LabelAlphabet
lookupLabel(Object) - Method in class cc.mallet.types.LabelAlphabet
lookupLabel(int) - Method in class cc.mallet.types.LabelAlphabet
lookupLogJoint(Assignment) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
lookupLogJoint(Assignment) - Method in class cc.mallet.grmm.inference.AbstractInferencer
lookupLogJoint(Assignment) - Method in class cc.mallet.grmm.inference.BruteForceInferencer
lookupLogJoint(Assignment) - Method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
lookupLogJoint(Assignment) - Method in interface cc.mallet.grmm.inference.Inferencer
  Returns the natural logarithm of the joint probability of a given assignment, computed in some factorized fashion.
lookupLogJoint(Assignment) - Method in class cc.mallet.grmm.inference.JunctionTree
lookupLogJoint(Assignment) - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
lookupMarginal(Variable) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
lookupMarginal(VarSet) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
lookupMarginal(VarSet) - Method in class cc.mallet.grmm.inference.AbstractInferencer
lookupMarginal(Variable) - Method in class cc.mallet.grmm.inference.AbstractInferencer
lookupMarginal(Variable) - Method in class cc.mallet.grmm.inference.BruteForceInferencer
lookupMarginal(VarSet) - Method in class cc.mallet.grmm.inference.BruteForceInferencer
lookupMarginal(Variable) - Method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
lookupMarginal(VarSet) - Method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
lookupMarginal(Variable) - Method in interface cc.mallet.grmm.inference.Inferencer
  Returns the computed marginal of a given variable.
lookupMarginal(VarSet) - Method in interface cc.mallet.grmm.inference.Inferencer
  Returns the computed marginal of a given clique in a graph.
lookupMarginal(Variable) - Method in class cc.mallet.grmm.inference.JunctionTree
lookupMarginal(Variable) - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
lookupMarginal(VarSet) - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
lookupMarginal(Variable) - Method in class cc.mallet.grmm.inference.SamplingInferencer
lookupMarginal(VarSet) - Method in class cc.mallet.grmm.inference.SamplingInferencer
lookupMarginal(Variable) - Method in class cc.mallet.grmm.inference.VariableElimination
lookupMinusLogZ(FactorGraph, Inferencer) - Static method in class cc.mallet.grmm.inference.Utils
  Returns ths value of -log Z in mdl according to the given inferencer.
lookupNumber(String) - Method in class cc.mallet.util.PropertyList
lookupNumberOfAssignment(Assignment) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledVarSet
lookupObject(int) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
lookupObject(int) - Method in class cc.mallet.types.Alphabet
lookupObject(String) - Method in class cc.mallet.util.PropertyList
lookupObjects(int[]) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
lookupObjects(int[], Object[]) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
  Returns an array of the objects corresponding to
lookupObjects(int[]) - Method in class cc.mallet.types.Alphabet
lookupObjects(int[], Object[]) - Method in class cc.mallet.types.Alphabet
  Returns an array of the objects corresponding to
lookupOutcome(int) - Method in class cc.mallet.grmm.types.Variable
lookupProjectionCache(VarSet) - Method in class cc.mallet.grmm.types.Universe
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.AbstractFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.Assignment
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.BetaFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.ConstantFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.NormalFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.PottsTableFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.SkeletonFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.UniformFactor
lookupValueInternal(int) - Method in class cc.mallet.grmm.types.UniNormalFactor
lookupVertex(int) - Method in class cc.mallet.grmm.types.Tree
LoopyBP - Class in cc.mallet.grmm.inference
  The loopy belief propagation algorithm for approximate inference in general graphical models.
LoopyBP() - Constructor for class cc.mallet.grmm.inference.LoopyBP
LoopyBP(int) - Constructor for class cc.mallet.grmm.inference.LoopyBP
LoopyBP(AbstractBeliefPropagation.MessageStrategy, int) - Constructor for class cc.mallet.grmm.inference.LoopyBP
lowerTriangularCrossproduct(double[], int) - Static method in class cc.mallet.util.MVNormal
  Returns L'L for lower triangular matrix L.
lowerTriangularProduct(double[], double[], int) - Static method in class cc.mallet.util.MVNormal
  Returns (lower-triangular) X = AB for square lower-triangular matrices A and B

## M

main(String[]) - Static method in class cc.mallet.classify.examples.DocumentClassifier
main(String[]) - Static method in class cc.mallet.classify.tests.TestClassifiers
main(String[]) - Static method in class cc.mallet.classify.tests.TestMaxEntTrainer
main(String[]) - Static method in class cc.mallet.classify.tests.TestNaiveBayes
main(String[]) - Static method in class cc.mallet.classify.tests.TestStaticParameters
main(String[]) - Static method in class cc.mallet.classify.tui.Calo2Classify
main(String[]) - Static method in class cc.mallet.classify.tui.Classifier2Info
main(String[]) - Static method in class cc.mallet.classify.tui.Csv2Classify
main(String[]) - Static method in class cc.mallet.classify.tui.Csv2Vectors
main(String[]) - Static method in class cc.mallet.classify.tui.SvmLight2Classify
main(String[]) - Static method in class cc.mallet.classify.tui.SvmLight2Vectors
main(String[]) - Static method in class cc.mallet.classify.tui.Text2Classify
main(String[]) - Static method in class cc.mallet.classify.tui.Text2Vectors
main(String[]) - Static method in class cc.mallet.classify.tui.Vectors2Classify
main(String[]) - Static method in class cc.mallet.classify.tui.Vectors2FeatureConstraints
main(String[]) - Static method in class cc.mallet.classify.tui.Vectors2Info
main(String[]) - Static method in class cc.mallet.classify.tui.Vectors2Vectors
main(String[]) - Static method in class cc.mallet.cluster.evaluate.tests.TestClusteringEvaluators
main(String[]) - Static method in class cc.mallet.cluster.examples.FirstOrderClusterExample
main(String[]) - Static method in class cc.mallet.cluster.iterator.tests.TestIterators
main(String[]) - Static method in class cc.mallet.cluster.Record
main(String[]) - Static method in class cc.mallet.cluster.tui.Clusterings2Clusterer
main(String[]) - Static method in class cc.mallet.cluster.tui.Clusterings2Clusterings
main(String[]) - Static method in class cc.mallet.cluster.tui.Clusterings2Info
main(String[]) - Static method in class cc.mallet.cluster.tui.Text2Clusterings
main(String[]) - Static method in class cc.mallet.cluster.util.PairwiseMatrix
main(String[]) - Static method in class cc.mallet.examples.TestCRFPipe
main(String[]) - Static method in class cc.mallet.examples.TrainCRF
main(String[]) - Static method in class cc.mallet.examples.TrainHMM
main(String[]) - Static method in class cc.mallet.extract.test.TestDocumentExtraction
main(String[]) - Static method in class cc.mallet.extract.test.TestDocumentViewer
main(String[]) - Static method in class cc.mallet.extract.test.TestLatticeViewer
main(String[]) - Static method in class cc.mallet.extract.test.TestPerDocumentF1Evaluator
main(String[]) - Static method in class cc.mallet.fst.SimpleTagger
  Command-line wrapper to train, test, or run a generic CRF-based tagger.
main(String[]) - Static method in class cc.mallet.fst.tests.TestCRF
main(String[]) - Static method in class cc.mallet.fst.tests.TestFeatureTransducer
main(String[]) - Static method in class cc.mallet.fst.tests.TestMEMM
main(String[]) - Static method in class cc.mallet.fst.tests.TestSumNegLogProb2
main(String[]) - Static method in class cc.mallet.grmm.examples.SimpleCrfExample
main(String[]) - Static method in class cc.mallet.grmm.examples.SimpleFactorExample
main(String[]) - Static method in class cc.mallet.grmm.examples.SimpleGraphExample
main(String[]) - Static method in class cc.mallet.grmm.learning.extract.AcrfExtractorTui
main(String[]) - Static method in class cc.mallet.grmm.learning.GenericAcrfTui
main(String[]) - Static method in class cc.mallet.grmm.test.TestAbstractBeliefPropagation
main(String[]) - Static method in class cc.mallet.grmm.test.TestAssignment
main(String[]) - Static method in class cc.mallet.grmm.test.TestAssignmentIterator
main(String[]) - Static method in class cc.mallet.grmm.test.TestBetaFactor
main(String[]) - Static method in class cc.mallet.grmm.test.TestBitVarSet
main(String[]) - Static method in class cc.mallet.grmm.test.TestDirectedModel
main(String[]) - Static method in class cc.mallet.grmm.test.TestFactorGraph
main(String[]) - Static method in class cc.mallet.grmm.test.TestFactors
main(String[]) - Static method in class cc.mallet.grmm.test.TestGenericAcrfData2TokenSequence
main(String[]) - Static method in class cc.mallet.grmm.test.TestGibbsSampler
main(String[]) - Static method in class cc.mallet.grmm.test.TestHashClique
main(String[]) - Static method in class cc.mallet.grmm.test.TestInference
main(String[]) - Static method in class cc.mallet.grmm.test.TestListVarSet
main(String[]) - Static method in class cc.mallet.grmm.test.TestLogTableFactor
main(String[]) - Static method in class cc.mallet.grmm.test.TestMIntInt2ObjectMap
main(String[]) - Static method in class cc.mallet.grmm.test.TestNormalFactor
main(String[]) - Static method in class cc.mallet.grmm.test.TestPottsFactor
main(String[]) - Static method in class cc.mallet.grmm.test.TestRandomGraphs
main(String[]) - Static method in class cc.mallet.grmm.test.TestTableFactor
main(String[]) - Static method in class cc.mallet.grmm.test.TestTRP
main(String[]) - Static method in class cc.mallet.grmm.test.TestUndirectedModel
main(String[]) - Static method in class cc.mallet.grmm.test.TestUniformFactor
main(String[]) - Static method in class cc.mallet.grmm.test.TestUniNormalFactor
main(String[]) - Static method in class cc.mallet.optimize.tests.TestOptimizable
main(String[]) - Static method in class cc.mallet.optimize.tests.TestOptimizer
main(String[]) - Static method in class cc.mallet.pipe.CharSequence2TokenSequence
main(String[]) - Static method in class cc.mallet.pipe.CharSequenceRemoveHTML
main(String[]) - Static method in class cc.mallet.pipe.iterator.tests.TestPatternMatchIterator
main(String[]) - Static method in class cc.mallet.pipe.SGML2TokenSequence
main(String[]) - Static method in class cc.mallet.pipe.tests.TestInstancePipe
main(String[]) - Static method in class cc.mallet.pipe.tests.TestIterators
main(String[]) - Static method in class cc.mallet.pipe.tests.TestPipeUtils
main(String[]) - Static method in class cc.mallet.pipe.tests.TestRainbowStyle
main(String[]) - Static method in class cc.mallet.pipe.tests.TestSGML2TokenSequence
main(String[]) - Static method in class cc.mallet.pipe.tests.TestSpacePipe
main(String[]) - Static method in class cc.mallet.pipe.tsf.tests.TestOffsetConjunctions
main(String[]) - Static method in class cc.mallet.pipe.tsf.tests.TestOffsetFeatureConjunctions
main(String[]) - Static method in class cc.mallet.pipe.tsf.tests.TestSequencePrintingPipe
main(String[]) - Static method in class cc.mallet.share.mccallum.ner.TUI
main(String[]) - Static method in class cc.mallet.share.upenn.MaxEntShell
  Command-line wrapper to train, test, or run a maxent classifier.
main(String[]) - Static method in class cc.mallet.share.weili.ner.enron.TUI
main(String[]) - Static method in class cc.mallet.topics.DMRTopicModel
main(String[]) - Static method in class cc.mallet.topics.HierarchicalLDA
  This method is primarily for testing purposes.
main(String[]) - Static method in class cc.mallet.topics.HierarchicalPAM
main(String[]) - Static method in class cc.mallet.topics.LDA
  Deprecated.
main(String[]) - Static method in class cc.mallet.topics.LDAHyper
  Deprecated.
main(String[]) - Static method in class cc.mallet.topics.MultinomialHMM
main(String[]) - Static method in class cc.mallet.topics.NPTopicModel
main(String[]) - Static method in class cc.mallet.topics.PAM4L
main(String[]) - Static method in class cc.mallet.topics.ParallelTopicModel
main(String[]) - Static method in class cc.mallet.topics.PolylingualTopicModel
main(String[]) - Static method in class cc.mallet.topics.SimpleLDA
main(String[]) - Static method in class cc.mallet.topics.TopicalNGrams
main(String[]) - Static method in class cc.mallet.topics.tui.DMRLoader
main(String[]) - Static method in class cc.mallet.topics.tui.EvaluateTopics
main(String[]) - Static method in class cc.mallet.topics.tui.HierarchicalLDATUI
main(String[]) - Static method in class cc.mallet.topics.tui.InferTopics
main(String[]) - Static method in class cc.mallet.topics.tui.TopicTrain
main(String[]) - Static method in class cc.mallet.topics.tui.Vectors2Topics
main(String[]) - Static method in class cc.mallet.types.Dirichlet
main(String[]) - Static method in class cc.mallet.types.InstanceListTUI
main(String[]) - Static method in class cc.mallet.types.Matrixn
main(String[]) - Static method in class cc.mallet.types.StringKernel
  Return string kernel between two strings
main(String[]) - Static method in class cc.mallet.types.tests.TestAlphabet
main(String[]) - Static method in class cc.mallet.types.tests.TestAugmentableFeatureVector
main(String[]) - Static method in class cc.mallet.types.tests.TestFeatureSequence
main(String[]) - Static method in class cc.mallet.types.tests.TestFeatureVector
main(String[]) - Static method in class cc.mallet.types.tests.TestHashedSparseVector
main(String[]) - Static method in class cc.mallet.types.tests.TestIndexedSparseVector
main(String[]) - Static method in class cc.mallet.types.tests.TestLabelAlphabet
main(String[]) - Static method in class cc.mallet.types.tests.TestLabelsSequence
main(String[]) - Static method in class cc.mallet.types.tests.TestLabelVector
main(String[]) - Static method in class cc.mallet.types.tests.TestMatrix
main(String[]) - Static method in class cc.mallet.types.tests.TestMatrixn
main(String[]) - Static method in class cc.mallet.types.tests.TestMultinomial
main(String[]) - Static method in class cc.mallet.types.tests.TestPagedInstanceList
main(String[]) - Static method in class cc.mallet.types.tests.TestRankedFeatureVector
main(String[]) - Static method in class cc.mallet.types.tests.TestSerializable
main(String[]) - Static method in class cc.mallet.types.tests.TestSparseMatrixn
main(String[]) - Static method in class cc.mallet.types.tests.TestSparseVector
main(String[]) - Static method in class cc.mallet.types.tests.TestToken
main(String[]) - Static method in class cc.mallet.util.BulkLoader
main(String[]) - Static method in class cc.mallet.util.CharSequenceLexer
main(String[]) - Static method in class cc.mallet.util.MVNormal
main(String[]) - Static method in class cc.mallet.util.Randoms
main(String[]) - Static method in class cc.mallet.util.resources.wn.Examples
main(String[]) - Static method in class cc.mallet.util.tests.TestAStar
main(String[]) - Static method in class cc.mallet.util.tests.TestMaths
main(String[]) - Static method in class cc.mallet.util.tests.TestPriorityQueue
main(String[]) - Static method in class cc.mallet.util.tests.TestPropertyList
main(String[]) - Static method in class cc.mallet.util.tests.TestRandom
main(String[]) - Static method in class cc.mallet.util.tests.TestStrings
majorityProb - Static variable in class cc.mallet.classify.tui.Vectors2FeatureConstraints
MakeAmpersandXMLFriendly - Class in cc.mallet.pipe
  convert & to &amp in tokens of a token sequence
MakeAmpersandXMLFriendly() - Constructor for class cc.mallet.pipe.MakeAmpersandXMLFriendly
makeBinary() - Method in class cc.mallet.types.SparseVector
makeBPInferencer() - Static method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
makeFactorial(Pipe, int) - Static method in class cc.mallet.grmm.learning.ACRF
makeFromLogMatrix(Variable[], Matrix) - Static method in class cc.mallet.grmm.types.LogTableFactor
makeFromLogValues(Variable[], double[]) - Static method in class cc.mallet.grmm.types.LogTableFactor
makeFromLogValues(Variable, double[]) - Static method in class cc.mallet.grmm.types.LogTableFactor
makeFromLogValues(VarSet, double[]) - Static method in class cc.mallet.grmm.types.TableFactor
makeFromMatrix(Variable[], SparseMatrixn) - Static method in class cc.mallet.grmm.types.LogTableFactor
makeFromReaders(FactorGraph, List) - Static method in class cc.mallet.grmm.inference.TRP.TreeListFactory
makeFromSingleIndex(VarSet, int) - Static method in class cc.mallet.grmm.types.Assignment
makeFromSubtree(Object, List) - Static method in class cc.mallet.grmm.types.Tree
makeFromValues(Variable[], double[]) - Static method in class cc.mallet.grmm.types.LogTableFactor
makeFromValues(Variable, double[]) - Static method in class cc.mallet.grmm.types.LogTableFactor
makeIdentityFactor(AbstractTableFactor) - Static method in class cc.mallet.grmm.types.AbstractTableFactor
  STATIC FACTORY METHODS
makeIdentityFactor() - Static method in class cc.mallet.grmm.types.ConstantFactor
makeKikuchiInferencer() - Static method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
makeList(Instance, Instance) - Static method in class cc.mallet.cluster.util.ClusterUtils
makeNonBinary() - Method in class cc.mallet.types.SparseVector
makeOnlyThread() - Method in class cc.mallet.topics.WorkerRunnable
  If there is only one thread, we don't need to go through communication overhead.
makeOutputFile() - Method in class cc.mallet.grmm.learning.ACRFEvaluator
makeSpacePredictionPipe() - Static method in class cc.mallet.fst.tests.TestMEMM
makeText(String[]) - Method in class cc.mallet.pipe.SimpleTaggerSentence2TokenSequence
  returns the first String in the array or "" if the array has length 0.
MalletLogger - Class in cc.mallet.util
MalletLogger(String, String) - Constructor for class cc.mallet.util.MalletLogger
MalletProgressMessageLogger - Class in cc.mallet.util
  Created by IntelliJ IDEA.
MalletProgressMessageLogger(String, String) - Constructor for class cc.mallet.util.MalletProgressMessageLogger
map(Method) - Method in class cc.mallet.types.SparseVector
  Applies the method argument to each value in a non-binary vector.
map(Collection, CollectionUtils.Fn) - Static method in class cc.mallet.util.CollectionUtils
  Returns a new collection whose elements consist of the function fn.f applied to all of the elements of the given collection.
marginalize(Variable[]) - Method in class cc.mallet.grmm.types.AbstractFactor
marginalize(Collection) - Method in class cc.mallet.grmm.types.AbstractFactor
marginalize(Variable) - Method in class cc.mallet.grmm.types.AbstractFactor
marginalize(Variable[]) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Returns the marginal of this distribution over the given variables.
marginalize(Collection) - Method in class cc.mallet.grmm.types.AbstractTableFactor
marginalize(Variable) - Method in class cc.mallet.grmm.types.AbstractTableFactor
marginalize(Variable[]) - Method in class cc.mallet.grmm.types.CPT
marginalize(Collection) - Method in class cc.mallet.grmm.types.CPT
marginalize(Variable) - Method in class cc.mallet.grmm.types.CPT
marginalize(Variable[]) - Method in interface cc.mallet.grmm.types.Factor
  Returns the marginal of this distribution over the given variables.
marginalize(Collection) - Method in interface cc.mallet.grmm.types.Factor
  Returns the marginal of this distribution over the given variables.
marginalize(Variable) - Method in interface cc.mallet.grmm.types.Factor
  Returns the marginal of this distribution over one variable.
marginalize(Variable[]) - Method in class cc.mallet.grmm.types.FactorGraph
marginalize(Collection) - Method in class cc.mallet.grmm.types.FactorGraph
marginalize(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.AbstractFactor
marginalizeInternal(AbstractTableFactor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.Assignment
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.BetaFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.ConstantFactor
marginalizeInternal(AbstractTableFactor) - Method in class cc.mallet.grmm.types.LogTableFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.NormalFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.PottsTableFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.SkeletonFactor
marginalizeInternal(AbstractTableFactor) - Method in class cc.mallet.grmm.types.TableFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.UniformFactor
marginalizeInternal(VarSet) - Method in class cc.mallet.grmm.types.UniNormalFactor
marginalizeOut(Variable) - Method in class cc.mallet.grmm.types.AbstractFactor
marginalizeOut(VarSet) - Method in class cc.mallet.grmm.types.AbstractFactor
marginalizeOut(Variable) - Method in class cc.mallet.grmm.types.AbstractTableFactor
marginalizeOut(VarSet) - Method in class cc.mallet.grmm.types.AbstractTableFactor
marginalizeOut(Variable) - Method in class cc.mallet.grmm.types.CPT
marginalizeOut(VarSet) - Method in class cc.mallet.grmm.types.CPT
marginalizeOut(Variable) - Method in interface cc.mallet.grmm.types.Factor
  Returns the marginal distribution attained by summing out the given variable.
marginalizeOut(VarSet) - Method in interface cc.mallet.grmm.types.Factor
  Returns the marginal distribution attained by summing out the given set of variables.
marginalizeOut(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
marginalizeOut(VarSet) - Method in class cc.mallet.grmm.types.FactorGraph
MarginalProbEstimator - Class in cc.mallet.topics
  An implementation of topic model marginal probability estimators presented in Wallach et al., "Evaluation Methods for Topic Models", ICML (2009)
MarginalProbEstimator(int, double[], double, double, int[][], int[]) - Constructor for class cc.mallet.topics.MarginalProbEstimator
MATCH - Static variable in class cc.mallet.types.StringEditVector
matches(String, String) - Method in class cc.mallet.extract.ExactMatchComparator
matches(String, String) - Method in interface cc.mallet.extract.FieldComparator
  Returns true if the given two slot fillers match.
matches(String, String) - Method in class cc.mallet.extract.PunctuationIgnoringComparator
Maths - Class in cc.mallet.util
Maths() - Constructor for class cc.mallet.util.Maths
Matrices - Class in cc.mallet.grmm.util
  Static Matrix constructors.
Matrices() - Constructor for class cc.mallet.grmm.util.Matrices
Matrix - Interface in cc.mallet.types
Matrix2 - Class in cc.mallet.types
  Deprecated.
Matrix2(double[], int, int) - Constructor for class cc.mallet.types.Matrix2
  Deprecated.
Matrix2(int, int) - Constructor for class cc.mallet.types.Matrix2
  Deprecated.
Matrix2(double[][]) - Constructor for class cc.mallet.types.Matrix2
  Deprecated.
Matrix2(double, int, int) - Constructor for class cc.mallet.types.Matrix2
  Deprecated.
Matrixn - Class in cc.mallet.types
  Implementation of Matrix that allows arbitrary number of dimensions.
Matrixn(double[]) - Constructor for class cc.mallet.types.Matrixn
  Create a 1-d matrix with the given values.
Matrixn(int[]) - Constructor for class cc.mallet.types.Matrixn
  Create a matrix with the given dimensions.
Matrixn(int[], double[]) - Constructor for class cc.mallet.types.Matrixn
  Create a matrix with the given dimensions and the given values.
MatrixOps - Class in cc.mallet.types
  A class of static utility functions for manipulating arrays of double.
MatrixOps() - Constructor for class cc.mallet.types.MatrixOps
max(double[]) - Static method in class cc.mallet.types.DenseVector
max(int[][]) - Static method in class cc.mallet.types.MatrixOps
max(int[]) - Static method in class cc.mallet.types.MatrixOps
max(double[]) - Static method in class cc.mallet.types.MatrixOps
max(double[][]) - Static method in class cc.mallet.types.MatrixOps
max() - Method in class cc.mallet.util.Univariate
maxAbsdiff(double[], double[]) - Static method in class cc.mallet.types.MatrixOps
  Returns the maximum elementwise absolute difference between two vectors.
maxDepth - Static variable in class cc.mallet.classify.DecisionTreeTrainer.Factory
MaxEnt - Class in cc.mallet.classify
  Maximum Entropy (AKA Multivariate Logistic Regression) classifier.
MaxEnt(Pipe, double[], FeatureSelection, FeatureSelection[]) - Constructor for class cc.mallet.classify.MaxEnt
MaxEnt(Pipe, double[], FeatureSelection) - Constructor for class cc.mallet.classify.MaxEnt
MaxEnt(Pipe, double[], FeatureSelection[]) - Constructor for class cc.mallet.classify.MaxEnt
MaxEnt(Pipe, double[]) - Constructor for class cc.mallet.classify.MaxEnt
MaxEntConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of a `Segment` extracted by a `Transducer` using a `MaxEnt` classifier to classify segments as "correct" or "incorrect." xxx needs some interface work
MaxEntConfidenceEstimator(Transducer, double) - Constructor for class cc.mallet.fst.confidence.MaxEntConfidenceEstimator
MaxEntConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.MaxEntConfidenceEstimator
MaxEntGETrainer - Class in cc.mallet.classify
  Training of MaxEnt models with labeled features using Generalized Expectation Criteria.
MaxEntGETrainer() - Constructor for class cc.mallet.classify.MaxEntGETrainer
MaxEntGETrainer(HashMap<Integer, double[]>) - Constructor for class cc.mallet.classify.MaxEntGETrainer
MaxEntGETrainer(HashMap<Integer, double[]>, MaxEnt) - Constructor for class cc.mallet.classify.MaxEntGETrainer
MaxEntL1Trainer - Class in cc.mallet.classify
MaxEntL1Trainer() - Constructor for class cc.mallet.classify.MaxEntL1Trainer
MaxEntL1Trainer(double) - Constructor for class cc.mallet.classify.MaxEntL1Trainer
MaxEntL1Trainer(MaxEnt) - Constructor for class cc.mallet.classify.MaxEntL1Trainer
MaxEntOptimizableByGE - Class in cc.mallet.classify
MaxEntOptimizableByGE(InstanceList, HashMap<Integer, double[]>, MaxEnt) - Constructor for class cc.mallet.classify.MaxEntOptimizableByGE
MaxEntOptimizableByLabelDistribution - Class in cc.mallet.classify
MaxEntOptimizableByLabelDistribution() - Constructor for class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
MaxEntOptimizableByLabelDistribution(InstanceList, MaxEnt) - Constructor for class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
MaxEntOptimizableByLabelLikelihood - Class in cc.mallet.classify
MaxEntOptimizableByLabelLikelihood() - Constructor for class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
MaxEntOptimizableByLabelLikelihood(InstanceList, MaxEnt) - Constructor for class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
MaxEntSequenceConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of a `Sequence` extracted by a `Transducer` using a `MaxEnt` classifier to classify Sequences as "correct" or "incorrect." xxx needs some interface work.
MaxEntSequenceConfidenceEstimator(Transducer, double) - Constructor for class cc.mallet.fst.confidence.MaxEntSequenceConfidenceEstimator
MaxEntSequenceConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.MaxEntSequenceConfidenceEstimator
MaxEntShell - Class in cc.mallet.share.upenn
  Simple wrapper for training a MALLET maxent classifier.
MaxEntTrainer - Class in cc.mallet.classify
  The trainer for a Maximum Entropy classifier.
MaxEntTrainer() - Constructor for class cc.mallet.classify.MaxEntTrainer
MaxEntTrainer(MaxEnt) - Constructor for class cc.mallet.classify.MaxEntTrainer
  Construct a MaxEnt trainer using a trained classifier as initial values.
MaxEntTrainer(double) - Constructor for class cc.mallet.classify.MaxEntTrainer
  Constructs a trainer with a parameter to avoid overtraining.
maxIndex(double[]) - Static method in class cc.mallet.types.MatrixOps
maxIndex(double[][]) - Static method in class cc.mallet.types.MatrixOps
maxL1MarginalDistance(FactorGraph, Inferencer, Inferencer) - Static method in class cc.mallet.grmm.inference.Utils
MaxLattice - Interface in cc.mallet.fst
  The interface to classes implementing the Viterbi algorithm, finding the best sequence of states for a given input sequence.
MaxLatticeDefault - Class in cc.mallet.fst
  Default, full dynamic programming version of the Viterbi "Max-(Product)-Lattice" algorithm.
MaxLatticeDefault(Transducer, Sequence) - Constructor for class cc.mallet.fst.MaxLatticeDefault
MaxLatticeDefault(Transducer, Sequence, Sequence) - Constructor for class cc.mallet.fst.MaxLatticeDefault
MaxLatticeDefault(Transducer, Sequence, Sequence, int) - Constructor for class cc.mallet.fst.MaxLatticeDefault
  Initiate Viterbi decoding of the inputSequence, contrained to match non-null parts of the outputSequence.
MaxLatticeDefault.Factory - Class in cc.mallet.fst
MaxLatticeDefault.Factory() - Constructor for class cc.mallet.fst.MaxLatticeDefault.Factory
MaxLatticeFactory - Class in cc.mallet.fst
MaxLatticeFactory() - Constructor for class cc.mallet.fst.MaxLatticeFactory
maxT - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
maxTime() - Method in class cc.mallet.grmm.util.LabelsAssignment
maxTopic - Variable in class cc.mallet.topics.NPTopicModel
MCMaxEnt - Class in cc.mallet.classify
  Maximum Entropy classifier.
MCMaxEnt(Pipe, double[], FeatureSelection, FeatureSelection[]) - Constructor for class cc.mallet.classify.MCMaxEnt
MCMaxEnt(Pipe, double[], FeatureSelection) - Constructor for class cc.mallet.classify.MCMaxEnt
MCMaxEnt(Pipe, double[], FeatureSelection[]) - Constructor for class cc.mallet.classify.MCMaxEnt
MCMaxEnt(Pipe, double[]) - Constructor for class cc.mallet.classify.MCMaxEnt
MCMaxEntTrainer - Class in cc.mallet.classify
  The trainer for a Maximum Entropy classifier.
MCMaxEntTrainer(CommandOption.List) - Constructor for class cc.mallet.classify.MCMaxEntTrainer
MCMaxEntTrainer(MCMaxEnt) - Constructor for class cc.mallet.classify.MCMaxEntTrainer
MCMaxEntTrainer() - Constructor for class cc.mallet.classify.MCMaxEntTrainer
MCMaxEntTrainer(boolean) - Constructor for class cc.mallet.classify.MCMaxEntTrainer
MCMaxEntTrainer(double) - Constructor for class cc.mallet.classify.MCMaxEntTrainer
  Constructs a trainer with a parameter to avoid overtraining.
MCMaxEntTrainer(double, boolean) - Constructor for class cc.mallet.classify.MCMaxEntTrainer
MCMaxEntTrainer(double, double) - Constructor for class cc.mallet.classify.MCMaxEntTrainer
mdlCurrent - Variable in class cc.mallet.grmm.inference.AbstractBeliefPropagation
mdlToGraph(FactorGraph) - Static method in class cc.mallet.grmm.util.Graphs
  Converts a FactorGraph into a plain graph where each Variable is a vertex, and two Variables are connected by an edge if they are arguments to the same factor.
mean(double[]) - Static method in class cc.mallet.types.MatrixOps
mean() - Method in class cc.mallet.util.Univariate
mean(InstanceList) - Static method in class cc.mallet.util.VectorStats
  Returns a `SparseVector` whose entries (taken from the union of those in the instances) are the expected values of those in the `InstanceList`.
mean(InstanceList, int) - Static method in class cc.mallet.util.VectorStats
  Returns a `SparseVector` whose entries (dense with the given number of indices) are the expected values of those in the `InstanceList`.
mean(InstanceList, int[]) - Static method in class cc.mallet.util.VectorStats
  Returns a `SparseVector` whose entries (the given indices) are the expected values of those in the `InstanceList`.
meanCorrect() - Method in class cc.mallet.classify.ConfidencePredictingClassifier
meanIncorrect() - Method in class cc.mallet.classify.ConfidencePredictingClassifier
median() - Method in class cc.mallet.util.Univariate
MedoidEvaluator - Class in cc.mallet.cluster.neighbor_evaluator
  Uses a `Classifier` over pairs of `Instances` to score `Neighbor`.
MedoidEvaluator(Classifier, String) - Constructor for class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator
MedoidEvaluator(Classifier, String, boolean, boolean) - Constructor for class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator
MedoidEvaluator.Average - Class in cc.mallet.cluster.neighbor_evaluator
MedoidEvaluator.Average() - Constructor for class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator.Average
MedoidEvaluator.CombiningStrategy - Interface in cc.mallet.cluster.neighbor_evaluator
  Specifies how to combine a set of pairwise scores into a cluster-wise score.
MedoidEvaluator.Maximum - Class in cc.mallet.cluster.neighbor_evaluator
MedoidEvaluator.Maximum() - Constructor for class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator.Maximum
MedoidEvaluator.Minimum - Class in cc.mallet.cluster.neighbor_evaluator
MedoidEvaluator.Minimum() - Constructor for class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator.Minimum
MEMM - Class in cc.mallet.fst
  A Maximum Entropy Markov Model.
MEMM(Pipe, Pipe) - Constructor for class cc.mallet.fst.MEMM
MEMM(Alphabet, Alphabet) - Constructor for class cc.mallet.fst.MEMM
MEMM(CRF) - Constructor for class cc.mallet.fst.MEMM
MEMM.State - Class in cc.mallet.fst
MEMM.State(String, int, double, double, String[], String[], String[][], CRF) - Constructor for class cc.mallet.fst.MEMM.State
MEMM.TransitionIterator - Class in cc.mallet.fst
MEMM.TransitionIterator(MEMM.State, FeatureVectorSequence, int, String, CRF) - Constructor for class cc.mallet.fst.MEMM.TransitionIterator
MEMM.TransitionIterator(MEMM.State, FeatureVector, String, CRF) - Constructor for class cc.mallet.fst.MEMM.TransitionIterator
MEMMTrainer - Class in cc.mallet.fst
  Trains and evaluates a `MEMM`.
MEMMTrainer(MEMM) - Constructor for class cc.mallet.fst.MEMMTrainer
MEMMTrainer.MEMMOptimizableByLabelLikelihood - Class in cc.mallet.fst
  Represents the terms in the objective function.
MEMMTrainer.MEMMOptimizableByLabelLikelihood(MEMM, InstanceList) - Constructor for class cc.mallet.fst.MEMMTrainer.MEMMOptimizableByLabelLikelihood
mergeClusters(Clustering, int, int) - Static method in class cc.mallet.cluster.util.ClusterUtils
  Relabels the clustering to reflect merging clusters i and j.
mergeInstances(Clustering, int[]) - Static method in class cc.mallet.cluster.util.ClusterUtils
  Merge clusters containing the specified instances.
mergeInstances(Clustering, int, int) - Static method in class cc.mallet.cluster.util.ClusterUtils
mergeInstancesWithSameLabel(Clustering) - Static method in class cc.mallet.cluster.util.ClusterUtils
MessageArray - Class in cc.mallet.grmm.inference
  Efficiently manages a array of messages in a factor graph from variables to factors and vice versa.
MessageArray(FactorGraph) - Constructor for class cc.mallet.grmm.inference.MessageArray
MessageArray.Iterator - Class in cc.mallet.grmm.inference
MessageArray.Iterator() - Constructor for class cc.mallet.grmm.inference.MessageArray.Iterator
MessageArray.ToMsgsIterator - Class in cc.mallet.grmm.inference
messages - Variable in class cc.mallet.grmm.inference.AbstractBeliefPropagation.AbstractMessageStrategy
MessageStrategy - Interface in cc.mallet.grmm.inference.gbp
  Created: May 29, 2005
Metric - Interface in cc.mallet.types
min(double[]) - Static method in class cc.mallet.types.MatrixOps
min() - Method in class cc.mallet.util.search.MinHeap
min() - Method in interface cc.mallet.util.search.PriorityQueue
  Return the top element of the queue.
min() - Method in class cc.mallet.util.Univariate
MinHeap - Class in cc.mallet.util.search
  Created by IntelliJ IDEA.
MinHeap(int) - Constructor for class cc.mallet.util.search.MinHeap
  Create a binary heap with initial capacity `capacity`.
MinHeap() - Constructor for class cc.mallet.util.search.MinHeap
  Create a binary heap with minimum initial capacity.
minIndex(double[]) - Static method in class cc.mallet.types.MatrixOps
minInfoGainSplit - Static variable in class cc.mallet.classify.DecisionTreeTrainer.Factory
Minkowski - Class in cc.mallet.types
Minkowski(double) - Constructor for class cc.mallet.types.Minkowski
  Constructor for Minkowski metric.
MinSegmentConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of an entire sequence by the least confidence segment.
MinSegmentConfidenceEstimator(Transducer, TransducerConfidenceEstimator) - Constructor for class cc.mallet.fst.confidence.MinSegmentConfidenceEstimator
MIntInt2ObjectMap - Class in cc.mallet.grmm.util
  Hash map that maps integer pairs to objects.
MIntInt2ObjectMap() - Constructor for class cc.mallet.grmm.util.MIntInt2ObjectMap
MIntInt2ObjectMap(int) - Constructor for class cc.mallet.grmm.util.MIntInt2ObjectMap
mix(AbstractTableFactor, AbstractTableFactor, double) - Static method in class cc.mallet.grmm.types.Factors
  Returns a new Factor `F = alpha * f1 + (1 - alpha) * f2`.
model - Variable in class cc.mallet.fst.confidence.TransducerConfidenceEstimator
model - Variable in class cc.mallet.fst.confidence.TransducerSequenceConfidenceEstimator
model - Variable in class cc.mallet.topics.LDAHyper.Topication
  Deprecated.
modelFilename - Variable in class cc.mallet.topics.ParallelTopicModel
modelLogLikelihood() - Method in class cc.mallet.topics.HierarchicalPAM
modelLogLikelihood() - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
modelLogLikelihood() - Method in class cc.mallet.topics.ParallelTopicModel
modelLogLikelihood() - Method in class cc.mallet.topics.PolylingualTopicModel
modelLogLikelihood() - Method in class cc.mallet.topics.SimpleLDA
ModelReader - Class in cc.mallet.grmm.util
  $Id: ModelReader.java,v 1.1 2007/10/22 21:37:58 mccallum Exp $
ModelReader() - Constructor for class cc.mallet.grmm.util.ModelReader
Models - Class in cc.mallet.grmm.util
  Static utilities that do useful things with factor graphs.
Models() - Constructor for class cc.mallet.grmm.util.Models
modifyPotential(ACRF.UnrolledGraph, ACRF.UnrolledVarSet, AbstractTableFactor) - Method in class cc.mallet.grmm.learning.ACRF.Template
  Modifies a factor computed from this template.
msgProduct(Factor, int, int) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation.AbstractMessageStrategy
msgProduct(Factor, int, int) - Method in interface cc.mallet.grmm.inference.AbstractBeliefPropagation.MessageStrategy
MUCEvaluator - Class in cc.mallet.cluster.evaluate
  Evaluate a Clustering using the MUC evaluation metric.
MUCEvaluator() - Constructor for class cc.mallet.cluster.evaluate.MUCEvaluator
MultiInstanceList - Class in cc.mallet.types
  An implementation of InstanceList that logically combines multiple instance lists so that they appear as one list without copying the original lists.
MultiInstanceList(InstanceList[]) - Constructor for class cc.mallet.types.MultiInstanceList
  Constructs a `MultiInstanceList` with an array of `InstanceList`
MultiInstanceList(List<InstanceList>) - Constructor for class cc.mallet.types.MultiInstanceList
  Constructs a `MultiInstanceList` with a `List` of `InstanceList`
Multinomial - Class in cc.mallet.types
  A probability distribution over a set of features represented as a `FeatureVector`.
Multinomial(double[], Alphabet, int, boolean, boolean) - Constructor for class cc.mallet.types.Multinomial
Multinomial(double[], Alphabet) - Constructor for class cc.mallet.types.Multinomial
Multinomial(double[], int) - Constructor for class cc.mallet.types.Multinomial
Multinomial(double[]) - Constructor for class cc.mallet.types.Multinomial
Multinomial.Estimator - Class in cc.mallet.types
  A hierarchy of classes used to produce estimates of probabilities, in the form of a Multinomial, from counts associated with the elements of an Alphabet.
Multinomial.Estimator(double[], int, Alphabet) - Constructor for class cc.mallet.types.Multinomial.Estimator
Multinomial.Estimator(double[], Alphabet) - Constructor for class cc.mallet.types.Multinomial.Estimator
Multinomial.Estimator() - Constructor for class cc.mallet.types.Multinomial.Estimator
Multinomial.Estimator(int) - Constructor for class cc.mallet.types.Multinomial.Estimator
Multinomial.Estimator(Alphabet) - Constructor for class cc.mallet.types.Multinomial.Estimator
Multinomial.LaplaceEstimator - Class in cc.mallet.types
  An MEstimator with m set to 1.
Multinomial.LaplaceEstimator() - Constructor for class cc.mallet.types.Multinomial.LaplaceEstimator
Multinomial.LaplaceEstimator(int) - Constructor for class cc.mallet.types.Multinomial.LaplaceEstimator
Multinomial.LaplaceEstimator(Alphabet) - Constructor for class cc.mallet.types.Multinomial.LaplaceEstimator
Multinomial.Logged - Class in cc.mallet.types
  A Multinomial in which the values associated with each feature index fi is Math.log(probability[fi]) instead of probability[fi].
Multinomial.Logged(double[], Alphabet, int, boolean) - Constructor for class cc.mallet.types.Multinomial.Logged
Multinomial.Logged(double[], Alphabet, boolean) - Constructor for class cc.mallet.types.Multinomial.Logged
Multinomial.Logged(double[], Alphabet, int) - Constructor for class cc.mallet.types.Multinomial.Logged
Multinomial.Logged(double[], Alphabet) - Constructor for class cc.mallet.types.Multinomial.Logged
Multinomial.Logged(Multinomial) - Constructor for class cc.mallet.types.Multinomial.Logged
Multinomial.Logged(double[]) - Constructor for class cc.mallet.types.Multinomial.Logged
Multinomial.MAPEstimator - Class in cc.mallet.types
  Unimplemented, but the MEstimators are.
Multinomial.MAPEstimator(Dirichlet) - Constructor for class cc.mallet.types.Multinomial.MAPEstimator
Multinomial.MEstimator - Class in cc.mallet.types
  An Estimator in which probability estimates in a Multinomial are generated by adding a constant m (specified at construction time) to each count before dividing by the total of the m-biased counts.
Multinomial.MEstimator(Alphabet, double) - Constructor for class cc.mallet.types.Multinomial.MEstimator
Multinomial.MEstimator(int, double) - Constructor for class cc.mallet.types.Multinomial.MEstimator
Multinomial.MEstimator(double) - Constructor for class cc.mallet.types.Multinomial.MEstimator
Multinomial.MLEstimator - Class in cc.mallet.types
  An MEstimator with m set to 0.
Multinomial.MLEstimator() - Constructor for class cc.mallet.types.Multinomial.MLEstimator
Multinomial.MLEstimator(int) - Constructor for class cc.mallet.types.Multinomial.MLEstimator
Multinomial.MLEstimator(Alphabet) - Constructor for class cc.mallet.types.Multinomial.MLEstimator
MultinomialHMM - Class in cc.mallet.topics
  Latent Dirichlet Allocation.
MultinomialHMM(int, String, int) - Constructor for class cc.mallet.topics.MultinomialHMM
multiply(Factor) - Method in class cc.mallet.grmm.types.AbstractFactor
multiply(Factor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Returns the elementwise product of this potential and another one.
multiply(Factor) - Method in class cc.mallet.grmm.types.ConstantFactor
multiply(Factor) - Method in class cc.mallet.grmm.types.CPT
multiply(Factor) - Method in interface cc.mallet.grmm.types.Factor
  Returns the elementwise product of this factor with another.
multiply(Factor) - Method in class cc.mallet.grmm.types.FactorGraph
multiplyAll(Collection) - Static method in class cc.mallet.grmm.types.Factors
multiplyAll(Collection) - Static method in class cc.mallet.grmm.types.LogTableFactor
multiplyAll(Factor[]) - Static method in class cc.mallet.grmm.types.TableFactor
multiplyAll(Collection) - Static method in class cc.mallet.grmm.types.TableFactor
  Returns the product of a collection of multinomial potentials.
multiplyBy(Factor) - Method in class cc.mallet.grmm.types.AbstractFactor
multiplyBy(Factor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Does the conceptual equivalent of this *= pot.
multiplyBy(Factor) - Method in class cc.mallet.grmm.types.BetaFactor
multiplyBy(Factor) - Method in class cc.mallet.grmm.types.ConstantFactor
multiplyBy(Factor) - Method in class cc.mallet.grmm.types.CPT
multiplyBy(Factor) - Method in interface cc.mallet.grmm.types.Factor
  Does this *= pot.
multiplyBy(Factor) - Method in class cc.mallet.grmm.types.FactorGraph
multiplyBy(Factor) - Method in class cc.mallet.grmm.types.NormalFactor
multiplyBy(Factor) - Method in class cc.mallet.grmm.types.UniformFactor
multiplyBy(Factor) - Method in class cc.mallet.grmm.types.UniNormalFactor
multiplyByInternal(DiscreteFactor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
multiplyByInternal(DiscreteFactor) - Method in class cc.mallet.grmm.types.LogTableFactor
  Does the conceptual equivalent of this *= pot.
multiplyByInternal(DiscreteFactor) - Method in class cc.mallet.grmm.types.TableFactor
MultiSegmentationEvaluator - Class in cc.mallet.fst
  Evaluates a transducer model, computes the precision, recall and F1 scores; considers segments that span across multiple tokens.
MultiSegmentationEvaluator(InstanceList[], String[], Object[], Object[]) - Constructor for class cc.mallet.fst.MultiSegmentationEvaluator
MultiSegmentationEvaluator(InstanceList, String, Object[], Object[]) - Constructor for class cc.mallet.fst.MultiSegmentationEvaluator
MultiSegmentationEvaluator(InstanceList, String, InstanceList, String, Object[], Object[]) - Constructor for class cc.mallet.fst.MultiSegmentationEvaluator
MultiSegmentationEvaluator(InstanceList, String, InstanceList, String, InstanceList, String, Object[], Object[]) - Constructor for class cc.mallet.fst.MultiSegmentationEvaluator
MultiSegmentationEvaluatorACRF - Class in cc.mallet.grmm.learning
MultiSegmentationEvaluatorACRF(Object[], Object[], boolean) - Constructor for class cc.mallet.grmm.learning.MultiSegmentationEvaluatorACRF
  This class WILL NOT WORK if segmentStartTags and segmentContinueTags are the same!!
MultiSegmentationEvaluatorACRF(Object[], Object[]) - Constructor for class cc.mallet.grmm.learning.MultiSegmentationEvaluatorACRF
  This class WILL NOT WORK if segmentStartTags and segmentContinueTags are the same!!
MultiSegmentationEvaluatorACRF(Object[], Object[], int) - Constructor for class cc.mallet.grmm.learning.MultiSegmentationEvaluatorACRF
MultiSegmentationEvaluatorACRF.TestResults - Class in cc.mallet.grmm.learning
MultiSegmentationEvaluatorACRF.TestResults(Object[], Object[]) - Constructor for class cc.mallet.grmm.learning.MultiSegmentationEvaluatorACRF.TestResults
mutualInformation(Factor) - Static method in class cc.mallet.grmm.types.Factors
  Given a joint distribution over two variables, returns their mutual information.
MVNormal - Class in cc.mallet.util
  Tools for working with multivariate normal distributions
MVNormal() - Constructor for class cc.mallet.util.MVNormal

## N

NaiveBayes - Class in cc.mallet.classify
  A classifier that classifies instances according to the NaiveBayes method.
NaiveBayes(Pipe, Multinomial.Logged, Multinomial.Logged[]) - Constructor for class cc.mallet.classify.NaiveBayes
  Construct a NaiveBayes classifier from a pipe, prior estimates for each Classification, and feature estimates of each Classification.
NaiveBayes(Pipe, Multinomial, Multinomial[]) - Constructor for class cc.mallet.classify.NaiveBayes
  Construct a NaiveBayes classifier from a pipe, prior estimates for each Classification, and feature estimates of each Classification.
NaiveBayesEMTrainer - Class in cc.mallet.classify
NaiveBayesEMTrainer() - Constructor for class cc.mallet.classify.NaiveBayesEMTrainer
NaiveBayesTrainer - Class in cc.mallet.classify
  Class used to generate a NaiveBayes classifier from a set of training data.
NaiveBayesTrainer(NaiveBayes) - Constructor for class cc.mallet.classify.NaiveBayesTrainer
NaiveBayesTrainer(Pipe) - Constructor for class cc.mallet.classify.NaiveBayesTrainer
NaiveBayesTrainer() - Constructor for class cc.mallet.classify.NaiveBayesTrainer
NaiveBayesTrainer.Factory - Class in cc.mallet.classify
NaiveBayesTrainer.Factory() - Constructor for class cc.mallet.classify.NaiveBayesTrainer.Factory
name(int) - Method in class cc.mallet.classify.evaluate.Graph.Legend
name - Variable in class cc.mallet.fst.semi_supervised.GECriterion
name - Variable in class cc.mallet.types.Instance
name2state - Variable in class cc.mallet.fst.CRF
NBestViterbiConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of an entire sequence by the probability that one of the the Viterbi paths rank 2->N is correct.
NBestViterbiConfidenceEstimator(Transducer, int) - Constructor for class cc.mallet.fst.confidence.NBestViterbiConfidenceEstimator
Neighbor - Class in cc.mallet.cluster.neighbor_evaluator
  A Clustering and a modified version of that Clustering.
Neighbor(Clustering, Clustering) - Constructor for class cc.mallet.cluster.neighbor_evaluator.Neighbor
NeighborEvaluator - Interface in cc.mallet.cluster.neighbor_evaluator
  Scores the value of changing the current `Clustering` to the modified `Clustering` specified in a `Neighbor` object.
NeighborIterator - Class in cc.mallet.cluster.iterator
  Sample Instances with data objects equal to `Neighbor`s.
NeighborIterator(Clustering) - Constructor for class cc.mallet.cluster.iterator.NeighborIterator
NEPipes - Class in cc.mallet.share.upenn.ner
NEPipes(File) - Constructor for class cc.mallet.share.upenn.ner.NEPipes
newClassifierTrainer(Classifier) - Method in class cc.mallet.classify.ClassifierTrainer.Factory
newClassifierTrainer() - Method in class cc.mallet.classify.ClassifierTrainer.Factory
newClassifierTrainer(Classifier) - Method in class cc.mallet.classify.DecisionTreeTrainer.Factory
newClassifierTrainer(Classifier) - Method in class cc.mallet.classify.NaiveBayesTrainer.Factory
newCRFOptimizable(CRF, InstanceList, int) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood.Factory
newCRFOptimizable(CRF, InstanceList) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood.Factory
newFeatureVector(FeatureVector, Alphabet, FeatureSelection) - Static method in class cc.mallet.types.FeatureVector
  Construct a new FeatureVector, selecting only those features in fs, and having new (presumably more compact, dense) Alphabet.
newIteratorFrom(Iterator<Instance>) - Method in class cc.mallet.pipe.BranchingPipe
  Deprecated.
newIteratorFrom(Iterator<Instance>) - Method in class cc.mallet.pipe.FeatureVectorSequence2FeatureVectors
newIteratorFrom(Iterator<Instance>) - Method in class cc.mallet.pipe.FilterEmptyFeatureVectors
newIteratorFrom(Iterator<Instance>) - Method in class cc.mallet.pipe.Pipe
  Given an InstanceIterator, return a new InstanceIterator whose instances have also been processed by this pipe.
newIteratorFrom(Iterator<Instance>) - Method in class cc.mallet.pipe.SerialPipes
newIteratorFrom(Iterator<Instance>) - Method in class cc.mallet.pipe.TokenSequence2TokenInstances
newMaxLattice(Transducer, Sequence, Sequence) - Method in class cc.mallet.fst.MaxLatticeDefault.Factory
newMaxLattice(Transducer, Sequence) - Method in class cc.mallet.fst.MaxLatticeFactory
newMaxLattice(Transducer, Sequence, Sequence) - Method in class cc.mallet.fst.MaxLatticeFactory
newMessages - Variable in class cc.mallet.grmm.inference.gbp.AbstractMessageStrategy
newPartiallyRankedFeatureVector(InstanceList, LabelVector[]) - Method in interface cc.mallet.types.PartiallyRankedFeatureVector.Factory
newPartiallyRankedFeatureVectors(InstanceList, LabelVector[]) - Method in interface cc.mallet.types.PartiallyRankedFeatureVector.PerLabelFactory
newRankedFeatureVector(InstanceList) - Method in class cc.mallet.types.ExpGain.Factory
newRankedFeatureVector(InstanceList) - Method in class cc.mallet.types.FeatureCounts.Factory
newRankedFeatureVector(InstanceList) - Method in class cc.mallet.types.GradientGain.Factory
newRankedFeatureVector(InstanceList) - Method in class cc.mallet.types.InfoGain.Factory
newRankedFeatureVector(InstanceList) - Method in interface cc.mallet.types.RankedFeatureVector.Factory
newRankedFeatureVectors(InstanceList) - Method in class cc.mallet.types.PerLabelFeatureCounts.Factory
newRankedFeatureVectors(InstanceList) - Method in class cc.mallet.types.PerLabelInfoGain.Factory
newRankedFeatureVectors(InstanceList) - Method in interface cc.mallet.types.RankedFeatureVector.PerLabelFactory
newSerialPipesFromRange(int, int) - Method in class cc.mallet.pipe.SerialPipes
newSerialPipesFromSuffix(SerialPipes.Predicate) - Method in class cc.mallet.pipe.SerialPipes
newState(String, int, double, double, String[], String[], String[][], CRF) - Method in class cc.mallet.fst.CRF
newState(String, int, double, double, String[], String[], String[][], CRF) - Method in class cc.mallet.fst.MEMM
newSumLattice(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean, LabelAlphabet) - Method in class cc.mallet.fst.SumLatticeBeam.Factory
newSumLattice(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean, LabelAlphabet) - Method in class cc.mallet.fst.SumLatticeDefault.Factory
newSumLattice(Transducer, Sequence) - Method in class cc.mallet.fst.SumLatticeFactory
newSumLattice(Transducer, Sequence, Transducer.Incrementor) - Method in class cc.mallet.fst.SumLatticeFactory
newSumLattice(Transducer, Sequence, Sequence) - Method in class cc.mallet.fst.SumLatticeFactory
newSumLattice(Transducer, Sequence, Sequence, Transducer.Incrementor) - Method in class cc.mallet.fst.SumLatticeFactory
newSumLattice(Transducer, Sequence, Sequence, Transducer.Incrementor, LabelAlphabet) - Method in class cc.mallet.fst.SumLatticeFactory
newSumLattice(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean) - Method in class cc.mallet.fst.SumLatticeFactory
newSumLattice(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean, LabelAlphabet) - Method in class cc.mallet.fst.SumLatticeFactory
  Returns a SumLattice object to run forward-backward.
newSumLattice(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean, LabelAlphabet) - Method in class cc.mallet.fst.SumLatticeScaling.Factory
newTSP() - Method in class cc.mallet.classify.tests.TestStaticParameters.Factory
next() - Method in class cc.mallet.cluster.iterator.AllPairsIterator
next() - Method in class cc.mallet.cluster.iterator.ClusterSampleIterator
next() - Method in class cc.mallet.cluster.iterator.NodeClusterSampleIterator
next() - Method in class cc.mallet.cluster.iterator.PairSampleIterator
next() - Method in class cc.mallet.fst.Transducer.TransitionIterator
next() - Method in class cc.mallet.grmm.inference.MessageArray.Iterator
next() - Method in class cc.mallet.grmm.inference.MessageArray.ToMsgsIterator
next() - Method in class cc.mallet.grmm.util.PipedIterator
  Deprecated.
next() - Method in class cc.mallet.pipe.iterator.ArrayDataAndTargetIterator
next() - Method in class cc.mallet.pipe.iterator.ArrayIterator
next() - Method in class cc.mallet.pipe.iterator.ConcatenatedInstanceIterator
next() - Method in class cc.mallet.pipe.iterator.CsvIterator
next() - Method in class cc.mallet.pipe.iterator.EmptyInstanceIterator
next() - Method in class cc.mallet.pipe.iterator.FileIterator
next() - Method in class cc.mallet.pipe.iterator.FileListIterator
next() - Method in class cc.mallet.pipe.iterator.FileUriIterator
next() - Method in class cc.mallet.pipe.iterator.LineGroupIterator
next() - Method in class cc.mallet.pipe.iterator.LineIterator
next() - Method in class cc.mallet.pipe.iterator.ParenGroupIterator
next() - Method in class cc.mallet.pipe.iterator.PatternMatchIterator
next() - Method in class cc.mallet.pipe.iterator.PipeExtendedIterator
  Deprecated.
next() - Method in class cc.mallet.pipe.iterator.PipeInputIterator
  Deprecated.
next() - Method in class cc.mallet.pipe.iterator.RandomFeatureVectorIterator
next() - Method in class cc.mallet.pipe.iterator.RandomTokenSequenceIterator
next() - Method in class cc.mallet.pipe.iterator.SegmentIterator
next() - Method in class cc.mallet.pipe.iterator.SelectiveFileLineIterator
next() - Method in class cc.mallet.pipe.iterator.SimpleFileLineIterator
next() - Method in class cc.mallet.pipe.iterator.StringArrayIterator
next() - Method in class cc.mallet.pipe.iterator.UnlabeledFileIterator
next() - Method in class cc.mallet.types.ChainedInstanceIterator
  Deprecated.
next() - Method in class cc.mallet.types.CrossValidationIterator
  Returns the next training/testing split.
next() - Method in class cc.mallet.types.FeatureVectorSequence.Iterator
next() - Method in class cc.mallet.types.InstanceList.CrossValidationIterator
next() - Method in class cc.mallet.types.LabelSequence.Iterator
next() - Method in class cc.mallet.types.SingleInstanceIterator
next() - Method in class cc.mallet.util.CharSequenceLexer
next() - Method in interface cc.mallet.util.Lexer
next() - Method in class cc.mallet.util.PropertyList.Iterator
next - Variable in class cc.mallet.util.PropertyList
next() - Method in class cc.mallet.util.search.AStar
next() - Method in class cc.mallet.util.search.SearchNode.NextNodeIterator
next() - Method in class cc.mallet.util.search.SearchState.NextStateIterator
nextAnswer() - Method in class cc.mallet.util.search.AStar
  Get the next search node for a final state.
nextBeta(double, double) - Method in class cc.mallet.util.Randoms
  Return a random double drawn from a Beta distribution with mean a/(a+b) and variance ab/((a+b+1)(a+b)^2).
nextBitSet(int, double) - Method in class cc.mallet.util.Randoms
  Return a random BitSet with "size" bits, each having probability p of being true.
nextBoolean() - Method in class cc.mallet.util.Randoms
  Return a random boolean, equally likely to be true or false.
nextBoolean(double) - Method in class cc.mallet.util.Randoms
  Return a random boolean, with probability p of being true.
nextChiSq() - Method in class cc.mallet.util.Randoms
  Return a random double drawn from an Chi-squarted distribution with mean 1 and variance 2.
nextChiSq(int) - Method in class cc.mallet.util.Randoms
  Return a random double drawn from an Chi-squared distribution with mean df and variance 2*df.
nextChiSq(int, double) - Method in class cc.mallet.util.Randoms
  Return a random double drawn from an Chi-squared distribution with mean df+lambda and variance 2*df.
nextDeselectedIndex(int) - Method in class cc.mallet.types.FeatureSelection
nextDiscrete(double[]) - Method in class cc.mallet.util.Randoms
  Draw a single sample from multinomial "a".
nextDiscrete(double[], double) - Method in class cc.mallet.util.Randoms
  draw a single sample from (unnormalized) multinomial "a", with normalizing factor "sum".
nextDistribution() - Method in class cc.mallet.types.Dirichlet
nextExp() - Method in class cc.mallet.util.Randoms
  Return a random double drawn from an Exponential distribution with mean 1 and variance 1.
nextExp(double) - Method in class cc.mallet.util.Randoms
  Return a random double drawn from an Exponential distribution with mean beta and variance beta^2.
nextExp(double, double) - Method in class cc.mallet.util.Randoms
  Return a random double drawn from an Exponential distribution with mean beta+lambda and variance beta^2.
nextFactor(VarSet) - Method in interface cc.mallet.grmm.inference.RandomGraphs.FactorGenerator
nextFactor(VarSet) - Method in class cc.mallet.grmm.inference.RandomGraphs.UniformFactorGenerator
nextFeatureVector(Alphabet, double[], double[], Randoms) - Static method in class cc.mallet.util.MVNormal
nextFile() - Method in class cc.mallet.pipe.iterator.FileIterator
nextFile() - Method in class cc.mallet.pipe.iterator.FileListIterator
nextFile() - Method in class cc.mallet.pipe.iterator.UnlabeledFileIterator
nextGamma() - Method in class cc.mallet.util.Randoms
  Return a random double drawn from a Gamma distribution with mean 1.0 and variance 1.0.
nextGamma(double) - Method in class cc.mallet.util.Randoms
  Return a random double drawn from a Gamma distribution with mean alpha and variance 1.0.
nextGamma(double, double) - Method in class cc.mallet.util.Randoms
  Return a random double drawn from a Gamma distribution with mean alpha*beta and variance alpha*beta^2.
nextGamma(double, double, double) - Method in class cc.mallet.util.Randoms
  Return a random double drawn from a Gamma distribution with mean alpha*beta+lamba and variance alpha*beta^2.
nextGaussian() - Method in class cc.mallet.util.Randoms
  Return a random double drawn from a Gaussian distribution with mean 0 and variance 1.
nextGaussian(double, double) - Method in class cc.mallet.util.Randoms
  Return a random double drawn from a Gaussian distribution with mean m and variance s2.
nextMVNormal(double[], double[], Randoms) - Static method in class cc.mallet.util.MVNormal
  Sample a multivariate normal from a precision matrix (ie inverse covariance matrix)
nextMVNormal(int, double[], double[], Randoms) - Static method in class cc.mallet.util.MVNormal
nextMVNormalPosterior(double[], double[], double[], double[], int, Randoms) - Static method in class cc.mallet.util.MVNormal
nextMVNormalWithCholesky(double[], double[], Randoms) - Static method in class cc.mallet.util.MVNormal
nextNode() - Method in class cc.mallet.util.search.AStarNode.NextNodeIterator
nextNode() - Method in class cc.mallet.util.search.SearchNode.NextNodeIterator
  The search tree node for the next state reached from the current state.
nextPoisson(double) - Method in class cc.mallet.util.Randoms
  Return random integer from Poission with parameter lambda.
nextPoisson() - Method in class cc.mallet.util.Randoms
  Return nextPoisson(1).
nextProperty() - Method in class cc.mallet.util.PropertyList.Iterator
nextSegment() - Method in class cc.mallet.pipe.iterator.SegmentIterator
nextSelectedIndex(int) - Method in class cc.mallet.types.FeatureSelection
nextSplit() - Method in class cc.mallet.types.CrossValidationIterator
  Returns the next training/testing split.
nextSplit(int) - Method in class cc.mallet.types.CrossValidationIterator
  Returns the next training/testing split.
nextSplit() - Method in class cc.mallet.types.InstanceList.CrossValidationIterator
  Returns the next training/testing split.
nextSplit(int) - Method in class cc.mallet.types.InstanceList.CrossValidationIterator
  Returns the next split, given the number of folds you want in the training data.
nextState() - Method in class cc.mallet.fst.CRF.TransitionIterator
nextState() - Method in class cc.mallet.fst.FeatureTransducer.TransitionIterator
nextState() - Method in class cc.mallet.fst.HMM.TransitionIterator
nextState() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  Deprecated.
nextState() - Method in class cc.mallet.util.search.SearchState.NextStateIterator
  Get the next reachable state.
nextTree(FactorGraph) - Method in class cc.mallet.grmm.inference.TRP.AlmostRandomTreeFactory
nextTree(FactorGraph) - Method in interface cc.mallet.grmm.inference.TRP.TreeFactory
nextTree(FactorGraph) - Method in class cc.mallet.grmm.inference.TRP.TreeListFactory
nextUniform() - Method in class cc.mallet.util.Randoms
  Return a random double in the range 0 to 1, inclusive, uniformly sampled from that range.
nextUniform(double, double) - Method in class cc.mallet.util.Randoms
  Return a random double in the range a to b, inclusive, uniformly sampled from that range.
nextWishart(double[], int, int, Randoms) - Static method in class cc.mallet.util.MVNormal
  A Wishart random variate, based on R code by Bill Venables.
nextWishartPosterior(double[], int, double[], int, int, Randoms) - Static method in class cc.mallet.util.MVNormal
nextZeroSumMVNormalWithCholesky(double[], double[], Randoms) - Static method in class cc.mallet.util.MVNormal
  Sample a vector x from N(m, (LL')-1, such that sum_i x_i = 0.
ngramify(CharSequence) - Method in class cc.mallet.pipe.CharSequence2CharNGrams
no_longer_needed_sumNegLogProb(double, double) - Static method in class cc.mallet.fst.Transducer
NodeClusterSampleIterator - Class in cc.mallet.cluster.iterator
  Samples merges of a singleton cluster with another (possibly non-singleton) cluster.
NodeClusterSampleIterator(Clustering, Randoms, double, int) - Constructor for class cc.mallet.cluster.iterator.NodeClusterSampleIterator
nodes - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice
noisify(double) - Method in class cc.mallet.types.InstanceList
  Deprecated.
NONMATCH - Static variable in class cc.mallet.types.StringEditVector
nonsingletonClusters - Variable in class cc.mallet.cluster.iterator.PairSampleIterator
Noop - Class in cc.mallet.pipe
  A pipe that does nothing to the instance fields but which has side effects on the dictionary.
Noop() - Constructor for class cc.mallet.pipe.Noop
Noop(Alphabet, Alphabet) - Constructor for class cc.mallet.pipe.Noop
  Pass through input without change, but force the creation of Alphabet's, so it can be shared by future DictionariedPipe's.
NoopTransducerTrainer - Class in cc.mallet.fst
  A TransducerTrainer that does no training, but simply acts as a container for a Transducer; for use in situations that require a TransducerTrainer, such as the TransducerEvaluator methods.
NoopTransducerTrainer(Transducer) - Constructor for class cc.mallet.fst.NoopTransducerTrainer
NormalFactor - Class in cc.mallet.grmm.types
  Multivariate Gaussian factor.
NormalFactor(VarSet, Vector, Matrix) - Constructor for class cc.mallet.grmm.types.NormalFactor
normalize() - Method in class cc.mallet.grmm.types.AbstractTableFactor
normalize() - Method in class cc.mallet.grmm.types.Assignment
normalize() - Method in class cc.mallet.grmm.types.BetaFactor
normalize() - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
normalize() - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
normalize() - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
normalize() - Method in class cc.mallet.grmm.types.ConstantFactor
normalize() - Method in class cc.mallet.grmm.types.CPT
normalize() - Method in interface cc.mallet.grmm.types.Factor
  Multiplies this potential by a constant such that it sums to 1.
normalize() - Method in class cc.mallet.grmm.types.FactorGraph
normalize() - Method in class cc.mallet.grmm.types.LogTableFactor
normalize() - Method in class cc.mallet.grmm.types.NormalFactor
normalize() - Method in class cc.mallet.grmm.types.PottsTableFactor
normalize() - Method in class cc.mallet.grmm.types.SkeletonFactor
normalize() - Method in class cc.mallet.grmm.types.TableFactor
  Multiplies every entry in the potential by a constant such that all the entries sum to 1.
normalize() - Method in class cc.mallet.grmm.types.UniformFactor
normalize() - Method in class cc.mallet.grmm.types.UniNormalFactor
normalize(double[]) - Static method in class cc.mallet.types.DenseVector
normalize(double[]) - Static method in class cc.mallet.types.MatrixOps
normalizeAll() - Method in class cc.mallet.grmm.inference.JunctionTree
  Normalizes all potentials in the tree, both node and sepset.
normalizeAsCpt(AbstractTableFactor, Variable) - Static method in class cc.mallet.grmm.types.Factors
normalizeBeliefs - Variable in class cc.mallet.grmm.inference.AbstractBeliefPropagation
NORMALIZED_COUNT - Static variable in class cc.mallet.pipe.tsf.CountMatches
NormalizedDotProductMetric - Class in cc.mallet.types
  Computes 1 - [ / sqrt (*)] aka 1 - cosine similarity
NormalizedDotProductMetric() - Constructor for class cc.mallet.types.NormalizedDotProductMetric
NPTopicModel - Class in cc.mallet.topics
  A non-parametric topic model that uses the "minimal path" assumption to reduce bookkeeping.
NPTopicModel(double, double, double) - Constructor for class cc.mallet.topics.NPTopicModel
NUM_LEVELS - Static variable in class cc.mallet.topics.HierarchicalPAM
numBatches - Variable in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
numberNext() - Method in class cc.mallet.fst.Transducer.TransitionIterator
  Deprecated.
numberSamples - Variable in class cc.mallet.cluster.iterator.PairSampleIterator
numClasses - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
numCombinations(int, int) - Static method in class cc.mallet.util.Maths
numConstraints - Static variable in class cc.mallet.classify.tui.Vectors2FeatureConstraints
numCorrect() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
numCorrectAtCoverage(double) - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
numDestinations() - Method in class cc.mallet.fst.CRF.State
numericIterator() - Method in class cc.mallet.util.PropertyList
numIncorrectSegments(Sequence, Sequence) - Method in class cc.mallet.fst.MultiSegmentationEvaluator
  Returns the number of incorrect segments in `predOutput`
numIterations - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
numIterations - Variable in class cc.mallet.topics.ParallelTopicModel
numIterations - Variable in class cc.mallet.topics.PolylingualTopicModel
numLabels - Variable in class cc.mallet.cluster.Clustering
numLevels() - Method in class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
numLocations() - Method in class cc.mallet.grmm.types.AbstractTableFactor
numLocations() - Method in class cc.mallet.grmm.types.CPT
numLocations() - Method in interface cc.mallet.grmm.types.DiscreteFactor
numLocations() - Method in class cc.mallet.types.AugmentableFeatureVector
numLocations() - Method in interface cc.mallet.types.ConstantMatrix
numLocations() - Method in class cc.mallet.types.DenseMatrix
numLocations() - Method in class cc.mallet.types.Label
numLocations() - Method in interface cc.mallet.types.Labeling
numLocations() - Method in class cc.mallet.types.SparseMatrixn
numLocations() - Method in class cc.mallet.types.SparseVector
numMaxViterbi - Static variable in class cc.mallet.extract.LatticeViewer
numParameters - Variable in class cc.mallet.fst.CRF
numPermutations(int, int) - Static method in class cc.mallet.util.Maths
numRanked() - Method in class cc.mallet.types.PartiallyRankedFeatureVector
numRows() - Method in class cc.mallet.grmm.types.Assignment
numSlices() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
numSlices() - Method in class cc.mallet.grmm.util.LabelsAssignment
numStates() - Method in class cc.mallet.fst.CRF
numStates() - Method in class cc.mallet.fst.FeatureTransducer
numStates() - Method in class cc.mallet.fst.HMM
numStates - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice
numStates - Variable in class cc.mallet.fst.semi_supervised.GECriteria
numStates - Variable in class cc.mallet.fst.semi_supervised.GELattice
numStates() - Method in class cc.mallet.fst.Transducer
numStopwords - Variable in class cc.mallet.topics.PolylingualTopicModel
numTopics - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
numTopics - Variable in class cc.mallet.topics.MarginalProbEstimator
numTopics - Variable in class cc.mallet.topics.NPTopicModel
numTopics - Variable in class cc.mallet.topics.ParallelTopicModel
numTopics - Variable in class cc.mallet.topics.PolylingualTopicModel
numTopics - Variable in class cc.mallet.topics.SimpleLDA
numTopics - Variable in class cc.mallet.topics.TopicInferencer
numTopics - Variable in class cc.mallet.topics.WorkerRunnable
numTypes - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
numTypes - Variable in class cc.mallet.topics.NPTopicModel
numTypes - Variable in class cc.mallet.topics.ParallelTopicModel
numTypes - Variable in class cc.mallet.topics.SimpleLDA
numTypes - Variable in class cc.mallet.topics.TopicInferencer
numTypes - Variable in class cc.mallet.topics.WorkerRunnable
numValues() - Method in class cc.mallet.extract.Field
numVariables() - Method in class cc.mallet.grmm.types.Assignment
numVariables() - Method in class cc.mallet.grmm.types.FactorGraph
  Returns the number of variable nodes in the graph.

## O

objectIterator() - Method in class cc.mallet.util.PropertyList
objectToUri(Object) - Static method in class cc.mallet.util.UriUtils
observedValue(Variable) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
OffsetConjunctions - Class in cc.mallet.pipe.tsf
OffsetConjunctions(boolean, Pattern, int[][]) - Constructor for class cc.mallet.pipe.tsf.OffsetConjunctions
OffsetConjunctions(boolean, int[][]) - Constructor for class cc.mallet.pipe.tsf.OffsetConjunctions
OffsetConjunctions(int[][]) - Constructor for class cc.mallet.pipe.tsf.OffsetConjunctions
OffsetFeatureConjunction - Class in cc.mallet.pipe.tsf
OffsetFeatureConjunction(String, String[], int[], boolean[], boolean) - Constructor for class cc.mallet.pipe.tsf.OffsetFeatureConjunction
  Create a Pipe for adding conjunctions of specified features.
OffsetFeatureConjunction(String, String[], int[], boolean) - Constructor for class cc.mallet.pipe.tsf.OffsetFeatureConjunction
OffsetFeatureConjunction(String, String[], int[]) - Constructor for class cc.mallet.pipe.tsf.OffsetFeatureConjunction
OffsetPropertyConjunctions - Class in cc.mallet.pipe.tsf
OffsetPropertyConjunctions(boolean, int[][]) - Constructor for class cc.mallet.pipe.tsf.OffsetPropertyConjunctions
OffsetPropertyConjunctions(int[][]) - Constructor for class cc.mallet.pipe.tsf.OffsetPropertyConjunctions
oldLogGamma(double) - Static method in class cc.mallet.util.Maths
oldMessages - Variable in class cc.mallet.grmm.inference.AbstractBeliefPropagation.AbstractMessageStrategy
oldMessages - Variable in class cc.mallet.grmm.inference.gbp.AbstractMessageStrategy
oldNextGamma(int) - Method in class cc.mallet.util.Randoms
ols(Univariate, Univariate) - Static method in class cc.mallet.util.StatFunctions
oneDistance(Factor, Factor) - Static method in class cc.mallet.grmm.types.Factors
oneDocTopicCounts - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
oneDocTopicCounts - Variable in class cc.mallet.topics.PolylingualTopicModel
oneDocTopicCounts - Variable in class cc.mallet.topics.SimpleLDA
oneNorm() - Method in class cc.mallet.types.AugmentableFeatureVector
oneNorm() - Method in interface cc.mallet.types.ConstantMatrix
oneNorm() - Method in class cc.mallet.types.DenseMatrix
oneNorm(double[]) - Static method in class cc.mallet.types.MatrixOps
oneNorm() - Method in class cc.mallet.types.SparseMatrixn
oneNorm() - Method in class cc.mallet.types.SparseVector
oneNormalize() - Method in class cc.mallet.types.DenseMatrix
oneNormalize() - Method in interface cc.mallet.types.Matrix
oneNormalize(double[]) - Static method in class cc.mallet.types.MatrixOps
oneNormalize() - Method in class cc.mallet.types.SparseMatrixn
openReader(File) - Static method in class cc.mallet.topics.tui.DMRLoader
optimizable - Variable in class cc.mallet.fst.ThreadedOptimizable
  optimizable to be parallelized
Optimizable - Interface in cc.mallet.optimize
Optimizable.ByBatchGradient - Interface in cc.mallet.optimize
Optimizable.ByCombiningBatchGradient - Interface in cc.mallet.optimize
Optimizable.ByGISUpdate - Interface in cc.mallet.optimize
Optimizable.ByGradient - Interface in cc.mallet.optimize
Optimizable.ByGradientValue - Interface in cc.mallet.optimize
Optimizable.ByHessian - Interface in cc.mallet.optimize
Optimizable.ByValue - Interface in cc.mallet.optimize
Optimizable.ByVotedPerceptron - Interface in cc.mallet.optimize
OptimizableCollection - Class in cc.mallet.optimize
OptimizableCollection() - Constructor for class cc.mallet.optimize.OptimizableCollection
OptimizableCollection.ByGradientValue - Class in cc.mallet.optimize
OptimizableCollection.ByGradientValue(Optimizable.ByGradientValue...) - Constructor for class cc.mallet.optimize.OptimizableCollection.ByGradientValue
OptimizationException - Exception in cc.mallet.optimize
  General exception thrown by optimization algorithms when there is an optimization-specific problem.
OptimizationException() - Constructor for exception cc.mallet.optimize.OptimizationException
OptimizationException(String) - Constructor for exception cc.mallet.optimize.OptimizationException
OptimizationException(String, Throwable) - Constructor for exception cc.mallet.optimize.OptimizationException
OptimizationException(Throwable) - Constructor for exception cc.mallet.optimize.OptimizationException
optimize() - Method in class cc.mallet.optimize.AGIS
optimize(int) - Method in class cc.mallet.optimize.AGIS
optimize(double[], double) - Method in class cc.mallet.optimize.BackTrackLineSearch
optimize() - Method in class cc.mallet.optimize.ConjugateGradient
optimize(int) - Method in class cc.mallet.optimize.ConjugateGradient
optimize() - Method in class cc.mallet.optimize.GradientAscent
optimize(int) - Method in class cc.mallet.optimize.GradientAscent
optimize(double[], double) - Method in class cc.mallet.optimize.GradientBracketLineOptimizer
optimize() - Method in class cc.mallet.optimize.LimitedMemoryBFGS
optimize(int) - Method in class cc.mallet.optimize.LimitedMemoryBFGS
optimize(double[], double) - Method in interface cc.mallet.optimize.LineOptimizer.ByGradient
  Returns the last step size used.
optimize(double[], double) - Method in interface cc.mallet.optimize.LineOptimizer
  Returns the last step size used.
optimize(int, int[]) - Method in interface cc.mallet.optimize.Optimizer.ByBatches
  Deprecated.
optimize(int, int, int[]) - Method in interface cc.mallet.optimize.Optimizer.ByBatches
  Deprecated.
optimize() - Method in interface cc.mallet.optimize.Optimizer
optimize(int) - Method in interface cc.mallet.optimize.Optimizer
optimize() - Method in class cc.mallet.optimize.OrthantWiseLimitedMemoryBFGS
optimize(int) - Method in class cc.mallet.optimize.OrthantWiseLimitedMemoryBFGS
optimize(int, int[]) - Method in class cc.mallet.optimize.StochasticMetaAscent
optimize(int, int, int[]) - Method in class cc.mallet.optimize.StochasticMetaAscent
optimizeAlpha(WorkerRunnable[]) - Method in class cc.mallet.topics.ParallelTopicModel
optimizeBeta(WorkerRunnable[]) - Method in class cc.mallet.topics.ParallelTopicModel
optimizeBetas() - Method in class cc.mallet.topics.PolylingualTopicModel
optimizeInterval - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
optimizeInterval - Variable in class cc.mallet.topics.ParallelTopicModel
optimizeInterval - Variable in class cc.mallet.topics.PolylingualTopicModel
Optimizer - Interface in cc.mallet.optimize
Optimizer.ByBatches - Interface in cc.mallet.optimize
  Deprecated.
OptimizerEvaluator - Interface in cc.mallet.optimize
  Callback interface that allows optimizer clients to perform some operation after every iteration.
OptimizerEvaluator.ByBatchGradient - Interface in cc.mallet.optimize
OptimizerEvaluator.ByGradient - Interface in cc.mallet.optimize
or(FeatureSelection) - Method in class cc.mallet.types.FeatureSelection
OrthantWiseLimitedMemoryBFGS - Class in cc.mallet.optimize
  Implementation of orthant-wise limited memory quasi Newton method for optimizing convex L1-regularized objectives.
OrthantWiseLimitedMemoryBFGS(Optimizable.ByGradientValue) - Constructor for class cc.mallet.optimize.OrthantWiseLimitedMemoryBFGS
OrthantWiseLimitedMemoryBFGS(Optimizable.ByGradientValue, double) - Constructor for class cc.mallet.optimize.OrthantWiseLimitedMemoryBFGS
output - Variable in class cc.mallet.types.SequencePair
output() - Method in class cc.mallet.types.SequencePair
outputAlphabet - Variable in class cc.mallet.fst.CRF
outputModelFilename - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
outputModelFilename - Variable in class cc.mallet.topics.PolylingualTopicModel
outputModelInterval - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
outputModelInterval - Variable in class cc.mallet.topics.PolylingualTopicModel
outputPipe - Variable in class cc.mallet.fst.Transducer
  A pipe that should expect the Transducer's output sequence in the "target" slot, and should produce something printable in the "source" slot that indicates the results of transduction.
OVER_MAX - Static variable in class cc.mallet.pipe.tsf.CountMatches

## P

PagedInstanceList - Class in cc.mallet.types
  An InstanceList which avoids OutOfMemoryErrors by saving Instances to disk when there is not enough memory to create a new Instance.
PagedInstanceList(Pipe, int, int, File) - Constructor for class cc.mallet.types.PagedInstanceList
  Creates a PagedInstanceList where "instancesPerPage" instances are swapped to disk in directory "swapDir" if the amount of free system memory drops below "minFreeMemory" bytes
PagedInstanceList(Pipe, int, int) - Constructor for class cc.mallet.types.PagedInstanceList
paint(Graphics) - Method in class cc.mallet.classify.evaluate.Graph
  Paint the graph outline
paint(Graphics) - Method in class cc.mallet.classify.evaluate.Graph2
PairF1Evaluator - Class in cc.mallet.cluster.evaluate
  Evaluates two clustering using pairwise comparisons.
PairF1Evaluator() - Constructor for class cc.mallet.cluster.evaluate.PairF1Evaluator
PairSampleIterator - Class in cc.mallet.cluster.iterator
  Sample pairs of Instances.
PairSampleIterator(Clustering, Randoms, double, int) - Constructor for class cc.mallet.cluster.iterator.PairSampleIterator
PairwiseEvaluator - Class in cc.mallet.cluster.neighbor_evaluator
  Uses a `Classifier` over pairs of `Instances` to score `Neighbor`.
PairwiseEvaluator(Classifier, String, PairwiseEvaluator.CombiningStrategy, boolean) - Constructor for class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator
PairwiseEvaluator.Average - Class in cc.mallet.cluster.neighbor_evaluator
PairwiseEvaluator.Average() - Constructor for class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator.Average
PairwiseEvaluator.CombiningStrategy - Interface in cc.mallet.cluster.neighbor_evaluator
  Specifies how to combine a set of pairwise scores into a cluster-wise score.
PairwiseEvaluator.Maximum - Class in cc.mallet.cluster.neighbor_evaluator
PairwiseEvaluator.Maximum() - Constructor for class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator.Maximum
PairwiseEvaluator.Minimum - Class in cc.mallet.cluster.neighbor_evaluator
PairwiseEvaluator.Minimum() - Constructor for class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator.Minimum
PairwiseMatrix - Class in cc.mallet.cluster.util
  2-D upper-triangular matrix.
PairwiseMatrix(int) - Constructor for class cc.mallet.cluster.util.PairwiseMatrix
PairwiseScorer - Class in cc.mallet.cluster.clustering_scorer
  For each pair of Instances, if the pair is predicted to be in the same cluster, increment the total by the evaluator's score for merging the two.
PairwiseScorer(NeighborEvaluator) - Constructor for class cc.mallet.cluster.clustering_scorer.PairwiseScorer
PAM4L - Class in cc.mallet.topics
  Four Level Pachinko Allocation with MLE learning, based on Andrew's Latent Dirichlet Allocation.
PAM4L(int, int) - Constructor for class cc.mallet.topics.PAM4L
PAM4L(int, int, double, double) - Constructor for class cc.mallet.topics.PAM4L
ParallelTopicModel - Class in cc.mallet.topics
  Simple parallel threaded implementation of LDA, following the UCI NIPS paper, with SparseLDA sampling scheme and data structure.
ParallelTopicModel(int) - Constructor for class cc.mallet.topics.ParallelTopicModel
ParallelTopicModel(int, double, double) - Constructor for class cc.mallet.topics.ParallelTopicModel
ParallelTopicModel(LabelAlphabet, double, double) - Constructor for class cc.mallet.topics.ParallelTopicModel
ParameterizedFactor - Interface in cc.mallet.grmm.types
  A factor that supports taking derivatives with respect to its continuous variables.
parameters - Variable in class cc.mallet.classify.MaxEnt
parameters - Variable in class cc.mallet.fst.CRF
ParenGroupIterator - Class in cc.mallet.pipe.iterator
  Iterator that takes a Reader, breaks up the input into top-level parenthesized expressions.
ParenGroupIterator(Reader) - Constructor for class cc.mallet.pipe.iterator.ParenGroupIterator
ParenGroupIterator(Reader, char, char) - Constructor for class cc.mallet.pipe.iterator.ParenGroupIterator
ParentChildGBP - Class in cc.mallet.grmm.inference.gbp
  Created: May 27, 2005
ParentChildGBP(RegionGraphGenerator) - Constructor for class cc.mallet.grmm.inference.gbp.ParentChildGBP
ParentChildGBP(RegionGraphGenerator, MessageStrategy) - Constructor for class cc.mallet.grmm.inference.gbp.ParentChildGBP
parseArg(String) - Method in class cc.mallet.util.CommandOption.Boolean
parseArg(String) - Method in class cc.mallet.util.CommandOption.Double
parseArg(String) - Method in class cc.mallet.util.CommandOption.DoubleArray
parseArg(String) - Method in class cc.mallet.util.CommandOption.File
parseArg(String) - Method in class cc.mallet.util.CommandOption.Integer
parseArg(String) - Method in class cc.mallet.util.CommandOption.IntegerArray
parseArg(String) - Method in class cc.mallet.util.CommandOption.Object
parseArg(String) - Method in class cc.mallet.util.CommandOption.ObjectFromBean
parseArg(String[], int) - Method in class cc.mallet.util.CommandOption
  Called after this CommandOption matches an argument.
parseArg(String) - Method in class cc.mallet.util.CommandOption
parseArg(String) - Method in class cc.mallet.util.CommandOption.Set
parseArg(String[], int) - Method in class cc.mallet.util.CommandOption.SpacedStrings
parseArg(String) - Method in class cc.mallet.util.CommandOption.String
parseFile(File) - Static method in class cc.mallet.cluster.tui.Text2Clusterings
parseSentence(String) - Method in class cc.mallet.pipe.SimpleTaggerSentence2TokenSequence
  Parses a string representing a sequence of rows of tokens into an array of arrays of tokens.
parseString(String) - Method in class cc.mallet.types.StringEditVector
PartiallyRankedFeatureVector - Class in cc.mallet.types
PartiallyRankedFeatureVector(Alphabet, int[], double[]) - Constructor for class cc.mallet.types.PartiallyRankedFeatureVector
PartiallyRankedFeatureVector(Alphabet, double[]) - Constructor for class cc.mallet.types.PartiallyRankedFeatureVector
PartiallyRankedFeatureVector(Alphabet, DenseVector) - Constructor for class cc.mallet.types.PartiallyRankedFeatureVector
PartiallyRankedFeatureVector(Alphabet, AugmentableFeatureVector) - Constructor for class cc.mallet.types.PartiallyRankedFeatureVector
PartiallyRankedFeatureVector(Alphabet, SparseVector) - Constructor for class cc.mallet.types.PartiallyRankedFeatureVector
PartiallyRankedFeatureVector.Factory - Interface in cc.mallet.types
PartiallyRankedFeatureVector.PerLabelFactory - Interface in cc.mallet.types
PatternMatchIterator - Class in cc.mallet.pipe.iterator
  Iterates over matching regular expresions.
PatternMatchIterator(CharSequence, Pattern) - Constructor for class cc.mallet.pipe.iterator.PatternMatchIterator
pbinom(int, int, double) - Static method in class cc.mallet.util.Maths
  Vastly inefficient O(x) method to compute cdf of B(n,p)
pchisq(double, double) - Method in class cc.mallet.util.StatFunctions
peekLineGroup() - Method in class cc.mallet.pipe.iterator.LineGroupIterator
PerClassAccuracyEvaluator - Class in cc.mallet.fst
  Determines the precision, recall and F1 on a per-class basis.
PerClassAccuracyEvaluator(InstanceList[], String[]) - Constructor for class cc.mallet.fst.PerClassAccuracyEvaluator
PerClassAccuracyEvaluator(InstanceList, String) - Constructor for class cc.mallet.fst.PerClassAccuracyEvaluator
PerClassAccuracyEvaluator(InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.fst.PerClassAccuracyEvaluator
perClassFeatureSelection - Variable in class cc.mallet.classify.MaxEnt
PerDocumentF1Evaluator - Class in cc.mallet.extract
  Created: Oct 8, 2004
PerDocumentF1Evaluator() - Constructor for class cc.mallet.extract.PerDocumentF1Evaluator
PerFieldF1Evaluator - Class in cc.mallet.extract
  Created: Oct 8, 2004
PerFieldF1Evaluator() - Constructor for class cc.mallet.extract.PerFieldF1Evaluator
PerLabelFeatureCounts - Class in cc.mallet.types
PerLabelFeatureCounts(InstanceList) - Constructor for class cc.mallet.types.PerLabelFeatureCounts
PerLabelFeatureCounts.Factory - Class in cc.mallet.types
PerLabelFeatureCounts.Factory() - Constructor for class cc.mallet.types.PerLabelFeatureCounts.Factory
PerLabelInfoGain - Class in cc.mallet.types
PerLabelInfoGain(InstanceList) - Constructor for class cc.mallet.types.PerLabelInfoGain
PerLabelInfoGain.Factory - Class in cc.mallet.types
PerLabelInfoGain.Factory() - Constructor for class cc.mallet.types.PerLabelInfoGain.Factory
pf(double, double, double) - Static method in class cc.mallet.util.StatFunctions
phi(DenseAssignmentIterator) - Method in class cc.mallet.grmm.types.AbstractFactor
PI_SQUARED_OVER_SIX - Static variable in class cc.mallet.types.Dirichlet
pickVertexToRemove(UndirectedGraph, ArrayList) - Method in class cc.mallet.grmm.inference.JunctionTreeInferencer
pipe(Instance) - Method in class cc.mallet.cluster.tui.Clusterings2Clusterer.ClusteringPipe
pipe(Instance) - Method in class cc.mallet.extract.pipe.TokenSequence2Tokenization
pipe(Instance) - Method in class cc.mallet.fst.SimpleTagger.SimpleTaggerSentence2FeatureVectorSequence
pipe(Instance) - Method in class cc.mallet.fst.tests.TestCRF.TestCRF2String
pipe(Instance) - Method in class cc.mallet.fst.tests.TestCRF.TestCRFTokenSequenceRemoveSpaces
pipe(Instance) - Method in class cc.mallet.fst.tests.TestMEMM.TestMEMM2String
pipe(Instance) - Method in class cc.mallet.fst.tests.TestMEMM.TestMEMMTokenSequenceRemoveSpaces
pipe(Instance) - Method in class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
pipe(Instance) - Method in class cc.mallet.grmm.util.LabelsSequence2Assignment
pipe(Instance) - Method in class cc.mallet.grmm.util.RememberTokenizationPipe
pipe(Instance) - Method in class cc.mallet.grmm.util.SliceLabelsSequence
pipe(Instance) - Method in class cc.mallet.pipe.AddClassifierTokenPredictions
  Add the token classifier's predictions as features to the instance.
pipe(Instance) - Method in class cc.mallet.pipe.Array2FeatureVector
  Convert the data in an `Instance` from an array to a `FeatureVector` leaving other fields unchanged.
pipe(Instance) - Method in class cc.mallet.pipe.AugmentableFeatureVectorAddConjunctions
pipe(Instance) - Method in class cc.mallet.pipe.AugmentableFeatureVectorLogScale
pipe(Instance) - Method in class cc.mallet.pipe.CharSequence2CharNGrams
pipe(Instance) - Method in class cc.mallet.pipe.CharSequence2TokenSequence
pipe(Instance) - Method in class cc.mallet.pipe.CharSequenceArray2TokenSequence
pipe(Instance) - Method in class cc.mallet.pipe.CharSequenceLowercase
pipe(Instance) - Method in class cc.mallet.pipe.CharSequenceRemoveHTML
pipe(Instance) - Method in class cc.mallet.pipe.CharSequenceRemoveUUEncodedBlocks
pipe(Instance) - Method in class cc.mallet.pipe.CharSequenceReplace
pipe(Instance) - Method in class cc.mallet.pipe.CharSubsequence
pipe(Instance) - Method in class cc.mallet.pipe.Classification2ConfidencePredictingFeatureVector
pipe(Instance) - Method in class cc.mallet.pipe.Csv2Array
  Convert the data in an `Instance` from a CharSequence of comma-separated-values to an array, where each index is the feature name.
pipe(Instance) - Method in class cc.mallet.pipe.Csv2FeatureVector
  Convert the data in the given `Instance` from a `CharSequence` of sparse feature-value pairs to a `FeatureVector`
pipe(Instance) - Method in class cc.mallet.pipe.Directory2FileIterator
pipe(File) - Method in class cc.mallet.pipe.Directory2FileIterator
pipe(URI) - Method in class cc.mallet.pipe.Directory2FileIterator
pipe(String) - Method in class cc.mallet.pipe.Directory2FileIterator
pipe(Instance) - Method in class cc.mallet.pipe.FeatureCountPipe
pipe(Instance) - Method in class cc.mallet.pipe.FeatureSequence2AugmentableFeatureVector
pipe(Instance) - Method in class cc.mallet.pipe.FeatureSequence2FeatureVector
pipe(Instance) - Method in class cc.mallet.pipe.FeatureSequenceConvolution
  construct word co-occurrence features from the original sequence do combinatoric, n choose 2, can be extended to n choose 3 public void convolution() { int fi = -1; int pre = -1; int i,j; int curLen = length; for(i = 0; i < curLen-1; i++) { for(j = i + 1; j < curLen; j++) { pre = features[i]; fi = features[j]; Object preO = dictionary.lookupObject(pre); Object curO = dictionary.lookupObject(fi); Object coO = preO.toString() + "_" + curO.toString(); add(coO); } } }
pipe(Instance) - Method in class cc.mallet.pipe.FeatureValueString2FeatureVector
pipe(Instance) - Method in class cc.mallet.pipe.FeatureVectorConjunctions
pipe(Instance) - Method in class cc.mallet.pipe.Filename2CharSequence
pipe(Reader) - Method in class cc.mallet.pipe.Filename2CharSequence
pipe(Instance) - Method in class cc.mallet.pipe.Input2CharSequence
pipe(URI) - Method in class cc.mallet.pipe.Input2CharSequence
pipe(File) - Method in class cc.mallet.pipe.Input2CharSequence
pipe(Reader) - Method in class cc.mallet.pipe.Input2CharSequence
pipe(CharSequence) - Method in class cc.mallet.pipe.Input2CharSequence
pipe(Instance) - Method in class cc.mallet.pipe.InstanceListTrimFeaturesByCount
pipe(Instance) - Method in class cc.mallet.pipe.LineGroupString2TokenSequence
pipe(Instance) - Method in class cc.mallet.pipe.MakeAmpersandXMLFriendly
pipe(Instance) - Method in class cc.mallet.pipe.Noop
Pipe - Class in cc.mallet.pipe
  The abstract superclass of all Pipes, which transform one data type to another.
Pipe() - Constructor for class cc.mallet.pipe.Pipe
  Construct a pipe with no data and target dictionaries
Pipe(Alphabet, Alphabet) - Constructor for class cc.mallet.pipe.Pipe
  Construct pipe with data and target dictionaries.
pipe(Instance) - Method in class cc.mallet.pipe.Pipe
  Really this should be 'protected', but isn't for historical reasons.
pipe(Instance) - Method in class cc.mallet.pipe.PrintInput
pipe(Instance) - Method in class cc.mallet.pipe.PrintInputAndTarget
pipe(Instance) - Method in class cc.mallet.pipe.PrintTokenSequenceFeatures
pipe(Instance) - Method in class cc.mallet.pipe.SaveDataInSource
pipe(Instance) - Method in class cc.mallet.pipe.SelectiveSGML2TokenSequence
pipe(Instance) - Method in class cc.mallet.pipe.SGML2TokenSequence
pipe(Instance) - Method in class cc.mallet.pipe.SimpleTaggerSentence2StringTokenization
  Takes an instance with data of type String or String[][] and creates an Instance of type StringTokenization.
pipe(Instance) - Method in class cc.mallet.pipe.SimpleTaggerSentence2TokenSequence
  Takes an instance with data of type String or String[][] and creates an Instance of type TokenSequence.
pipe(Instance) - Method in class cc.mallet.pipe.SimpleTokenizer
pipe(Instance) - Method in class cc.mallet.pipe.SourceLocation2TokenSequence
pipe(File) - Method in class cc.mallet.pipe.SourceLocation2TokenSequence
pipe(BufferedReader) - Method in class cc.mallet.pipe.SourceLocation2TokenSequence
pipe(Instance) - Method in class cc.mallet.pipe.StringAddNewLineDelimiter
pipe(Instance) - Method in class cc.mallet.pipe.StringList2FeatureSequence
pipe(Instance) - Method in class cc.mallet.pipe.SvmLight2FeatureVectorAndLabel
pipe(Instance) - Method in class cc.mallet.pipe.Target2FeatureSequence
pipe(Instance) - Method in class cc.mallet.pipe.Target2Label
pipe(Instance) - Method in class cc.mallet.pipe.Target2LabelSequence
pipe(Instance) - Method in class cc.mallet.pipe.TargetRememberLastLabel
pipe(Instance) - Method in class cc.mallet.pipe.TargetStringToFeatures
pipe(Instance) - Method in class cc.mallet.pipe.tests.TestInstancePipe.Array2ArrayIterator
pipe(Instance) - Method in class cc.mallet.pipe.tests.TestSGML2TokenSequence.Array2ArrayIterator
pipe(Instance) - Method in class cc.mallet.pipe.Token2FeatureVector
pipe(Instance) - Method in class cc.mallet.pipe.TokenSequence2FeatureSequence
pipe(Instance) - Method in class cc.mallet.pipe.TokenSequence2FeatureSequenceWithBigrams
pipe(Instance) - Method in class cc.mallet.pipe.TokenSequence2FeatureVectorSequence
pipe(Instance) - Method in class cc.mallet.pipe.TokenSequenceLowercase
pipe(Instance) - Method in class cc.mallet.pipe.TokenSequenceMatchDataAndTarget
pipe(Instance) - Method in class cc.mallet.pipe.TokenSequenceNGrams
pipe(Instance) - Method in class cc.mallet.pipe.TokenSequenceParseFeatureString
pipe(Instance) - Method in class cc.mallet.pipe.TokenSequenceRemoveNonAlpha
pipe(Instance) - Method in class cc.mallet.pipe.TokenSequenceRemoveStopwords
pipe(Instance) - Method in class cc.mallet.pipe.tsf.CountMatches
pipe(Instance) - Method in class cc.mallet.pipe.tsf.CountMatchesAlignedWithOffsets
pipe(Instance) - Method in class cc.mallet.pipe.tsf.CountMatchesMatching
pipe(Instance) - Method in class cc.mallet.pipe.tsf.FeaturesInWindow
pipe(Instance) - Method in class cc.mallet.pipe.tsf.FeaturesOfFirstMention
pipe(Instance) - Method in class cc.mallet.pipe.tsf.LexiconMembership
pipe(Instance) - Method in class cc.mallet.pipe.tsf.OffsetConjunctions
pipe(Instance) - Method in class cc.mallet.pipe.tsf.OffsetFeatureConjunction
pipe(Instance) - Method in class cc.mallet.pipe.tsf.OffsetPropertyConjunctions
pipe(Instance) - Method in class cc.mallet.pipe.tsf.RegexMatches
pipe(Instance) - Method in class cc.mallet.pipe.tsf.SequencePrintingPipe
pipe(Instance) - Method in class cc.mallet.pipe.tsf.Target2BIOFormat
pipe(Instance) - Method in class cc.mallet.pipe.tsf.TokenFirstPosition
pipe(Instance) - Method in class cc.mallet.pipe.tsf.TokenText
pipe(Instance) - Method in class cc.mallet.pipe.tsf.TokenTextCharNGrams
pipe(Instance) - Method in class cc.mallet.pipe.tsf.TokenTextCharPrefix
pipe(Instance) - Method in class cc.mallet.pipe.tsf.TokenTextCharSuffix
pipe(Instance) - Method in class cc.mallet.pipe.tsf.TokenTextNGrams
pipe(Instance) - Method in class cc.mallet.pipe.tsf.TrieLexiconMembership
pipe(Instance) - Method in class cc.mallet.share.casutton.ner.ConllNer2003Sentence2TokenSequence
pipe(Instance) - Method in class cc.mallet.share.mccallum.ner.ConllNer2003Sentence2TokenSequence
pipe(Instance) - Method in class cc.mallet.share.mccallum.ner.TokenSequenceDocHeader
pipe(Instance) - Method in class cc.mallet.share.upenn.ner.FeatureWindow
pipe(Instance) - Method in class cc.mallet.share.upenn.ner.LengthBins
pipe(Instance) - Method in class cc.mallet.share.upenn.ner.ListMember
pipe(Instance) - Method in class cc.mallet.share.upenn.ner.LongRegexMatches
pipe(Instance) - Method in class cc.mallet.share.weili.ner.enron.EnronMessage2TokenSequence
PipedInstanceWithConfidence - Class in cc.mallet.fst.confidence
  Helper class to store confidence of an Instance.
PipedInstanceWithConfidence(Instance, double, boolean) - Constructor for class cc.mallet.fst.confidence.PipedInstanceWithConfidence
PipedIterator - Class in cc.mallet.grmm.util
  Deprecated.
PipedIterator(Iterator<Instance>, Pipe) - Constructor for class cc.mallet.grmm.util.PipedIterator
  Deprecated.
PipeException - Exception in cc.mallet.pipe
PipeException() - Constructor for exception cc.mallet.pipe.PipeException
PipeExtendedIterator - Class in cc.mallet.pipe.iterator
  Deprecated.
PipeExtendedIterator(Iterator<Instance>, Pipe) - Constructor for class cc.mallet.pipe.iterator.PipeExtendedIterator
  Deprecated. Creates a new `PipeExtendedIterator` instance.
pipeInput(Object) - Method in class cc.mallet.extract.CRFExtractor
PipeInputIterator - Class in cc.mallet.pipe.iterator
  Deprecated.
PipeInputIterator() - Constructor for class cc.mallet.pipe.iterator.PipeInputIterator
  Deprecated.
pipeInstances(Iterator<Instance>) - Method in class cc.mallet.extract.CRFExtractor
pipes() - Method in class cc.mallet.pipe.SerialPipes
  Allows access to the underlying collection of Pipes.
PipeUtils - Class in cc.mallet.pipe
  Created: Aug 28, 2005
PlainLogFormatter - Class in cc.mallet.util
PlainLogFormatter() - Constructor for class cc.mallet.util.PlainLogFormatter
plusEquals(CRF.Factors, double) - Method in class cc.mallet.fst.CRF.Factors
plusEquals(CRF.Factors, double, boolean) - Method in class cc.mallet.fst.CRF.Factors
plusEquals(double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Adds a constant to all values in the table.
plusEquals(Factor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
plusEquals(AugmentableFeatureVector, double) - Method in class cc.mallet.types.AugmentableFeatureVector
plusEquals(SparseVector, double) - Method in class cc.mallet.types.AugmentableFeatureVector
plusEquals(SparseVector) - Method in class cc.mallet.types.AugmentableFeatureVector
plusEquals(double) - Method in class cc.mallet.types.DenseMatrix
plusEquals(ConstantMatrix) - Method in class cc.mallet.types.DenseMatrix
plusEquals(ConstantMatrix, double) - Method in class cc.mallet.types.DenseMatrix
plusEquals(double[], double[]) - Static method in class cc.mallet.types.DenseMatrix
plusEquals(double[], double[], double) - Static method in class cc.mallet.types.DenseMatrix
plusEquals(ConstantMatrix) - Method in interface cc.mallet.types.Matrix
plusEquals(ConstantMatrix, double) - Method in interface cc.mallet.types.Matrix
plusEquals(int, int, double) - Method in class cc.mallet.types.Matrix2
  Deprecated.
plusEquals(double[], double) - Static method in class cc.mallet.types.MatrixOps
  Adds a scalar to every element in an array.
plusEquals(double[], double[]) - Static method in class cc.mallet.types.MatrixOps
plusEquals(double[], double[], double) - Static method in class cc.mallet.types.MatrixOps
plusEquals(double[][], double[][], double) - Static method in class cc.mallet.types.MatrixOps
plusEquals(ConstantMatrix) - Method in class cc.mallet.types.SparseMatrixn
plusEquals(ConstantMatrix, double) - Method in class cc.mallet.types.SparseMatrixn
plusEqualsAtLocation(int, double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
plusEqualsAtLocation(int, double) - Method in class cc.mallet.grmm.types.LogTableFactor
plusEqualsAtLocation(int, double) - Method in class cc.mallet.grmm.types.TableFactor
plusEqualsGaussianPriorGradient(CRF.Factors, double) - Method in class cc.mallet.fst.CRF.Factors
plusEqualsHyperbolicPriorGradient(CRF.Factors, double, double) - Method in class cc.mallet.fst.CRF.Factors
plusEqualsInternal(DiscreteFactor) - Method in class cc.mallet.grmm.types.AbstractTableFactor
plusEqualsInternal(DiscreteFactor) - Method in class cc.mallet.grmm.types.LogTableFactor
  Does the conceptual equivalent of this += pot.
plusEqualsInternal(DiscreteFactor) - Method in class cc.mallet.grmm.types.TableFactor
plusEqualsSparse(SparseVector, double) - Method in class cc.mallet.types.HashedSparseVector
plusEqualsSparse(SparseVector) - Method in class cc.mallet.types.HashedSparseVector
plusEqualsSparse(SparseVector, double) - Method in class cc.mallet.types.IndexedSparseVector
plusEqualsSparse(SparseVector) - Method in class cc.mallet.types.IndexedSparseVector
plusEqualsSparse(SparseVector) - Method in class cc.mallet.types.SparseVector
  For each index i that is present in this vector, set this[i] += v[i].
plusEqualsSparse(SparseVector, double) - Method in class cc.mallet.types.SparseVector
  For each index i that is present in this vector, set this[i] += factor * v[i].
pnorm(double, boolean) - Static method in class cc.mallet.util.StatFunctions
pnorm(double, boolean, double, double) - Static method in class cc.mallet.util.StatFunctions
pointBiserialCorrelation() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
  Correlation when one variable (X) is binary: r = (bar(x1) - bar(x0)) * sqrt(p(1-p)) / sx , where bar(x1) = mean of X when Y is 1 bar(x0) = mean of X when Y is 0 sx = standard deviation of X p = proportion of values where Y=1
PolylingualTopicModel - Class in cc.mallet.topics
  Latent Dirichlet Allocation for loosely parallel corpora in arbitrary languages
PolylingualTopicModel(int) - Constructor for class cc.mallet.topics.PolylingualTopicModel
PolylingualTopicModel(int, double) - Constructor for class cc.mallet.topics.PolylingualTopicModel
PolylingualTopicModel(int, double, Randoms) - Constructor for class cc.mallet.topics.PolylingualTopicModel
PolylingualTopicModel(LabelAlphabet, double, Randoms) - Constructor for class cc.mallet.topics.PolylingualTopicModel
PolylingualTopicModel.TopicAssignment - Class in cc.mallet.topics
PolylingualTopicModel.TopicAssignment(Instance[], LabelSequence[]) - Constructor for class cc.mallet.topics.PolylingualTopicModel.TopicAssignment
positiveCount - Variable in class cc.mallet.cluster.iterator.PairSampleIterator
positiveProportion - Variable in class cc.mallet.cluster.iterator.PairSampleIterator
positiveTarget - Variable in class cc.mallet.cluster.iterator.PairSampleIterator
postParsing(CommandOption.List) - Method in class cc.mallet.util.CommandOption
  To be overridden by subclasses; "list" is the the CommandOption.List that called this option
PottsTableFactor - Class in cc.mallet.grmm.types
  A factor over a continuous variable alpha and discrete variables `x` such that `phi(x|alpha)`is Potts.``
PottsTableFactor(VarSet, Variable) - Constructor for class cc.mallet.grmm.types.PottsTableFactor
PottsTableFactor(Variable, Variable, Variable) - Constructor for class cc.mallet.grmm.types.PottsTableFactor
pow(int) - Static method in class cc.mallet.grmm.util.Flops
preamble(ClassifierTrainer) - Method in class cc.mallet.classify.ClassifierEvaluator
preamble(TransducerTrainer) - Method in class cc.mallet.fst.CRFWriter
preamble(TransducerTrainer) - Method in class cc.mallet.fst.TransducerEvaluator
preamble(TransducerTrainer) - Method in class cc.mallet.fst.ViterbiWriter
preceedingPipeDataAlphabetNotification(Alphabet) - Method in class cc.mallet.pipe.Pipe
preceedingPipeTargetAlphabetNotification(Alphabet) - Method in class cc.mallet.pipe.Pipe
precision - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
precondition(TransducerTrainer) - Method in class cc.mallet.fst.TransducerEvaluator
  If this returns false, then the body of the evaluate(TransducerTrainer) method will not run.
precondition(Instance) - Method in class cc.mallet.pipe.Pipe
  Each instance processed is tested by this method.
predicate(Pipe) - Method in class cc.mallet.pipe.SerialPipes.Predicate
predict(InstanceList) - Method in class cc.mallet.fst.CRF
  Deprecated.
print() - Method in class cc.mallet.classify.C45.Node
  Prints the tree rooted at this node
print(String) - Method in class cc.mallet.classify.C45.Node
print() - Method in class cc.mallet.classify.C45
  Prints the tree
print() - Method in class cc.mallet.classify.Classification
print(PrintWriter) - Method in class cc.mallet.classify.Classification
print() - Method in class cc.mallet.classify.Classifier
  Outputs human-readable description of classifier (e.g., list of weights, decision tree) to System.out
print(PrintWriter) - Method in class cc.mallet.classify.Classifier
print() - Method in class cc.mallet.classify.DecisionTree.Node
print() - Method in class cc.mallet.classify.MaxEnt
print(PrintStream) - Method in class cc.mallet.classify.MaxEnt
print() - Method in class cc.mallet.classify.MCMaxEnt
print() - Method in class cc.mallet.classify.RankMaxEnt
print(PrintWriter) - Method in class cc.mallet.extract.Extraction
print() - Method in class cc.mallet.fst.CRF
print(PrintWriter) - Method in class cc.mallet.fst.CRF
print() - Method in class cc.mallet.fst.CRF.State
print() - Method in class cc.mallet.fst.HMM
print() - Method in class cc.mallet.fst.HMM.State
print(Alphabet) - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Prints the constraints.
print() - Method in class cc.mallet.fst.Transducer
print(OutputStream) - Method in class cc.mallet.grmm.learning.ACRF
print(String, PrintWriter) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
print() - Method in class cc.mallet.types.AugmentableFeatureVector
print() - Method in interface cc.mallet.types.ConstantMatrix
print() - Method in class cc.mallet.types.DenseMatrix
print(double[]) - Static method in class cc.mallet.types.DenseVector
print(int[]) - Static method in class cc.mallet.types.DenseVector
print() - Method in class cc.mallet.types.Dirichlet
print() - Method in class cc.mallet.types.Matrix2
  Deprecated.
print(double[]) - Static method in class cc.mallet.types.MatrixOps
  Prints a double array to standard output
print(PrintWriter, double[]) - Static method in class cc.mallet.types.MatrixOps
  Prints a double array to the given PrintWriter.
print(double[][]) - Static method in class cc.mallet.types.MatrixOps
print(int[][]) - Static method in class cc.mallet.types.MatrixOps
print(int[]) - Static method in class cc.mallet.types.MatrixOps
print() - Method in class cc.mallet.types.Multinomial.Estimator
print() - Method in class cc.mallet.types.SparseMatrixn
print() - Method in class cc.mallet.types.SparseVector
print(double[]) - Static method in class cc.mallet.util.ArrayUtils
print(int[]) - Static method in class cc.mallet.util.ArrayUtils
print(Collection) - Static method in class cc.mallet.util.CollectionUtils
print(Collection, String) - Static method in class cc.mallet.util.CollectionUtils
print() - Method in class cc.mallet.util.PrintUtilities
print(Graphics, PageFormat, int) - Method in class cc.mallet.util.PrintUtilities
print() - Method in class cc.mallet.util.PropertyList
printAsDot(PrintWriter) - Method in class cc.mallet.grmm.types.FactorGraph
printAsDot(PrintWriter, Assignment) - Method in class cc.mallet.grmm.types.FactorGraph
printAverageScores() - Method in class cc.mallet.classify.ConfidencePredictingClassifier
printByRank(OutputStream) - Method in class cc.mallet.types.RankedFeatureVector
  Prints a human-readable version of this vector, with features listed in ranked order.
printByRank(PrintWriter) - Method in class cc.mallet.types.RankedFeatureVector
  Prints a human-readable version of this vector, with features listed in ranked order.
printComponent(Component) - Static method in class cc.mallet.util.PrintUtilities
printConfidenceAccuracy() - Method in class cc.mallet.classify.ConfidencePredictingClassifier
printDocumentTopics(File) - Method in class cc.mallet.topics.LDA
  Deprecated.
printDocumentTopics(PrintWriter) - Method in class cc.mallet.topics.LDA
  Deprecated.
printDocumentTopics(PrintWriter, double, int) - Method in class cc.mallet.topics.LDA
  Deprecated.
printDocumentTopics(File) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
printDocumentTopics(PrintWriter) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
printDocumentTopics(PrintWriter, double, int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
printDocumentTopics(ArrayList<LDAHyper.Topication>, File) - Method in class cc.mallet.topics.LDAStream
printDocumentTopics(ArrayList<LDAHyper.Topication>, PrintWriter) - Method in class cc.mallet.topics.LDAStream
printDocumentTopics(ArrayList<LDAHyper.Topication>, PrintWriter, double, int) - Method in class cc.mallet.topics.LDAStream
printDocumentTopics(File) - Method in class cc.mallet.topics.PAM4L
printDocumentTopics(PrintWriter, double, int) - Method in class cc.mallet.topics.PAM4L
printDocumentTopics(File) - Method in class cc.mallet.topics.ParallelTopicModel
printDocumentTopics(PrintWriter) - Method in class cc.mallet.topics.ParallelTopicModel
printDocumentTopics(PrintWriter, double, int) - Method in class cc.mallet.topics.ParallelTopicModel
printDocumentTopics(File) - Method in class cc.mallet.topics.PolylingualTopicModel
printDocumentTopics(PrintWriter) - Method in class cc.mallet.topics.PolylingualTopicModel
printDocumentTopics(PrintWriter, double, int) - Method in class cc.mallet.topics.PolylingualTopicModel
printDocumentTopics(File, double, int) - Method in class cc.mallet.topics.SimpleLDA
printDocumentTopics(File) - Method in class cc.mallet.topics.TopicalNGrams
printDocumentTopics(PrintWriter) - Method in class cc.mallet.topics.TopicalNGrams
printDocumentTopics(PrintWriter, double, int) - Method in class cc.mallet.topics.TopicalNGrams
printExtremeFeatures(PrintWriter, int) - Method in class cc.mallet.classify.MaxEnt
printGradient - Variable in class cc.mallet.fst.CRFTrainerByLabelLikelihood
printGradientAbsNorm() - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
PrintInput - Class in cc.mallet.pipe
  Print the data field of each instance.
PrintInput(String) - Constructor for class cc.mallet.pipe.PrintInput
PrintInput() - Constructor for class cc.mallet.pipe.PrintInput
PrintInput(PrintStream) - Constructor for class cc.mallet.pipe.PrintInput
PrintInput(String, PrintStream) - Constructor for class cc.mallet.pipe.PrintInput
PrintInputAndTarget - Class in cc.mallet.pipe
  Print the data and target fields of each instance.
PrintInputAndTarget(String) - Constructor for class cc.mallet.pipe.PrintInputAndTarget
PrintInputAndTarget() - Constructor for class cc.mallet.pipe.PrintInputAndTarget
printInRows(double[]) - Static method in class cc.mallet.types.MatrixOps
printInstanceLists() - Method in class cc.mallet.fst.MEMMTrainer
printLogLikelihood - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
printLogLikelihood - Variable in class cc.mallet.topics.NPTopicModel
printLogLikelihood - Variable in class cc.mallet.topics.ParallelTopicModel
printLogLikelihood - Variable in class cc.mallet.topics.PolylingualTopicModel
printLogLikelihood - Variable in class cc.mallet.topics.SimpleLDA
printLowerK(PrintWriter, int) - Method in class cc.mallet.types.RankedFeatureVector
printNode(HierarchicalLDA.NCRPNode, int) - Method in class cc.mallet.topics.HierarchicalLDA
printNodes() - Method in class cc.mallet.topics.HierarchicalLDA
printOptionValues(Class) - Static method in class cc.mallet.util.CommandOption
printPhi(File, double) - Method in class cc.mallet.topics.LDAStream
printRank(PrintWriter) - Method in class cc.mallet.classify.Classification
printRank(PrintWriter) - Method in class cc.mallet.classify.MaxEnt
printSizes() - Method in class cc.mallet.grmm.types.AbstractTableFactor
printState() - Method in class cc.mallet.topics.HierarchicalLDA
  Writes the current sampling state to the file specified in `stateFile`.
printState(PrintWriter) - Method in class cc.mallet.topics.HierarchicalLDA
  Write a text file describing the current sampling state.
printState(File) - Method in class cc.mallet.topics.HierarchicalPAM
printState(PrintWriter) - Method in class cc.mallet.topics.HierarchicalPAM
printState(File) - Method in class cc.mallet.topics.LDA
  Deprecated.
printState(PrintWriter) - Method in class cc.mallet.topics.LDA
  Deprecated.
printState(File) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
printState(PrintStream) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
printState(ArrayList<LDAHyper.Topication>, File) - Method in class cc.mallet.topics.LDAStream
printState(ArrayList<LDAHyper.Topication>, PrintStream) - Method in class cc.mallet.topics.LDAStream
printState(File) - Method in class cc.mallet.topics.NPTopicModel
printState(PrintStream) - Method in class cc.mallet.topics.NPTopicModel
printState(File) - Method in class cc.mallet.topics.PAM4L
printState(PrintWriter) - Method in class cc.mallet.topics.PAM4L
printState(File) - Method in class cc.mallet.topics.ParallelTopicModel
printState(PrintStream) - Method in class cc.mallet.topics.ParallelTopicModel
printState(File) - Method in class cc.mallet.topics.PolylingualTopicModel
printState(PrintStream) - Method in class cc.mallet.topics.PolylingualTopicModel
printState(File) - Method in class cc.mallet.topics.SimpleLDA
printState(PrintStream) - Method in class cc.mallet.topics.SimpleLDA
printState(File) - Method in class cc.mallet.topics.TopicalNGrams
printState(PrintWriter) - Method in class cc.mallet.topics.TopicalNGrams
printStateTransitions() - Method in class cc.mallet.topics.MultinomialHMM
printTheta(ArrayList<LDAHyper.Topication>, File, double, int) - Method in class cc.mallet.topics.LDAStream
PrintTokenSequenceFeatures - Class in cc.mallet.pipe
  Print properties of the token sequence in the data field and the corresponding value of any token in a token sequence or feature in a featur sequence in the target field.
PrintTokenSequenceFeatures(String) - Constructor for class cc.mallet.pipe.PrintTokenSequenceFeatures
PrintTokenSequenceFeatures() - Constructor for class cc.mallet.pipe.PrintTokenSequenceFeatures
printTopicWordWeights(File) - Method in class cc.mallet.topics.ParallelTopicModel
printTopicWordWeights(PrintWriter) - Method in class cc.mallet.topics.ParallelTopicModel
  Print an unnormalized weight for every word in every topic.
printTopK(PrintWriter, int) - Method in class cc.mallet.types.RankedFeatureVector
printTopWords(PrintStream, int, boolean) - Method in class cc.mallet.topics.DMRTopicModel
printTopWords(int, boolean) - Method in class cc.mallet.topics.HierarchicalPAM
printTopWords(int, boolean) - Method in class cc.mallet.topics.LDA
  Deprecated.
printTopWords(File, int, boolean) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
printTopWords(PrintStream, int, boolean) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
printTopWords(int, boolean) - Method in class cc.mallet.topics.PAM4L
printTopWords(File, int, boolean) - Method in class cc.mallet.topics.ParallelTopicModel
printTopWords(PrintStream, int, boolean) - Method in class cc.mallet.topics.ParallelTopicModel
printTopWords(File, int, boolean) - Method in class cc.mallet.topics.PolylingualTopicModel
printTopWords(PrintStream, int, boolean) - Method in class cc.mallet.topics.PolylingualTopicModel
printTopWords(int, boolean) - Method in class cc.mallet.topics.TopicalNGrams
printTypeTopicCounts(File) - Method in class cc.mallet.topics.ParallelTopicModel
  Write the internal representation of type-topic counts (count/topic pairs in descending order by count) to a file.
printUsage(boolean) - Method in class cc.mallet.util.CommandOption.List
PrintUtilities - Class in cc.mallet.util
  A simple utility class that lets you very simply print an arbitrary component.
PrintUtilities(Component) - Constructor for class cc.mallet.util.PrintUtilities
printValues() - Method in class cc.mallet.grmm.types.AbstractTableFactor
printWordCounts() - Method in class cc.mallet.topics.PAM4L
printWords(int) - Method in class cc.mallet.classify.NaiveBayes
PriorityQueue - Interface in cc.mallet.util.search
  Created by IntelliJ IDEA.
priorVariance - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
probability(int) - Method in class cc.mallet.types.Multinomial.Logged
probability(int) - Method in class cc.mallet.types.Multinomial
probability(Object) - Method in class cc.mallet.types.Multinomial
probs - Variable in class cc.mallet.grmm.types.AbstractTableFactor
process(ACRF.UnrolledGraph, Instance) - Method in interface cc.mallet.grmm.learning.ACRF.GraphPostProcessor
process(String[]) - Method in class cc.mallet.util.CommandOption.List
  Parse and process command-line options in args.
process(String[], int) - Method in class cc.mallet.util.CommandOption
  Give this CommandOption the opportunity to process the index'th argument in args.
process(Class, String[]) - Static method in class cc.mallet.util.CommandOption
processOptions(String[]) - Method in class cc.mallet.util.CommandOption.List
ProgressMessageLogFormatter - Class in cc.mallet.util
  Format ProgressMessages destined for screen.
ProgressMessageLogFormatter() - Constructor for class cc.mallet.util.ProgressMessageLogFormatter
ProgressMessageLogRecord - Class in cc.mallet.util
  A log message that is to be written in place (no newline) if the message is headed for the user's terminal.
ProgressMessageLogRecord(LogRecord) - Constructor for class cc.mallet.util.ProgressMessageLogRecord
propagateTopicWeight(TObjectDoubleHashMap<HierarchicalLDA.NCRPNode>, HierarchicalLDA.NCRPNode, double) - Method in class cc.mallet.topics.HierarchicalLDA
  Propagate a topic weight to a node and all its children.
PropertyHolder - Interface in cc.mallet.types
  Author: saunders Created Nov 15, 2005 Copyright (C) Univ.
PropertyList - Class in cc.mallet.util
PropertyList() - Constructor for class cc.mallet.util.PropertyList
PropertyList(String, PropertyList) - Constructor for class cc.mallet.util.PropertyList
PropertyList.Iterator - Class in cc.mallet.util
PropertyList.Iterator(PropertyList) - Constructor for class cc.mallet.util.PropertyList.Iterator
PropertyList.NumericIterator - Class in cc.mallet.util
PropertyList.NumericIterator(PropertyList) - Constructor for class cc.mallet.util.PropertyList.NumericIterator
PropertyList.ObjectIterator - Class in cc.mallet.util
PropertyList.ObjectIterator(PropertyList) - Constructor for class cc.mallet.util.PropertyList.ObjectIterator
prune() - Method in class cc.mallet.classify.C45
  Prune the tree using minimum description length
prune(double[], Alphabet, int) - Method in class cc.mallet.types.FeatureSequence
  Remove features from the sequence that occur fewer than `cutoff` times in the corpus, as indicated by the provided counts.
pt(double, double) - Static method in class cc.mallet.util.StatFunctions
PunctuationIgnoringComparator - Class in cc.mallet.extract
  Created: Nov 23, 2004
PunctuationIgnoringComparator() - Constructor for class cc.mallet.extract.PunctuationIgnoringComparator
put(Factor, Variable, Factor) - Method in class cc.mallet.grmm.inference.MessageArray
put(Variable, Factor, Factor) - Method in class cc.mallet.grmm.inference.MessageArray
put(int, int, Factor) - Method in class cc.mallet.grmm.inference.MessageArray
put(int, int, Object) - Method in class cc.mallet.grmm.util.MIntInt2ObjectMap
put(Object, Object) - Method in class cc.mallet.grmm.util.THashMultiMap
  Adds `value` to the list of things mapped to by key.
put(int, int) - Method in class cc.mallet.types.FeatureCounter
put(Object, int) - Method in class cc.mallet.types.FeatureCounter

## Q

QBCSequenceConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of an entire sequence by the "disagreement" among a committee of CRFs.
QBCSequenceConfidenceEstimator(Transducer, Transducer[]) - Constructor for class cc.mallet.fst.confidence.QBCSequenceConfidenceEstimator
qnorm(double, boolean) - Static method in class cc.mallet.util.StatFunctions
qnorm(double, boolean, double, double) - Static method in class cc.mallet.util.StatFunctions
qt(double, double, boolean) - Static method in class cc.mallet.util.StatFunctions
quant(double) - Method in class cc.mallet.util.Univariate
query(FactorGraph, Assignment) - Method in class cc.mallet.grmm.inference.AbstractInferencer
query(FactorGraph, Assignment) - Method in interface cc.mallet.grmm.inference.Inferencer
  Computes the marginal probability of a given assignment to a small number of model variables.
query(DirectedModel, Variable) - Method in class cc.mallet.grmm.inference.TRP
QueueElement - Interface in cc.mallet.util.search
  Created by IntelliJ IDEA.

## R

rainbow(int, float, float) - Static method in class cc.mallet.util.ColorUtils
  Returns a list of hex color names of length n.
random - Variable in class cc.mallet.cluster.iterator.PairSampleIterator
random - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
random - Variable in class cc.mallet.topics.MarginalProbEstimator
random - Variable in class cc.mallet.topics.NPTopicModel
random - Variable in class cc.mallet.topics.PolylingualTopicModel
random - Variable in class cc.mallet.topics.SimpleLDA
random - Variable in class cc.mallet.topics.TopicInferencer
random - Variable in class cc.mallet.topics.WorkerRunnable
randomAttractiveGrid(int, double, Random) - Static method in class cc.mallet.grmm.inference.RandomGraphs
  Constructs a square grid of a given size with random attractive potentials.
RandomConfidenceEstimator - Class in cc.mallet.fst.confidence
  Randomly assigns values between 0-1 to the confidence of a `Segment`.
RandomConfidenceEstimator(int, Transducer) - Constructor for class cc.mallet.fst.confidence.RandomConfidenceEstimator
RandomConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.RandomConfidenceEstimator
randomDirichlet(Randoms, double) - Method in class cc.mallet.types.Dirichlet
RandomEvaluator - Class in cc.mallet.cluster.neighbor_evaluator
  Randomly scores `Neighbor`s.
RandomEvaluator(Randoms) - Constructor for class cc.mallet.cluster.neighbor_evaluator.RandomEvaluator
randomFeatureSequence(Randoms, int) - Method in class cc.mallet.types.Dirichlet
randomFeatureSequence(Randoms, int) - Method in class cc.mallet.types.Multinomial
randomFeatureVector(Randoms, int) - Method in class cc.mallet.types.Dirichlet
randomFeatureVector(Randoms, int) - Method in class cc.mallet.types.Multinomial
RandomFeatureVectorIterator - Class in cc.mallet.pipe.iterator
RandomFeatureVectorIterator(Randoms, Dirichlet, double, double, double, double, String[]) - Constructor for class cc.mallet.pipe.iterator.RandomFeatureVectorIterator
RandomFeatureVectorIterator(Randoms, Alphabet, String[]) - Constructor for class cc.mallet.pipe.iterator.RandomFeatureVectorIterator
RandomFeatureVectorIterator(Randoms, int, int) - Constructor for class cc.mallet.pipe.iterator.RandomFeatureVectorIterator
randomFrustratedGrid(int, double, Random) - Static method in class cc.mallet.grmm.inference.RandomGraphs
  Constructs a square grid of a given size with random frustrated potentials.
randomFrustratedTree(int, int, double, Random) - Static method in class cc.mallet.grmm.inference.RandomGraphs
RandomGraphs - Class in cc.mallet.grmm.inference
  Utility class for generating many useful kinds of random graphical models.
RandomGraphs() - Constructor for class cc.mallet.grmm.inference.RandomGraphs
RandomGraphs.FactorGenerator - Interface in cc.mallet.grmm.inference
RandomGraphs.UniformFactorGenerator - Class in cc.mallet.grmm.inference
RandomGraphs.UniformFactorGenerator() - Constructor for class cc.mallet.grmm.inference.RandomGraphs.UniformFactorGenerator
randomIndex(Randoms) - Method in class cc.mallet.types.Multinomial
randomMultinomial(Randoms) - Method in class cc.mallet.types.Dirichlet
randomNodePotential(Random, Variable) - Static method in class cc.mallet.grmm.inference.RandomGraphs
randomObject(Randoms) - Method in class cc.mallet.types.Multinomial
randomRawMultinomial(Randoms) - Method in class cc.mallet.types.Dirichlet
randomRepulsiveGrid(int, double, Random) - Static method in class cc.mallet.grmm.inference.RandomGraphs
  Constructs a square grid of a given size with random repulsive potentials.
Randoms - Class in cc.mallet.util
Randoms(int) - Constructor for class cc.mallet.util.Randoms
Randoms() - Constructor for class cc.mallet.util.Randoms
randomSeed - Variable in class cc.mallet.topics.ParallelTopicModel
RandomSequenceConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of an entire sequence randomly.
RandomSequenceConfidenceEstimator(int, Transducer) - Constructor for class cc.mallet.fst.confidence.RandomSequenceConfidenceEstimator
RandomSequenceConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.RandomSequenceConfidenceEstimator
randomTokenSequence(Randoms, int) - Method in class cc.mallet.types.Dirichlet
RandomTokenSequenceIterator - Class in cc.mallet.pipe.iterator
RandomTokenSequenceIterator(Randoms, Dirichlet, double, double, double, double, String[]) - Constructor for class cc.mallet.pipe.iterator.RandomTokenSequenceIterator
RandomTokenSequenceIterator(Randoms, Alphabet, String[]) - Constructor for class cc.mallet.pipe.iterator.RandomTokenSequenceIterator
RandomTokenSequenceIterator(Randoms, int, int) - Constructor for class cc.mallet.pipe.iterator.RandomTokenSequenceIterator
randomVector(Randoms) - Method in class cc.mallet.types.Dirichlet
randomVector(int, Random) - Static method in class cc.mallet.types.MatrixOps
RankedFeatureVector - Class in cc.mallet.types
RankedFeatureVector(Alphabet, int[], double[]) - Constructor for class cc.mallet.types.RankedFeatureVector
RankedFeatureVector(Alphabet, double[]) - Constructor for class cc.mallet.types.RankedFeatureVector
RankedFeatureVector(Alphabet, double[], int, int) - Constructor for class cc.mallet.types.RankedFeatureVector
RankedFeatureVector(Alphabet, DenseVector) - Constructor for class cc.mallet.types.RankedFeatureVector
RankedFeatureVector(Alphabet, AugmentableFeatureVector) - Constructor for class cc.mallet.types.RankedFeatureVector
RankedFeatureVector(Alphabet, SparseVector) - Constructor for class cc.mallet.types.RankedFeatureVector
RankedFeatureVector.Factory - Interface in cc.mallet.types
RankedFeatureVector.PerLabelFactory - Interface in cc.mallet.types
RankingNeighborEvaluator - Class in cc.mallet.cluster.neighbor_evaluator
  Uses a `Classifier` that scores an array of `Neighbor`s.
RankingNeighborEvaluator(Classifier) - Constructor for class cc.mallet.cluster.neighbor_evaluator.RankingNeighborEvaluator
rankInstancesByConfidence(InstanceList, Object[], Object[]) - Method in class cc.mallet.fst.confidence.TransducerSequenceConfidenceEstimator
  Ranks all `Sequences`s in this `InstanceList` by confidence estimate.
RankMaxEnt - Class in cc.mallet.classify
  Rank Maximum Entropy classifier.
RankMaxEnt(Pipe, double[], FeatureSelection, FeatureSelection[]) - Constructor for class cc.mallet.classify.RankMaxEnt
RankMaxEnt(Pipe, double[], FeatureSelection) - Constructor for class cc.mallet.classify.RankMaxEnt
RankMaxEnt(Pipe, double[], FeatureSelection[]) - Constructor for class cc.mallet.classify.RankMaxEnt
RankMaxEnt(Pipe, double[]) - Constructor for class cc.mallet.classify.RankMaxEnt
RankMaxEntTrainer - Class in cc.mallet.classify
  The trainer for a `RankMaxEnt` classifier.
RankMaxEntTrainer() - Constructor for class cc.mallet.classify.RankMaxEntTrainer
RankMaxEntTrainer(double) - Constructor for class cc.mallet.classify.RankMaxEntTrainer
  Constructs a trainer with a parameter to avoid overtraining.
rankPipedInstancesByConfidence(InstanceList, Object[], Object[]) - Method in class cc.mallet.fst.confidence.MaxEntSequenceConfidenceEstimator
rankSegmentsByConfidence(InstanceList, Object[], Object[]) - Method in class cc.mallet.fst.confidence.TransducerConfidenceEstimator
  Ranks all `Segment`s in this `InstanceList` by confidence estimate.
rankSegmentsByConfidence(Instance, Object[], Object[]) - Method in class cc.mallet.fst.confidence.TransducerConfidenceEstimator
  ranks the segments in one `Instance`
rawValue(int) - Method in class cc.mallet.grmm.types.AbstractTableFactor
rawValue(Assignment) - Method in class cc.mallet.grmm.types.LogTableFactor
rawValue(int) - Method in class cc.mallet.grmm.types.LogTableFactor
rawValue(Assignment) - Method in class cc.mallet.grmm.types.TableFactor
rawValue(int) - Method in class cc.mallet.grmm.types.TableFactor
read(File) - Static method in class cc.mallet.topics.LDAHyper
  Deprecated.
read(File) - Static method in class cc.mallet.topics.MarginalProbEstimator
read(File) - Static method in class cc.mallet.topics.ParallelTopicModel
read(File) - Static method in class cc.mallet.topics.TopicInferencer
readClusterings(String) - Static method in class cc.mallet.cluster.tui.Clusterings2Clusterer
readConstraintsFromFile(String, InstanceList) - Static method in class cc.mallet.classify.FeatureConstraintUtil
  Reads feature constraints from a file, whether they are stored using Strings or indices.
readConstraintsFromFileIndex(String, InstanceList) - Static method in class cc.mallet.classify.FeatureConstraintUtil
  Reads feature constraints stored using strings from a file.
readConstraintsFromFileString(String, InstanceList) - Static method in class cc.mallet.classify.FeatureConstraintUtil
  Reads feature constraints stored using strings from a file.
readFile(File) - Static method in class cc.mallet.util.FileUtils
  Reads every line from a given text file.
readFromFile(File) - Method in class cc.mallet.util.CommandOption.List
  Load configuration information from a file.
readFromFiles(FactorGraph, List) - Static method in class cc.mallet.grmm.inference.TRP.TreeListFactory
readFromMatrix(VarSet, Reader) - Static method in class cc.mallet.grmm.util.ModelReader
readGzippedObject(File) - Static method in class cc.mallet.util.FileUtils
  Reads a serialized object from a file that has been compressed using gzip.
readModel(BufferedReader) - Method in class cc.mallet.grmm.util.ModelReader
readObject(File) - Static method in class cc.mallet.util.FileUtils
  Reads a Serialized object, which may or may not be zipped.
readResolve() - Method in class cc.mallet.pipe.Pipe
  This gets called after readObject; it lets the object decide whether to return itself or return a previously read in version.
readResolve() - Method in class cc.mallet.types.Alphabet
  This gets called after readObject; it lets the object decide whether to return itself or return a previously read in version.
readUnzippedObject(File) - Static method in class cc.mallet.util.FileUtils
  Reads a serialized object from a file.
readWeightsFromText(Reader) - Method in class cc.mallet.grmm.learning.ACRF
recall - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
recenter() - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Multiplies this factor by the constant 1/max().
recenter() - Method in class cc.mallet.grmm.types.LogTableFactor
recenter() - Method in class cc.mallet.grmm.types.TableFactor
Record - Class in cc.mallet.cluster
Record(Alphabet, Alphabet) - Constructor for class cc.mallet.cluster.Record
Record(Alphabet, Alphabet, String[][]) - Constructor for class cc.mallet.cluster.Record
Record - Class in cc.mallet.extract
  Created: Oct 12, 2004
Record(String, LabeledSpans) - Constructor for class cc.mallet.extract.Record
RegexFieldCleaner - Class in cc.mallet.extract
  A field cleaner that removes all occurrences of a given regex.
RegexFieldCleaner(String) - Constructor for class cc.mallet.extract.RegexFieldCleaner
RegexFieldCleaner(Pattern) - Constructor for class cc.mallet.extract.RegexFieldCleaner
RegexFileFilter - Class in cc.mallet.util
RegexFileFilter(Pattern, Pattern) - Constructor for class cc.mallet.util.RegexFileFilter
RegexFileFilter(String, String) - Constructor for class cc.mallet.util.RegexFileFilter
RegexFileFilter(Pattern) - Constructor for class cc.mallet.util.RegexFileFilter
RegexFileFilter(String) - Constructor for class cc.mallet.util.RegexFileFilter
RegexMatches - Class in cc.mallet.pipe.tsf
RegexMatches(String, Pattern) - Constructor for class cc.mallet.pipe.tsf.RegexMatches
RegionGraphGenerator - Interface in cc.mallet.grmm.inference.gbp
  Interface for strategies that construct region graphs from arbitrary graphical models.
RememberTokenizationPipe - Class in cc.mallet.grmm.util
  Created: Mar 17, 2005
RememberTokenizationPipe() - Constructor for class cc.mallet.grmm.util.RememberTokenizationPipe
remove() - Method in class cc.mallet.cluster.iterator.NeighborIterator
remove() - Method in class cc.mallet.fst.Transducer.TransitionIterator
remove() - Method in class cc.mallet.grmm.inference.MessageArray.Iterator
remove(Variable) - Method in class cc.mallet.grmm.types.FactorGraph
  Removes a variable from this model, along with all of its factors.
remove(Collection) - Method in class cc.mallet.grmm.types.FactorGraph
  Removes a Collection of variables from this model, along with all of its factors.
remove(Object) - Method in class cc.mallet.grmm.types.HashVarSet
remove(Object) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
remove() - Method in class cc.mallet.grmm.util.PipedIterator
  Deprecated.
remove() - Method in class cc.mallet.pipe.iterator.ArrayDataAndTargetIterator
remove() - Method in class cc.mallet.pipe.iterator.ArrayIterator
remove() - Method in class cc.mallet.pipe.iterator.ConcatenatedInstanceIterator
remove() - Method in class cc.mallet.pipe.iterator.CsvIterator
remove() - Method in class cc.mallet.pipe.iterator.EmptyInstanceIterator
remove() - Method in class cc.mallet.pipe.iterator.FileIterator
remove() - Method in class cc.mallet.pipe.iterator.FileListIterator
remove() - Method in class cc.mallet.pipe.iterator.LineGroupIterator
remove() - Method in class cc.mallet.pipe.iterator.LineIterator
remove() - Method in class cc.mallet.pipe.iterator.ParenGroupIterator
remove() - Method in class cc.mallet.pipe.iterator.PatternMatchIterator
remove() - Method in class cc.mallet.pipe.iterator.PipeExtendedIterator
  Deprecated.
remove() - Method in class cc.mallet.pipe.iterator.PipeInputIterator
  Deprecated.
remove() - Method in class cc.mallet.pipe.iterator.RandomFeatureVectorIterator
remove() - Method in class cc.mallet.pipe.iterator.RandomTokenSequenceIterator
remove() - Method in class cc.mallet.pipe.iterator.SegmentIterator
remove() - Method in class cc.mallet.pipe.iterator.SelectiveFileLineIterator
remove() - Method in class cc.mallet.pipe.iterator.SimpleFileLineIterator
remove() - Method in class cc.mallet.pipe.iterator.StringArrayIterator
remove() - Method in class cc.mallet.pipe.iterator.UnlabeledFileIterator
remove() - Method in class cc.mallet.types.ChainedInstanceIterator
  Deprecated.
remove() - Method in class cc.mallet.types.CrossValidationIterator
remove(Object) - Method in class cc.mallet.types.FeatureSelection
remove(int) - Method in class cc.mallet.types.FeatureSelection
remove() - Method in class cc.mallet.types.FeatureVectorSequence.Iterator
remove() - Method in class cc.mallet.types.InstanceList.CrossValidationIterator
remove(int) - Method in class cc.mallet.types.InstanceList
remove(Instance) - Method in class cc.mallet.types.InstanceList
remove() - Method in class cc.mallet.types.LabelSequence.Iterator
remove(Instance) - Method in class cc.mallet.types.MultiInstanceList
remove(int) - Method in class cc.mallet.types.MultiInstanceList
remove(Object) - Method in class cc.mallet.types.MultiInstanceList
remove() - Method in class cc.mallet.types.SingleInstanceIterator
remove() - Method in class cc.mallet.util.CharSequenceLexer
remove() - Method in interface cc.mallet.util.Lexer
remove() - Method in class cc.mallet.util.PropertyList.Iterator
remove(String, PropertyList) - Static method in class cc.mallet.util.PropertyList
remove() - Method in class cc.mallet.util.search.AStar
remove() - Method in class cc.mallet.util.search.SearchNode.NextNodeIterator
remove() - Method in class cc.mallet.util.search.SearchState.NextStateIterator
REMOVE_PUNCT - Static variable in class cc.mallet.extract.RegexFieldCleaner
removeAll(Collection) - Method in class cc.mallet.grmm.types.HashVarSet
removeAll(Collection) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
removeConstantFactors(FactorGraph) - Static method in class cc.mallet.grmm.util.Models
removeDuplicates(int) - Method in class cc.mallet.types.AugmentableFeatureVector
removeDuplicates(int) - Method in class cc.mallet.types.SparseVector
removeEvaluator(TransducerEvaluator) - Method in class cc.mallet.fst.TransducerTrainer
removeItem(String) - Method in class cc.mallet.classify.evaluate.Graph
removeLast() - Method in class cc.mallet.types.TokenSequence
removeSources() - Method in class cc.mallet.types.InstanceList
  Sets the "source" field to `null` in all instances.
removeStopWords(String[]) - Method in class cc.mallet.pipe.TokenSequenceRemoveStopwords
removeStopWords(File) - Method in class cc.mallet.pipe.TokenSequenceRemoveStopwords
  Remove whitespace-separated tokens in file "wordlist" to the stoplist.
removeSubsumedRegions(List) - Static method in class cc.mallet.grmm.inference.gbp.ClusterVariationalRegionGenerator
removeTargets() - Method in class cc.mallet.types.InstanceList
  Sets the "target" field to `null` in all instances.
report() - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
report(String) - Method in class cc.mallet.util.Timing
  Like tick(), but doesn't reset the counter.
reportTime() - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
reportTime() - Method in class cc.mallet.grmm.inference.AbstractInferencer
reportTime() - Method in interface cc.mallet.grmm.inference.Inferencer
  Outputs some measure of the total time spent in this inferencer.
reset() - Method in class cc.mallet.cluster.GreedyAgglomerative
  Reset convergence to false so a new round of clustering can begin.
reset() - Method in class cc.mallet.cluster.GreedyAgglomerativeByDensity
  Reset convergence to false and clear state so a new round of clustering can begin.
reset() - Method in class cc.mallet.cluster.HillClimbingClusterer
  Perform any cleanup of the clustering algorithm prior to clustering.
reset() - Method in class cc.mallet.cluster.neighbor_evaluator.ClassifyingNeighborEvaluator
reset() - Method in class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator
reset() - Method in interface cc.mallet.cluster.neighbor_evaluator.NeighborEvaluator
  Reset the state of the evaluator.
reset() - Method in class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator
reset() - Method in class cc.mallet.cluster.neighbor_evaluator.RandomEvaluator
  Reset the state of the evaluator.
reset() - Method in class cc.mallet.cluster.neighbor_evaluator.RankingNeighborEvaluator
reset() - Method in class cc.mallet.fst.FeatureTransducer
reset() - Method in class cc.mallet.fst.HMM
  Deprecated.
reset() - Method in class cc.mallet.grmm.inference.TRP.ConvergenceTerminator
reset() - Method in class cc.mallet.grmm.inference.TRP.DefaultConvergenceTerminator
reset() - Method in class cc.mallet.grmm.inference.TRP.IterationTerminator
reset() - Method in interface cc.mallet.grmm.inference.TRP.TerminationCondition
reset() - Method in class cc.mallet.optimize.ConjugateGradient
reset() - Method in class cc.mallet.optimize.LimitedMemoryBFGS
  Resets the previous gradients and values that are used to approximate the Hessian.
reset() - Method in class cc.mallet.pipe.iterator.RandomFeatureVectorIterator
reset() - Method in class cc.mallet.pipe.iterator.RandomTokenSequenceIterator
reset() - Method in class cc.mallet.types.Multinomial.Estimator
resetBeta(double, double) - Method in class cc.mallet.topics.WorkerRunnable
resetMessagesSentAtStart() - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
ResidualBP - Class in cc.mallet.grmm.inference
  A dynamic BP schedule where The loopy belief propagation algorithm for approximate inference in general graphical models.
ResidualBP() - Constructor for class cc.mallet.grmm.inference.ResidualBP
ResidualBP(int) - Constructor for class cc.mallet.grmm.inference.ResidualBP
ResidualBP(AbstractBeliefPropagation.MessageStrategy, int) - Constructor for class cc.mallet.grmm.inference.ResidualBP
restriction(Assignment, VarSet) - Static method in class cc.mallet.grmm.types.Assignment
  Deprecated. marginalize
retainAll(Collection) - Method in class cc.mallet.grmm.types.HashVarSet
retainAll(Collection) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
retainMass(DiscreteFactor, double) - Static method in class cc.mallet.grmm.types.Factors
returnedCounts - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
ROCData - Class in cc.mallet.types
  Tracks ROC data for instances in `Trial` results.
ROCData(double[], LabelAlphabet) - Constructor for class cc.mallet.types.ROCData
  Constructs a new object
ROOT_TOPIC - Static variable in class cc.mallet.topics.HierarchicalPAM
rowDotProduct(int, Vector) - Method in class cc.mallet.types.Matrix2
  Deprecated.
rowDotProduct(int, Vector, int, FeatureSelection) - Method in class cc.mallet.types.Matrix2
  Deprecated. Skip all column indices higher than "maxCi".
rowDotProduct(double[], int, int, Vector, int, FeatureSelection) - Static method in class cc.mallet.types.MatrixOps
rowDotProduct(double[], int, int, Vector, double, int, FeatureSelection) - Static method in class cc.mallet.types.MatrixOps
rowPlusEquals(int, Vector, double) - Method in class cc.mallet.types.Matrix2
  Deprecated.
rowPlusEquals(int, double, double) - Method in class cc.mallet.types.Matrix2
  Deprecated.
rowPlusEquals(double[], int, int, Vector, double) - Static method in class cc.mallet.types.MatrixOps
rowSetAll(int, double, FeatureSelection, boolean) - Method in class cc.mallet.types.Matrix2
  Deprecated. If "ifSelected" is false, it reverses the selection.
rowSetAll(double[], int, int, double, FeatureSelection, boolean) - Static method in class cc.mallet.types.MatrixOps
  If "ifSelected" is false, it reverses the selection.
run() - Method in class cc.mallet.cluster.examples.FirstOrderClusterExample
run() - Method in class cc.mallet.topics.WorkerRunnable
runComparison() - Static method in class cc.mallet.types.Dirichlet
runEvaluators() - Method in class cc.mallet.fst.TransducerTrainer
  This method should be called by subclasses whenever evaluators should be run.
runJunctionTree() - Method in class cc.mallet.grmm.test.TestInference

## S

sample(FactorGraph, int) - Method in class cc.mallet.grmm.inference.ExactSampler
sample(FactorGraph, int) - Method in class cc.mallet.grmm.inference.GibbsSampler
sample(FactorGraph, int) - Method in interface cc.mallet.grmm.inference.Sampler
  Samples from the distribution of a given undirected model.
sample(Randoms) - Method in class cc.mallet.grmm.types.AbstractFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.AbstractTableFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.Assignment
sample(Randoms) - Method in class cc.mallet.grmm.types.BetaFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.ConstantFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.CPT
sample(Randoms) - Method in interface cc.mallet.grmm.types.Factor
  Return an assignment sampled from this factor, interpreting it as an unnormalized probability distribution.
sample(Randoms) - Method in class cc.mallet.grmm.types.FactorGraph
sample(Randoms) - Method in class cc.mallet.grmm.types.NormalFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.PottsTableFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.SkeletonFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.UniformFactor
sample(Randoms) - Method in class cc.mallet.grmm.types.UniNormalFactor
sample() - Method in class cc.mallet.topics.MultinomialHMM
sample(int) - Method in class cc.mallet.topics.NPTopicModel
sample(int) - Method in class cc.mallet.topics.SimpleLDA
sampleContinuousVars(Randoms) - Method in class cc.mallet.grmm.types.FactorGraph
  Samples the continuous variables in this factor graph.
sampleFromArray(int[], Randoms, int) - Method in class cc.mallet.cluster.iterator.ClusterSampleIterator
  Samples a subset of elements from this array.
sampleLocation(Randoms) - Method in class cc.mallet.grmm.types.AbstractTableFactor
sampleLocation(Randoms) - Method in class cc.mallet.grmm.types.CPT
sampleLocation(Randoms) - Method in interface cc.mallet.grmm.types.DiscreteFactor
samplePath(int, int) - Method in class cc.mallet.topics.HierarchicalLDA
Sampler - Interface in cc.mallet.grmm.inference
  Interface for methods from sampling the distribution given by a graphical model.
sampleSplitFromArray(int[], Randoms, int) - Method in class cc.mallet.cluster.iterator.ClusterSampleIterator
  Samples a two disjoint subset of elements from this array.
sampleTopics(int) - Method in class cc.mallet.topics.HierarchicalLDA
sampleTopicsForAllDocs(Randoms) - Method in class cc.mallet.topics.LDA
  Deprecated.
sampleTopicsForDocs(int, int, Randoms) - Method in class cc.mallet.topics.LDA
  Deprecated.
sampleTopicsForOneDoc(FeatureSequence, FeatureSequence, boolean, boolean) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
sampleTopicsForOneDoc(FeatureSequence, FeatureSequence) - Method in class cc.mallet.topics.NPTopicModel
sampleTopicsForOneDoc(PolylingualTopicModel.TopicAssignment, boolean) - Method in class cc.mallet.topics.PolylingualTopicModel
sampleTopicsForOneDoc(FeatureSequence, FeatureSequence) - Method in class cc.mallet.topics.SimpleLDA
sampleTopicsForOneDoc(FeatureSequence, FeatureSequence, boolean) - Method in class cc.mallet.topics.WorkerRunnable
sampleWithInstanceWeights(Random) - Method in class cc.mallet.types.InstanceList
  Deprecated.
sampleWithReplacement(Random, int) - Method in class cc.mallet.types.InstanceList
sampleWithWeights(Random, double[]) - Method in class cc.mallet.types.InstanceList
  Returns an `InstanceList` of the same size, where the instances come from the random sampling (with replacement) of this list using the given weights.
SamplingInferencer - Class in cc.mallet.grmm.inference
  Approximate inferencer for graphical models using sampling.
SamplingInferencer(Sampler, int) - Constructor for class cc.mallet.grmm.inference.SamplingInferencer
satisfiedBy(FeatureVector) - Method in class cc.mallet.types.FeatureConjunction
save(File) - Method in class cc.mallet.types.InstanceList
  Saves this `InstanceList` to `file`.
SaveDataInSource - Class in cc.mallet.pipe
  Set the source field of each instance to its data field.
SaveDataInSource() - Constructor for class cc.mallet.pipe.SaveDataInSource
saveModelInterval - Variable in class cc.mallet.topics.ParallelTopicModel
saveOldSv() - Static method in class cc.mallet.types.tests.TestHashedSparseVector
saveSampleInterval - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
saveSampleInterval - Variable in class cc.mallet.topics.ParallelTopicModel
saveSampleInterval - Variable in class cc.mallet.topics.PolylingualTopicModel
saveStateInterval - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
saveStateInterval - Variable in class cc.mallet.topics.ParallelTopicModel
saveStateInterval - Variable in class cc.mallet.topics.PolylingualTopicModel
saveXis - Static variable in class cc.mallet.fst.SumLatticeDefault
saveXis - Static variable in class cc.mallet.fst.SumLatticeScaling
scalingFactor - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
score(Clustering) - Method in interface cc.mallet.cluster.clustering_scorer.ClusteringScorer
score(Clustering) - Method in class cc.mallet.cluster.clustering_scorer.PairwiseScorer
scoreCache - Variable in class cc.mallet.cluster.GreedyAgglomerative
  Cache for calls to `NeighborhoodEvaluator`.
SE() - Method in class cc.mallet.util.Univariate
SearchNode - Class in cc.mallet.util.search
  Created by IntelliJ IDEA.
SearchNode(SearchState, SearchNode, double) - Constructor for class cc.mallet.util.search.SearchNode
  Create a search node with given state, parent, and cost.
SearchNode.NextNodeIterator - Class in cc.mallet.util.search
  This iterator generates search nodes that refer to the states reachable from the state pertaining to a this search node.
SearchNode.NextNodeIterator() - Constructor for class cc.mallet.util.search.SearchNode.NextNodeIterator
SearchState - Interface in cc.mallet.util.search
  Created by IntelliJ IDEA.
SearchState.NextStateIterator - Class in cc.mallet.util.search
  Iterator over the states with transitions from a given state.
SearchState.NextStateIterator() - Constructor for class cc.mallet.util.search.SearchState.NextStateIterator
secondDerivative(Factor, Variable, Assignment) - Method in class cc.mallet.grmm.types.PottsTableFactor
Segment - Class in cc.mallet.fst
  Represents a labelled chunk of a `Sequence` segmented by a `Transducer`, usually corresponding to some object extracted from an input `Sequence`.
Segment(Sequence, Sequence, Sequence, int, int, Object, Object) - Constructor for class cc.mallet.fst.Segment
  Initializes the segment.
SegmentationEvaluator - Class in cc.mallet.fst
SegmentationEvaluator(InstanceList[], String[]) - Constructor for class cc.mallet.fst.SegmentationEvaluator
SegmentationEvaluator(InstanceList, String) - Constructor for class cc.mallet.fst.SegmentationEvaluator
SegmentationEvaluator(InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.fst.SegmentationEvaluator
SegmentationEvaluator(InstanceList, String, InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.fst.SegmentationEvaluator
SegmentIterator - Class in cc.mallet.pipe.iterator
  Iterates over `Segment`s extracted by a `Transducer` for some `InstanceList`.
SegmentIterator(Transducer, InstanceList, Object[], Object[]) - Constructor for class cc.mallet.pipe.iterator.SegmentIterator
  NOTE!: Assumes that `segmentStartTags[i]` corresponds to `segmentContinueTags[i]`.
SegmentIterator(Transducer, Instance, Object[], Object[]) - Constructor for class cc.mallet.pipe.iterator.SegmentIterator
  Iterates over `Segment`s for only one `Instance`.
SegmentIterator(InstanceList, Object[], Object[], ArrayList) - Constructor for class cc.mallet.pipe.iterator.SegmentIterator
  Useful when no `Transduce` is specified.
SegmentIterator(Instance, Object[], Object[], Sequence) - Constructor for class cc.mallet.pipe.iterator.SegmentIterator
  Iterate over segments in one instance.
SegmentIterator(Sequence, Sequence, Sequence, Object[], Object[]) - Constructor for class cc.mallet.pipe.iterator.SegmentIterator
  Iterate over segments in one labeled sequence
SegmentProductConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of an entire sequence by combining the output of a segment confidence estimator for each segment.
SegmentProductConfidenceEstimator(Transducer, TransducerConfidenceEstimator) - Constructor for class cc.mallet.fst.confidence.SegmentProductConfidenceEstimator
selectFeaturesByInfoGain(InstanceList, int) - Static method in class cc.mallet.classify.FeatureConstraintUtil
  Select features with the highest information gain.
selectFeaturesFor(InstanceList) - Method in class cc.mallet.types.FeatureSelector
selectFeaturesForAllLabels(InstanceList) - Method in class cc.mallet.types.FeatureSelector
selectFeaturesForPerLabel(InstanceList) - Method in class cc.mallet.types.FeatureSelector
SelectiveFileLineIterator - Class in cc.mallet.pipe.iterator
  Very similar to the SimpleFileLineIterator, but skips lines that match a regular expression.
SelectiveFileLineIterator(Reader, String) - Constructor for class cc.mallet.pipe.iterator.SelectiveFileLineIterator
SelectiveSGML2TokenSequence - Class in cc.mallet.pipe
  Similar to `SGML2TokenSequence`, except that only the tags listed in `allowedTags` are converted to `Label`s.
SelectiveSGML2TokenSequence(CharSequenceLexer, String, Set) - Constructor for class cc.mallet.pipe.SelectiveSGML2TokenSequence
SelectiveSGML2TokenSequence(String, String, Set) - Constructor for class cc.mallet.pipe.SelectiveSGML2TokenSequence
SelectiveSGML2TokenSequence(Set) - Constructor for class cc.mallet.pipe.SelectiveSGML2TokenSequence
SelectiveSGML2TokenSequence(CharSequenceLexer, Set) - Constructor for class cc.mallet.pipe.SelectiveSGML2TokenSequence
selectTopLDAFeatures(int, ParallelTopicModel, Alphabet) - Static method in class cc.mallet.classify.FeatureConstraintUtil
  Select top features in LDA topics.
sendMessage(FactorGraph, Factor, Variable) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation.MaxProductMessageStrategy
sendMessage(FactorGraph, Variable, Factor) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation.MaxProductMessageStrategy
sendMessage(FactorGraph, Factor, Variable) - Method in interface cc.mallet.grmm.inference.AbstractBeliefPropagation.MessageStrategy
sendMessage(FactorGraph, Variable, Factor) - Method in interface cc.mallet.grmm.inference.AbstractBeliefPropagation.MessageStrategy
sendMessage(FactorGraph, Variable, Factor) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
sendMessage(FactorGraph, Factor, Variable) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
sendMessage(FactorGraph, Factor, Variable) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation.SumProductMessageStrategy
sendMessage(FactorGraph, Variable, Factor) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation.SumProductMessageStrategy
sendMessage(RegionEdge) - Method in class cc.mallet.grmm.inference.gbp.FullMessageStrategy
sendMessage(RegionEdge) - Method in interface cc.mallet.grmm.inference.gbp.MessageStrategy
sendMessage(RegionEdge) - Method in class cc.mallet.grmm.inference.gbp.SparseMessageSender
sep - Static variable in class cc.mallet.pipe.iterator.FileIterator
  Use as label names the directories specified in the constructor, optionally removing common prefix of all starting directories
sepsetPotentials() - Method in class cc.mallet.grmm.inference.JunctionTree
Sequence<E> - Interface in cc.mallet.types
SequenceConfidenceInstance - Class in cc.mallet.fst.confidence
  Stores a `Sequence` and a PropertyList, used when extracting features from a Sequence in a pipe for confidence prediction
SequenceConfidenceInstance(Instance) - Constructor for class cc.mallet.fst.confidence.SequenceConfidenceInstance
SequencePair<I,O> - Class in cc.mallet.types
SequencePair(Sequence<I>, Sequence<O>) - Constructor for class cc.mallet.types.SequencePair
SequencePair() - Constructor for class cc.mallet.types.SequencePair
SequencePairAlignment<I,O> - Class in cc.mallet.types
SequencePairAlignment(Sequence<I>, Sequence<O>, double) - Constructor for class cc.mallet.types.SequencePairAlignment
SequencePairAlignment() - Constructor for class cc.mallet.types.SequencePairAlignment
SequencePrintingPipe - Class in cc.mallet.pipe.tsf
  Created: Jul 6, 2005
SequencePrintingPipe(PrintWriter) - Constructor for class cc.mallet.pipe.tsf.SequencePrintingPipe
Sequences - Class in cc.mallet.util
  Utility methods for cc.mallet.types.Sequence and similar classes.
Sequences() - Constructor for class cc.mallet.util.Sequences
sequenceToString() - Method in class cc.mallet.fst.Segment
SerialPipes - Class in cc.mallet.pipe
  Convert an instance through a sequence of pipes.
SerialPipes() - Constructor for class cc.mallet.pipe.SerialPipes
SerialPipes(Pipe[]) - Constructor for class cc.mallet.pipe.SerialPipes
SerialPipes(Collection<Pipe>) - Constructor for class cc.mallet.pipe.SerialPipes
SerialPipes.Predicate - Class in cc.mallet.pipe
SerialPipes.Predicate() - Constructor for class cc.mallet.pipe.SerialPipes.Predicate
set(int, Clustering) - Method in class cc.mallet.cluster.Clusterings
set(int, int, double) - Method in class cc.mallet.cluster.util.PairwiseMatrix
set(ConstantMatrix) - Method in class cc.mallet.types.DenseMatrix
set(int, double) - Method in class cc.mallet.types.IDSorter
  Reinitialize an IDSorter
set(int, Instance) - Method in class cc.mallet.types.InstanceList
set(int, Label) - Method in class cc.mallet.types.Labels
set(ConstantMatrix) - Method in interface cc.mallet.types.Matrix
set(double[], double[]) - Static method in class cc.mallet.types.MatrixOps
set(int, Instance) - Method in class cc.mallet.types.MultiInstanceList
set(int, Instance) - Method in class cc.mallet.types.PagedInstanceList
  Replaces the `Instance` at position `index` with a new one.
set(int, double) - Method in class cc.mallet.types.RankedFeatureVector
set(ConstantMatrix) - Method in class cc.mallet.types.SparseMatrixn
set(int, double) - Method in class cc.mallet.util.DoubleList
setAbsTolx(double) - Method in class cc.mallet.optimize.BackTrackLineSearch
  Sets the tolerance of absolute diff in function value.
setAddNoFactors(boolean) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
  Use this method to specify whether or not factors are added to the CRF by this trainer.
setAddNoFactors(boolean) - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
  Use this method to specify whether or not factors are added to the CRF by this trainer.
setAll(double) - Method in class cc.mallet.types.AugmentableFeatureVector
setAll(double) - Method in class cc.mallet.types.DenseMatrix
setAll(double) - Method in class cc.mallet.types.HashedSparseVector
setAll(double) - Method in class cc.mallet.types.IndexedSparseVector
setAll(double) - Method in interface cc.mallet.types.Matrix
setAll(double) - Method in class cc.mallet.types.Matrix2
  Deprecated.
setAll(double, FeatureSelection, boolean) - Method in class cc.mallet.types.Matrix2
  Deprecated. If "ifSelected" is false, it reverses the selection.
setAll(double[], double) - Static method in class cc.mallet.types.MatrixOps
  Sets every element of a double array to a given value.
setAll(double[][][], double) - Static method in class cc.mallet.types.MatrixOps
setAll(double[][], double) - Static method in class cc.mallet.types.MatrixOps
setAll(double) - Method in class cc.mallet.types.SparseMatrixn
setAll(double) - Method in class cc.mallet.types.SparseVector
  Sets every present index in the vector to v.
setAlpha(double) - Method in class cc.mallet.topics.HierarchicalLDA
setAlphabet(Alphabet) - Method in class cc.mallet.types.Multinomial.Estimator
setAlphas() - Method in class cc.mallet.topics.DMRTopicModel
  Use only the default features to set the topic prior (use no document features)
setAlphas(int) - Method in class cc.mallet.topics.DMRTopicModel
  This method sets the alphas for a hypothetical "document" that contains a single non-default feature.
setAlphas(Instance) - Method in class cc.mallet.topics.DMRTopicModel
  Set alpha based on features in an instance
setAsStartState(CRF.State) - Method in class cc.mallet.fst.CRF
setBeamWidth(int) - Method in class cc.mallet.fst.SumLatticeBeam
setBinner(SimilarTokensTemplate.FeatureVectorBinner) - Method in class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
setBounds(int, int, int, int) - Method in class cc.mallet.classify.evaluate.Graph
  Set bounds of canvas
setBurnin(int) - Method in class cc.mallet.grmm.inference.GibbsSampler
setBurninPeriod(int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
setBurninPeriod(int) - Method in class cc.mallet.topics.MultinomialHMM
setBurninPeriod(int) - Method in class cc.mallet.topics.ParallelTopicModel
setBurninPeriod(int) - Method in class cc.mallet.topics.PolylingualTopicModel
setCacheUnrolledGraphs(boolean) - Method in class cc.mallet.grmm.learning.ACRF
setCacheUnrolledGraphs(boolean) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setCaseSensitive(boolean) - Method in class cc.mallet.pipe.TokenSequenceRemoveStopwords
setCharSequence(CharSequence) - Method in class cc.mallet.util.CharSequenceLexer
setCheckpointDirectory(File) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setClassifier(MaxEnt) - Method in class cc.mallet.classify.MaxEntTrainer
  Initialize parameters using the provided classifier.
setCollectGarbage(boolean) - Method in class cc.mallet.types.PagedInstanceList
setComparator(FieldComparator) - Method in class cc.mallet.extract.AccuracyCoverageEvaluator
setComparator(FieldComparator) - Method in class cc.mallet.extract.PerDocumentF1Evaluator
setComparator(FieldComparator) - Method in class cc.mallet.extract.PerFieldF1Evaluator
setConfidence(double) - Method in class cc.mallet.fst.Segment
setConstraintBits(InstanceList, int, int) - Method in class cc.mallet.fst.semi_supervised.GECriteria
  Sets a bit for each instance if it has at least one feature constraint (anywhere in the sequence).
setConstraintsFile(String) - Method in class cc.mallet.classify.MaxEntGETrainer
setCorrect(boolean) - Method in class cc.mallet.fst.Segment
setCount(double) - Method in class cc.mallet.fst.semi_supervised.GECriterion
setCounts(Label, double, int[]) - Method in class cc.mallet.types.ROCData
  Sets the raw counts for a specified label and threshold.
setCPF(VarSet, Factor) - Method in class cc.mallet.grmm.inference.JunctionTree
setCurIter(int) - Method in class cc.mallet.fst.SumLatticeBeam
setData(InstanceList, InstanceList) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setData(Object) - Method in class cc.mallet.types.Instance
setDataAlphabet(Alphabet) - Method in class cc.mallet.pipe.Pipe
setDataSource(Iterator<Instance>, Iterator<Instance>) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setDataSubsets(Random, double, double) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setDefaultFeatureIndex(int) - Method in class cc.mallet.classify.MaxEnt
setDefaultWeight(int, double) - Method in class cc.mallet.fst.CRF
setDefaultWeight(int, double) - Method in class cc.mallet.grmm.learning.ACRF.Template
setDefaultWeights(double[]) - Method in class cc.mallet.fst.CRF
setDefaultWeights(SparseVector) - Method in class cc.mallet.grmm.learning.ACRF.Template
setDepthLimited(boolean) - Method in class cc.mallet.classify.C45Trainer
setDistinguishEndpts(boolean) - Method in class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
setDocLengthNormalization(double) - Method in class cc.mallet.classify.NaiveBayesEMTrainer
setDocLengthNormalization(double) - Method in class cc.mallet.classify.NaiveBayesTrainer.Factory
setDocLengthNormalization(double) - Method in class cc.mallet.classify.NaiveBayesTrainer
setDoPruning(boolean) - Method in class cc.mallet.classify.C45Trainer
setDoSizeScale(boolean) - Method in class cc.mallet.grmm.learning.ACRF
setDouble(int, Variable, double) - Method in class cc.mallet.grmm.types.Assignment
setEntropyWeight(double) - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByEntropyRegularization
  Sets the scaling factor for the entropy regularization term.
setErrorOutputStream(OutputStream) - Method in class cc.mallet.extract.AccuracyCoverageEvaluator
setErrorOutputStream(OutputStream) - Method in class cc.mallet.extract.PerDocumentF1Evaluator
setErrorOutputStream(OutputStream) - Method in class cc.mallet.extract.PerFieldF1Evaluator
setEta(double) - Method in class cc.mallet.topics.HierarchicalLDA
setEvaluator(ACRFEvaluator) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setEvaluator(OptimizerEvaluator.ByGradient) - Method in class cc.mallet.optimize.ConjugateGradient
setEvaluator(OptimizerEvaluator.ByGradient) - Method in class cc.mallet.optimize.GradientAscent
setEvaluator(OptimizerEvaluator.ByGradient) - Method in class cc.mallet.optimize.LimitedMemoryBFGS
setExcludeAdjacent(boolean) - Method in class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
setExpectation(double[]) - Method in class cc.mallet.fst.semi_supervised.GECriterion
setFactory(TRP.TreeFactory) - Method in class cc.mallet.grmm.inference.TRP
setFeatureMultinomialEstimator(Multinomial.Estimator) - Method in class cc.mallet.classify.NaiveBayesEMTrainer
setFeatureMultinomialEstimator(Multinomial.Estimator) - Method in class cc.mallet.classify.NaiveBayesTrainer.Factory
setFeatureMultinomialEstimator(Multinomial.Estimator) - Method in class cc.mallet.classify.NaiveBayesTrainer
  Set the Multinomial Estimator used for features.
setFeaturePipe(Pipe) - Method in class cc.mallet.extract.CRFExtractor
setFeatures(PropertyList) - Method in interface cc.mallet.types.PropertyHolder
setFeatures(PropertyList) - Method in class cc.mallet.types.Token
setFeatureSelection(FeatureSelection) - Method in class cc.mallet.classify.MaxEnt
setFeatureSelection(int, FeatureSelection) - Method in class cc.mallet.fst.CRF
setFeatureSelection(FeatureSelection) - Method in class cc.mallet.types.InstanceList
setFeaturesIncludeToken(boolean) - Method in class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
  If true, then the first feature in the list is considered to be the token's text.
setFeatureValue(String, double) - Method in class cc.mallet.fst.confidence.SequenceConfidenceInstance
setFeatureValue(String, double) - Method in interface cc.mallet.types.PropertyHolder
setFeatureValue(String, double) - Method in class cc.mallet.types.Token
setFinalWeight(double) - Method in class cc.mallet.fst.CRF.State
setFinalWeight(double) - Method in class cc.mallet.fst.FeatureTransducer.State
setFinalWeight(double) - Method in class cc.mallet.fst.HMM.State
setFinalWeight(double) - Method in class cc.mallet.fst.Transducer.State
setFirstString(String) - Method in class cc.mallet.types.StringEditVector
setFixedPotentials(ACRF.Template[]) - Method in class cc.mallet.grmm.learning.ACRF
setGamma(double) - Method in class cc.mallet.topics.HierarchicalLDA
setGamma(double) - Method in class cc.mallet.topics.MultinomialHMM
setGaussianPriorVariance(double) - Method in class cc.mallet.classify.MaxEntGETrainer
setGaussianPriorVariance(double) - Method in class cc.mallet.classify.MaxEntOptimizableByGE
  Sets the variance for Gaussian prior or equivalently the inverse of the weight of the L2 regularization term.
setGaussianPriorVariance(double) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
  Sets a parameter to prevent overtraining.
setGaussianPriorVariance(double) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
  Sets a parameter to prevent overtraining.
setGaussianPriorVariance(double) - Method in class cc.mallet.classify.MaxEntTrainer
  Sets a parameter to prevent overtraining.
setGaussianPriorVariance(double) - Method in class cc.mallet.classify.MCMaxEntTrainer
  Sets a parameter to prevent overtraining.
setGaussianPriorVariance(double) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
setGaussianPriorVariance(double) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
setGaussianPriorVariance(double) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
setGaussianPriorVariance(double) - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
setGaussianPriorVariance(double) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
setGaussianPriorVariance(double) - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByEntropyRegularization
setGaussianPriorVariance(double) - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByGE
setGaussianPriorVariance(double) - Method in class cc.mallet.grmm.learning.ACRF
setGraphProcessor(ACRF.GraphPostProcessor) - Method in class cc.mallet.grmm.learning.ACRF
setGrowAlphabet(boolean) - Method in class cc.mallet.pipe.TokenSequence2FeatureVectorSequence
setHyperbolicPriorSharpness(double) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
setHyperbolicPriorSharpness(double) - Method in class cc.mallet.classify.MCMaxEntTrainer
setHyperbolicPriorSharpness(double) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
setHyperbolicPriorSharpness(double) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
setHyperbolicPriorSharpness(double) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
setHyperbolicPriorSlope(double) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
setHyperbolicPriorSlope(double) - Method in class cc.mallet.classify.MCMaxEntTrainer
setHyperbolicPriorSlope(double) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
setHyperbolicPriorSlope(double) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
setHyperbolicPriorSlope(double) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
setIncludeTokenText(boolean) - Method in class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
setInertiaWeight(double) - Method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
setInferenceCache(Class, Object) - Method in class cc.mallet.grmm.types.FactorGraph
  Caches some information about this graph that is specific to a given type of inferencer (e.g., a junction tree).
setInferencer(Inferencer) - Method in class cc.mallet.grmm.learning.ACRF
setInferencer(Inferencer) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setInitialStep(double) - Method in class cc.mallet.optimize.StochasticMetaAscent
setInitialStepSize(double) - Method in class cc.mallet.optimize.ConjugateGradient
setInitialStepSize(double) - Method in class cc.mallet.optimize.GradientAscent
setInitialWeight(double) - Method in class cc.mallet.fst.CRF.State
setInitialWeight(double) - Method in class cc.mallet.fst.FeatureTransducer.State
setInitialWeight(double) - Method in class cc.mallet.fst.HMM.State
setInitialWeight(double) - Method in class cc.mallet.fst.Transducer.State
setInProduction(boolean) - Method in class cc.mallet.pipe.AddClassifierTokenPredictions
setInProduction(Pipe, boolean) - Static method in class cc.mallet.pipe.AddClassifierTokenPredictions
setInstance(int, Instance) - Method in class cc.mallet.types.InstanceList
  Replaces the `Instance` at position `index` with a new one.
setInstance(int, Instance) - Method in class cc.mallet.types.MultiInstanceList
setInstanceId(VMID) - Method in class cc.mallet.types.Alphabet
setInstanceWeight(int, double) - Method in class cc.mallet.types.InstanceList
setInstanceWeight(Instance, double) - Method in class cc.mallet.types.InstanceList
setInstanceWeight(Instance, double) - Method in class cc.mallet.types.MultiInstanceList
setInterceptGaussianPriorVariance(double) - Method in class cc.mallet.topics.DMROptimizable
  Set the variance for the default features (aka intercept terms), generally larger than the variance for the regular features.
setKLeps(double) - Method in class cc.mallet.fst.SumLatticeBeam
setL1RegularizationWeight(double) - Method in class cc.mallet.fst.CRFTrainerByL1LabelLikelihood
setL1Weight(double) - Method in class cc.mallet.classify.MaxEntTrainer
  Use an L1 prior.
setLabel(int, int) - Method in class cc.mallet.cluster.Clustering
  Set the cluster label for a particular instance.
setLabel(String) - Method in class cc.mallet.grmm.types.BitVarSet
setLabel(String) - Method in class cc.mallet.grmm.types.Variable
setLabeling(Labeling) - Method in class cc.mallet.types.Instance
setLabelsAtEnd(boolean) - Method in class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
setLearningRate(double) - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
setLearningRateByLikelihood(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
  Automatically sets the learning rate to one that would be good
setLineMaximizer(LineOptimizer.ByGradient) - Method in class cc.mallet.optimize.ConjugateGradient
setLogValue(Assignment, double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Use of this method is discouraged.
setLogValue(AssignmentIterator, double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Use of this method is discouraged.
setLogValue(Assignment, double) - Method in class cc.mallet.grmm.types.LogTableFactor
setLogValue(AssignmentIterator, double) - Method in class cc.mallet.grmm.types.LogTableFactor
setLogValue(Assignment, double) - Method in class cc.mallet.grmm.types.TableFactor
setLogValue(AssignmentIterator, double) - Method in class cc.mallet.grmm.types.TableFactor
setLogValues(double[]) - Method in class cc.mallet.grmm.types.AbstractTableFactor
setLogValues(double[]) - Method in class cc.mallet.grmm.types.LogTableFactor
setLogValues(double[]) - Method in class cc.mallet.grmm.types.TableFactor
setMarkDeletions(boolean) - Method in class cc.mallet.pipe.TokenSequenceRemoveStopwords
setMatch(int) - Method in class cc.mallet.types.StringEditVector
setMaxDepth(int) - Method in class cc.mallet.classify.C45Trainer
setMaxDepth(int) - Method in class cc.mallet.classify.DecisionTreeTrainer
setMaxer(Optimizer) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
setMaxLatticeFactory(MaxLatticeFactory) - Method in class cc.mallet.fst.Transducer
setMaxResets(int) - Method in class cc.mallet.fst.CRFTrainerByValueGradients
  Sets the max.
setMaxStepSize(double) - Method in class cc.mallet.optimize.GradientAscent
setMessageArray(MessageArray, MessageArray) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation.AbstractMessageStrategy
setMessageArray(MessageArray, MessageArray) - Method in interface cc.mallet.grmm.inference.AbstractBeliefPropagation.MessageStrategy
setMessageArray(MessageArray, MessageArray) - Method in class cc.mallet.grmm.inference.gbp.AbstractMessageStrategy
setMessageArray(MessageArray, MessageArray) - Method in interface cc.mallet.grmm.inference.gbp.MessageStrategy
setMessager(AbstractBeliefPropagation.MessageStrategy) - Method in class cc.mallet.grmm.inference.AbstractBeliefPropagation
setMinInfoGainSplit(double) - Method in class cc.mallet.classify.DecisionTreeTrainer
setMinNumInsts(int) - Method in class cc.mallet.classify.C45Trainer
setModelOutput(int, String) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
setModelOutput(int, String) - Method in class cc.mallet.topics.PolylingualTopicModel
setMu(double) - Method in class cc.mallet.optimize.StochasticMetaAscent
setName(Object) - Method in class cc.mallet.types.Instance
setNumCheckpointIterations(int) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setNumComponents(int) - Static method in class cc.mallet.optimize.tests.TestOptimizable
  Sets the number of gradient components that will be checked.
setNumericProperty(String, double) - Method in class cc.mallet.grmm.types.Variable
setNumericProperty(String, double) - Method in class cc.mallet.types.Instance
setNumericProperty(String, double) - Method in interface cc.mallet.types.PropertyHolder
setNumericProperty(String, double) - Method in class cc.mallet.types.Token
setNumericProperty(String, double) - Method in class cc.mallet.types.TokenSequence
setNumFeaturesToDisplay(int) - Static method in class cc.mallet.extract.LatticeViewer
setNumIterations(int) - Method in class cc.mallet.classify.MaxEntGETrainer
  Specifies the maximum number of iterations to run during a single call to `train` or `trainWithFeatureInduction`.
setNumIterations(int) - Method in class cc.mallet.classify.MaxEntTrainer
  Specifies the maximum number of iterations to run during a single call to `train` or `trainWithFeatureInduction`.
setNumIterations(int) - Method in class cc.mallet.classify.MCMaxEntTrainer
  Specifies the maximum number of iterations to run during a single call to `train` or `trainWithFeatureInduction`.
setNumIterations(int) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setNumIterations(int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
setNumIterations(int) - Method in class cc.mallet.topics.MultinomialHMM
setNumIterations(int) - Method in class cc.mallet.topics.ParallelTopicModel
setNumIterations(int) - Method in class cc.mallet.topics.PolylingualTopicModel
setNumIterToSkip(int) - Method in class cc.mallet.grmm.learning.ACRFEvaluator
setNumIterToWait(int) - Method in class cc.mallet.grmm.learning.ACRFEvaluator
setNumLabels(int) - Method in class cc.mallet.cluster.Clustering
  Set the number of clusters
setNumThreads(int) - Method in class cc.mallet.topics.ParallelTopicModel
setObserved(Variable, int) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
setOptimizeInterval(int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
setOptimizeInterval(int) - Method in class cc.mallet.topics.MultinomialHMM
setOptimizeInterval(int) - Method in class cc.mallet.topics.ParallelTopicModel
  Interval for optimizing Dirichlet hyperparameters
setOptimizeInterval(int) - Method in class cc.mallet.topics.PolylingualTopicModel
setOrCheckDataAlphabet(Alphabet) - Method in class cc.mallet.pipe.Pipe
setOrCheckTargetAlphabet(Alphabet) - Method in class cc.mallet.pipe.Pipe
setOutputPrefix(File) - Method in class cc.mallet.grmm.learning.ACRFEvaluator
setOutputPrefix(File) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
setParameter(int, int, double) - Method in class cc.mallet.classify.MaxEnt
setParameter(int, double) - Method in class cc.mallet.classify.MaxEntOptimizableByGE
setParameter(int, double) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
setParameter(int, double) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
setParameter(int, int, double) - Method in class cc.mallet.classify.MCMaxEnt
setParameter(int, double) - Method in class cc.mallet.fst.CRF.Factors
setParameter(int, int, int, double) - Method in class cc.mallet.fst.CRF
  Only sets the parameter from the first group of parameters.
setParameter(int, int, int, int, double) - Method in class cc.mallet.fst.CRF
setParameter(int, double) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
setParameter(int, double) - Method in class cc.mallet.fst.CRFOptimizableByGradientValues
setParameter(int, double) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
setParameter(int, double) - Method in class cc.mallet.fst.CRFTrainerByValueGradients.OptimizableCRF
setParameter(int, double) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
setParameter(int, double) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
setParameter(int, double) - Method in class cc.mallet.fst.ThreadedOptimizable
setParameter(int, double) - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
setParameter(int, double) - Method in interface cc.mallet.optimize.Optimizable
setParameter(int, double) - Method in class cc.mallet.optimize.OptimizableCollection.ByGradientValue
setParameter(int, double) - Method in class cc.mallet.topics.DMROptimizable
setParameters(double[]) - Method in class cc.mallet.classify.MaxEnt
setParameters(double[]) - Method in class cc.mallet.classify.MaxEntOptimizableByGE
setParameters(double[]) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
setParameters(double[]) - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
setParameters(double[]) - Method in class cc.mallet.fst.CRF.Factors
setParameters(double[]) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
setParameters(double[]) - Method in class cc.mallet.fst.CRFOptimizableByGradientValues
setParameters(double[]) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
setParameters(double[]) - Method in class cc.mallet.fst.CRFTrainerByValueGradients.OptimizableCRF
setParameters(double[]) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
setParameters(double[]) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
setParameters(double[]) - Method in class cc.mallet.fst.ThreadedOptimizable
setParameters(double[]) - Method in class cc.mallet.grmm.learning.ACRF.MaximizableACRF
setParameters(double[]) - Method in interface cc.mallet.optimize.Optimizable
setParameters(double[]) - Method in class cc.mallet.optimize.OptimizableCollection.ByGradientValue
setParameters(double[]) - Method in class cc.mallet.topics.DMROptimizable
setPattern(String) - Method in class cc.mallet.util.CharSequenceLexer
setPerClassFeatureSelection(FeatureSelection[]) - Method in class cc.mallet.classify.MaxEnt
setPerLabelFeatureSelection(FeatureSelection[]) - Method in class cc.mallet.types.InstanceList
setPerTemplateIterations(int) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setPipe(Pipe) - Method in class cc.mallet.types.InstanceList
  Change the default Pipe associated with InstanceList.
setPipes(Pipe, Pipe) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setPosition(int) - Method in interface cc.mallet.util.search.QueueElement
  Set the current queue position for this element.
setPosition(int) - Method in class cc.mallet.util.search.SearchNode
setPredicted(Sequence) - Method in class cc.mallet.fst.Segment
setPriority(double) - Method in interface cc.mallet.util.search.QueueElement
  Set the priority of this element.
setPriority(double) - Method in class cc.mallet.util.search.SearchNode
setPriorMultinomialEstimator(Multinomial.Estimator) - Method in class cc.mallet.classify.NaiveBayesEMTrainer
setPriorMultinomialEstimator(Multinomial.Estimator) - Method in class cc.mallet.classify.NaiveBayesTrainer.Factory
setPriorMultinomialEstimator(Multinomial.Estimator) - Method in class cc.mallet.classify.NaiveBayesTrainer
  Set the Multinomial Estimator used for priors.
setProgressDisplay(boolean) - Method in class cc.mallet.topics.HierarchicalLDA
  This parameter determines whether the sampler outputs shows progress by outputting a character after every iteration.
setProgressDisplayInterval(int) - Method in class cc.mallet.pipe.iterator.SimpleFileLineIterator
  Set the iterator to periodically print the total number of lines read to standard out.
setProperties(PropertyList) - Method in interface cc.mallet.types.PropertyHolder
setProperties(PropertyList) - Method in class cc.mallet.types.Token
setProperty(String, Object) - Method in class cc.mallet.types.Instance
setProperty(String, Object) - Method in interface cc.mallet.types.PropertyHolder
setProperty(String, Object) - Method in class cc.mallet.types.Token
setProperty(String, Object) - Method in class cc.mallet.types.TokenSequence
setPropertyList(PropertyList) - Method in class cc.mallet.types.Instance
  Deprecated.
setPunctuationPattern(Pattern) - Method in class cc.mallet.extract.PunctuationIgnoringComparator
setRand(Random) - Method in class cc.mallet.grmm.inference.LoopyBP
setRand(Random) - Method in class cc.mallet.grmm.inference.ResidualBP
setRandom(Randoms) - Method in class cc.mallet.grmm.inference.ExactSampler
setRandom(Randoms) - Method in class cc.mallet.grmm.inference.GibbsSampler
setRandom(Randoms) - Method in interface cc.mallet.grmm.inference.Sampler
  Sets the random seed used by this sampler.
setRandomSeed(long) - Method in class cc.mallet.grmm.inference.TRP
setRandomSeed(int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
setRandomSeed(int) - Method in class cc.mallet.topics.MultinomialHMM
setRandomSeed(int) - Method in class cc.mallet.topics.NPTopicModel
setRandomSeed(int) - Method in class cc.mallet.topics.ParallelTopicModel
setRandomSeed(int) - Method in class cc.mallet.topics.PolylingualTopicModel
setRandomSeed(int) - Method in class cc.mallet.topics.SimpleLDA
setRandomSeed(int) - Method in class cc.mallet.topics.TopicInferencer
setRankOrder(int, boolean) - Method in class cc.mallet.types.PartiallyRankedFeatureVector
setRankOrder() - Method in class cc.mallet.types.RankedFeatureVector
setRankOrder(int, boolean) - Method in class cc.mallet.types.RankedFeatureVector
setRankOrder(int) - Method in class cc.mallet.types.RankedFeatureVector
setRawValue(Assignment, double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
setRawValue(AssignmentIterator, double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
setRawValue(int, double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
setRegularGaussianPriorVariance(double) - Method in class cc.mallet.topics.DMROptimizable
  Set the variance for regular (non default) features, generally smaller than the variance for the default features.
setRelTolx(double) - Method in class cc.mallet.optimize.BackTrackLineSearch
  Sets the tolerance of relative diff in function value.
setRethrowExceptions(boolean) - Static method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
setReverseRankOrder(int, boolean) - Method in class cc.mallet.types.RankedFeatureVector
setRmin(double) - Method in class cc.mallet.fst.SumLatticeBeam
setRow(int, Assignment) - Method in class cc.mallet.grmm.types.Assignment
setRow(int, int[]) - Method in class cc.mallet.grmm.types.Assignment
setSaveSerializedModel(int, String) - Method in class cc.mallet.topics.ParallelTopicModel
  Define how often and where to save a serialized model.
setSaveState(int, String) - Method in class cc.mallet.topics.LDAHyper
  Deprecated. Define how often and where to save the state
setSaveState(int, String) - Method in class cc.mallet.topics.ParallelTopicModel
  Define how often and where to save a text representation of the current state.
setSaveState(int, String) - Method in class cc.mallet.topics.PolylingualTopicModel
  Define how often and where to save the state
setScalingFactor(double) - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByEntropyRegularization
setSecondString(String) - Method in class cc.mallet.types.StringEditVector
setSegmentEndTag(Object) - Method in class cc.mallet.fst.SegmentationEvaluator
setSegmentStartTag(Object) - Method in class cc.mallet.fst.SegmentationEvaluator
setSingle(int, double) - Method in class cc.mallet.types.Matrix2
  Deprecated.
setSingleValue(int, double) - Method in class cc.mallet.types.DenseMatrix
setSingleValue(int, double) - Method in interface cc.mallet.types.Matrix
setSingleValue(int, double) - Method in class cc.mallet.types.SparseMatrixn
setSlice(int) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
setSource(Object) - Method in class cc.mallet.types.Instance
setStateFile(String) - Method in class cc.mallet.topics.HierarchicalLDA
setStateLabelMap(StateLabelMap) - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByGE
setStpmax(double) - Method in class cc.mallet.optimize.GradientAscent
setSubFactor(DiscreteFactor) - Method in class cc.mallet.grmm.types.CPT
setSumLatticeFactory(SumLatticeFactory) - Method in class cc.mallet.fst.Transducer
setSummary(String) - Method in class cc.mallet.util.CommandOption.List
setSummary(Class, String) - Static method in class cc.mallet.util.CommandOption
setSupportedOnly(boolean) - Method in class cc.mallet.grmm.learning.ACRF
  Sets all templates of this ACRF to use supported features only.
setSymmetricAlpha(boolean) - Method in class cc.mallet.topics.ParallelTopicModel
setTarget(Object) - Method in class cc.mallet.types.Instance
setTargetAlphabet(Alphabet) - Method in class cc.mallet.pipe.Pipe
setTargetProcessing(boolean) - Method in class cc.mallet.pipe.Pipe
  Set whether input is taken from target field of instance during processing.
setTargetProcessing(boolean) - Method in class cc.mallet.pipe.SerialPipes
setTargetsUsingData(InstanceList, ArrayList<Integer>) - Static method in class cc.mallet.classify.FeatureConstraintUtil
  Set target distributions using estimates from data.
setTargetsUsingFeatureVoting(HashMap<Integer, ArrayList<Integer>>, InstanceList) - Static method in class cc.mallet.classify.FeatureConstraintUtil
  Set target distributions using feature voting heuristic described in "Learning from Labeled Features using Generalized Expectation Criteria" Gregory Druck, Gideon Mann, Andrew McCallum.
setTargetsUsingHeuristic(HashMap<Integer, ArrayList<Integer>>, int, double) - Static method in class cc.mallet.classify.FeatureConstraintUtil
  Set target distributions using "Schapire" heuristic described in "Learning from Labeled Features using Generalized Expectation Criteria" Gregory Druck, Gideon Mann, Andrew McCallum.
setTemperature(double) - Method in class cc.mallet.classify.MaxEntGETrainer
setTemperature(double) - Method in class cc.mallet.classify.MaxEntOptimizableByGE
  Set the temperature, 1 / the exponent model predicted probabilities are raised to when computing model expectations.
setTemperingInterval(int) - Method in class cc.mallet.topics.ParallelTopicModel
setTemplates(ACRF.Template[]) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setTerminator(TRP.TerminationCondition) - Method in class cc.mallet.grmm.inference.TRP
setTestingInstances(InstanceList) - Method in class cc.mallet.topics.LDAHyper
  Deprecated. Held-out instances for empirical likelihood calculation
setText(String) - Method in class cc.mallet.types.Token
setTextFeaturePrefix(String) - Method in class cc.mallet.grmm.learning.GenericAcrfData2TokenSequence
setTokenizatioFilter(TokenizationFilter) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setTokenizationFilter(TokenizationFilter) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
setTokenizationPipe(Pipe) - Method in class cc.mallet.extract.CRFExtractor
setTokenizationPipe(Pipe) - Method in interface cc.mallet.extract.Extractor
  Sets the pipe used by this extractor for tokenization.
setTokenizationPipe(Pipe) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractor
setTokensAsFeatures - Variable in class cc.mallet.pipe.SimpleTaggerSentence2TokenSequence
setTolerance(double) - Method in class cc.mallet.optimize.ConjugateGradient
setTolerance(double) - Method in class cc.mallet.optimize.LimitedMemoryBFGS
setTopicDisplay(int, int) - Method in class cc.mallet.topics.HierarchicalLDA
setTopicDisplay(int, int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
setTopicDisplay(int, int) - Method in class cc.mallet.topics.NPTopicModel
setTopicDisplay(int, int) - Method in class cc.mallet.topics.ParallelTopicModel
setTopicDisplay(int, int) - Method in class cc.mallet.topics.PolylingualTopicModel
setTopicDisplay(int, int) - Method in class cc.mallet.topics.SimpleLDA
setTopicDisplayInterval(int) - Method in class cc.mallet.topics.MultinomialHMM
setTrainable(boolean) - Method in class cc.mallet.fst.FeatureTransducer
setTrainable(boolean) - Method in class cc.mallet.grmm.learning.ACRF.FixedFactorTemplate
setTrainable(boolean) - Method in class cc.mallet.grmm.learning.ACRF.Template
setTrainingMethod(ACRFTrainer) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setUnlabeledDataWeight(double) - Method in class cc.mallet.classify.NaiveBayesEMTrainer
setUp() - Method in class cc.mallet.classify.tests.TestClassifiers
setUp() - Method in class cc.mallet.classify.tests.TestMaxEntTrainer
setUp() - Method in class cc.mallet.classify.tests.TestNaiveBayes
setUp() - Method in class cc.mallet.classify.tests.TestStaticParameters
setUp() - Method in class cc.mallet.cluster.evaluate.tests.TestClusteringEvaluators
setUp() - Method in class cc.mallet.cluster.iterator.tests.TestIterators
setUp() - Method in class cc.mallet.fst.tests.TestFeatureTransducer
setUp() - Method in class cc.mallet.grmm.test.TestAssignment
setUp() - Method in class cc.mallet.grmm.test.TestFactorGraph
setUp() - Method in class cc.mallet.grmm.test.TestInference
setUp() - Method in class cc.mallet.grmm.test.TestPottsFactor
setUp() - Method in class cc.mallet.optimize.tests.TestOptimizable
setUp() - Method in class cc.mallet.pipe.iterator.tests.TestPatternMatchIterator
setUp() - Method in class cc.mallet.pipe.tests.TestInstancePipe
setUp() - Method in class cc.mallet.pipe.tests.TestRainbowStyle
setUp() - Method in class cc.mallet.pipe.tests.TestSGML2TokenSequence
setUp() - Method in class cc.mallet.pipe.tsf.tests.TestOffsetConjunctions
setUp() - Method in class cc.mallet.types.tests.TestFeatureSequence
setUp() - Method in class cc.mallet.types.tests.TestFeatureVector
setUp() - Method in class cc.mallet.types.tests.TestHashedSparseVector
setUp() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
setUp() - Method in class cc.mallet.types.tests.TestLabelVector
setUp() - Method in class cc.mallet.types.tests.TestMatrix
setUp() - Method in class cc.mallet.types.tests.TestMultinomial
setUp() - Method in class cc.mallet.types.tests.TestRankedFeatureVector
setUp() - Method in class cc.mallet.types.tests.TestSparseVector
setUp() - Method in class cc.mallet.types.tests.TestToken
setUp() - Method in class cc.mallet.util.tests.TestPropertyList
setupData() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setUseCaching(boolean) - Method in class cc.mallet.grmm.inference.LoopyBP
setUseCaching(boolean) - Method in class cc.mallet.grmm.inference.ResidualBP
setUseForwardBackwardBeam(boolean) - Method in class cc.mallet.fst.SumLatticeBeam
setUseHessian(boolean) - Method in class cc.mallet.optimize.StochasticMetaAscent
setUseHyperbolicPrior(boolean) - Method in class cc.mallet.classify.MCMaxEntTrainer
setUseHyperbolicPrior(boolean) - Method in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
setUseHyperbolicPrior(boolean) - Method in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
setUseHyperbolicPrior(boolean) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
setUseInertia(boolean) - Method in class cc.mallet.grmm.inference.gbp.ParentChildGBP
setUsePerTemplateTrain(boolean) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setUseSomeUnsupportedTrick(boolean) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
  Sets whether to use the 'some unsupported trick.' This trick is, if training a CRF where some training has been done and sparse weights are used, to add a few weights for feaures that do not occur in the tainig data.
setUseSomeUnsupportedTrick(boolean) - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
  Sets whether to use the 'some unsupported trick.' This trick is, if training a CRF where some training has been done and sparse weights are used, to add a few weights for feaures that do not occur in the tainig data.
setUseSparseWeights(boolean) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
setUseSparseWeights(boolean) - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
setValidationInstances(InstanceList) - Method in class cc.mallet.classify.ClassifierTrainer
setValue(AssignmentIterator, double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Use of this method is discouraged.
setValue(Variable, int) - Method in class cc.mallet.grmm.types.Assignment
setValue(int, Variable, int) - Method in class cc.mallet.grmm.types.Assignment
setValue(AssignmentIterator, double) - Method in class cc.mallet.grmm.types.LogTableFactor
setValue(AssignmentIterator, double) - Method in class cc.mallet.grmm.types.TableFactor
setValue(int, double) - Method in class cc.mallet.types.AugmentableFeatureVector
setValue(int[], double) - Method in class cc.mallet.types.DenseMatrix
setValue(int[], double) - Method in class cc.mallet.types.DenseVector
setValue(int, double) - Method in class cc.mallet.types.DenseVector
setValue(int, double) - Method in class cc.mallet.types.HashedSparseVector
setValue(int, double) - Method in class cc.mallet.types.IndexedSparseVector
setValue(int[], double) - Method in interface cc.mallet.types.Matrix
setValue(int, int, double) - Method in class cc.mallet.types.Matrix2
  Deprecated.
setValue(int[], double) - Method in class cc.mallet.types.Matrix2
  Deprecated.
setValue(int[], double) - Method in class cc.mallet.types.Matrixn
setValue(int[], double) - Method in class cc.mallet.types.SparseMatrixn
setValue(int, double) - Method in class cc.mallet.types.SparseVector
  Sets the value at the given index.
setValueAtLocation(int, double) - Method in class cc.mallet.types.AugmentableFeatureVector
setValueAtLocation(int, double) - Method in class cc.mallet.types.DenseMatrix
setValueAtLocation(int, double) - Method in class cc.mallet.types.HashedSparseVector
setValueAtLocation(int, double) - Method in class cc.mallet.types.IndexedSparseVector
setValueAtLocation(int, double) - Method in interface cc.mallet.types.Matrix
setValueAtLocation(int, double) - Method in class cc.mallet.types.SparseMatrixn
setValueAtLocation(int, double) - Method in class cc.mallet.types.SparseVector
  Sets the value at the given location.
setValues(Matrix) - Method in class cc.mallet.grmm.types.AbstractTableFactor
setValues(double[]) - Method in class cc.mallet.grmm.types.AbstractTableFactor
setValues(double[]) - Method in class cc.mallet.grmm.types.LogTableFactor
setValues(double[]) - Method in class cc.mallet.grmm.types.TableFactor
setVarSet(VarSet) - Method in class cc.mallet.grmm.types.AbstractFactor
setVerboseOutputDirectory(File) - Method in class cc.mallet.grmm.inference.TRP
setVerboseOutputDirectory(File) - Method in class cc.mallet.grmm.learning.ACRF
setViterbiInferencer(Inferencer) - Method in class cc.mallet.grmm.learning.ACRF
setViterbiInferencer(Inferencer) - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
setWeight(double) - Method in class cc.mallet.classify.MaxEntOptimizableByGE
  The weight of GE term in the objective function.
setWeights(int, SparseVector) - Method in class cc.mallet.fst.CRF
setWeights(String, SparseVector) - Method in class cc.mallet.fst.CRF
setWeights(SparseVector[]) - Method in class cc.mallet.fst.CRF
setWeights(SparseVector[]) - Method in class cc.mallet.grmm.learning.ACRF.Template
setWeights() - Method in class cc.mallet.types.tests.TestInstanceListWeights
setWeightsDimensionAsIn(InstanceList) - Method in class cc.mallet.fst.CRF
setWeightsDimensionAsIn(InstanceList, boolean) - Method in class cc.mallet.fst.CRF
setWeightsDimensionDensely() - Method in class cc.mallet.fst.CRF
setWithAddend(ConstantMatrix, double) - Method in class cc.mallet.types.DenseMatrix
setWithAddend(ConstantMatrix, double) - Method in interface cc.mallet.types.Matrix
setWithAddend(ConstantMatrix, double) - Method in class cc.mallet.types.SparseMatrixn
setWithFactor(ConstantMatrix, double) - Method in class cc.mallet.types.DenseMatrix
setWithFactor(ConstantMatrix, double) - Method in interface cc.mallet.types.Matrix
setWithFactor(ConstantMatrix, double) - Method in class cc.mallet.types.SparseMatrixn
SGML2TokenSequence - Class in cc.mallet.pipe
  Converts a string containing simple SGML tags into a dta TokenSequence of words, paired with a target TokenSequence containing the SGML tags in effect for each word.
SGML2TokenSequence(CharSequenceLexer, String, boolean) - Constructor for class cc.mallet.pipe.SGML2TokenSequence
SGML2TokenSequence(CharSequenceLexer, String) - Constructor for class cc.mallet.pipe.SGML2TokenSequence
SGML2TokenSequence(String, String) - Constructor for class cc.mallet.pipe.SGML2TokenSequence
SGML2TokenSequence() - Constructor for class cc.mallet.pipe.SGML2TokenSequence
shallowClone() - Method in class cc.mallet.types.InstanceList
shallowClone() - Method in class cc.mallet.types.MultiInstanceList
shallowClone() - Method in class cc.mallet.types.PagedInstanceList
shallowCopy() - Method in class cc.mallet.cluster.Clustering
shallowCopy() - Method in class cc.mallet.types.Instance
ShallowTransducerTrainer - Class in cc.mallet.fst
  Deprecated. Use `NoopTransducerTrainer` instead
ShallowTransducerTrainer(Transducer) - Constructor for class cc.mallet.fst.ShallowTransducerTrainer
  Deprecated.
shatterInstances(Clustering, int[]) - Static method in class cc.mallet.cluster.util.ClusterUtils
shouldContinue(TRP) - Method in class cc.mallet.grmm.inference.TRP.ConvergenceTerminator
shouldContinue(TRP) - Method in class cc.mallet.grmm.inference.TRP.DefaultConvergenceTerminator
shouldContinue(TRP) - Method in class cc.mallet.grmm.inference.TRP.IterationTerminator
shouldContinue(TRP) - Method in interface cc.mallet.grmm.inference.TRP.TerminationCondition
shouldDoEvaluate(int) - Method in class cc.mallet.grmm.learning.ACRFEvaluator
showTopicsInterval - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
showTopicsInterval - Variable in class cc.mallet.topics.NPTopicModel
showTopicsInterval - Variable in class cc.mallet.topics.ParallelTopicModel
showTopicsInterval - Variable in class cc.mallet.topics.PolylingualTopicModel
showTopicsInterval - Variable in class cc.mallet.topics.SimpleLDA
shuffle(Random) - Method in class cc.mallet.types.InstanceList
shuffle(Random) - Method in class cc.mallet.types.MultiInstanceList
shutdown() - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
shutdown() - Method in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
shutdown() - Method in class cc.mallet.fst.ThreadedOptimizable
  Shuts down the executor used to start and run threads to compute values and gradients.
sigmod(double) - Static method in class cc.mallet.util.Maths
sigmod_rev(double) - Static method in class cc.mallet.util.Maths
SimilarTokensTemplate - Class in cc.mallet.grmm.learning.templates
  Template for adding "skip edges" as in
SimilarTokensTemplate(int) - Constructor for class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
SimilarTokensTemplate(int, boolean) - Constructor for class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
SimilarTokensTemplate(int, boolean, boolean) - Constructor for class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
SimilarTokensTemplate(int, boolean, SimilarTokensTemplate.FeatureVectorBinner) - Constructor for class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
SimilarTokensTemplate(int, boolean, boolean, SimilarTokensTemplate.FeatureVectorBinner) - Constructor for class cc.mallet.grmm.learning.templates.SimilarTokensTemplate
SimilarTokensTemplate.CapWordsBinner - Class in cc.mallet.grmm.learning.templates
SimilarTokensTemplate.CapWordsBinner() - Constructor for class cc.mallet.grmm.learning.templates.SimilarTokensTemplate.CapWordsBinner
SimilarTokensTemplate.FeatureVectorBinner - Interface in cc.mallet.grmm.learning.templates
  Interface for classes that ssigns each features vector to a String-valued bin.
SimilarTokensTemplate.WordFeatureBinner - Class in cc.mallet.grmm.learning.templates
SimilarTokensTemplate.WordFeatureBinner() - Constructor for class cc.mallet.grmm.learning.templates.SimilarTokensTemplate.WordFeatureBinner
SimilarTokensTemplate.WordFeatureBinner(Pattern) - Constructor for class cc.mallet.grmm.learning.templates.SimilarTokensTemplate.WordFeatureBinner
SimpleCrfExample - Class in cc.mallet.grmm.examples
  $Id: SimpleCrfExample.java,v 1.1 2007/10/22 21:38:02 mccallum Exp $
SimpleCrfExample() - Constructor for class cc.mallet.grmm.examples.SimpleCrfExample
SimpleFactorExample - Class in cc.mallet.grmm.examples
  A simple example to demonstrate the row-major indexing of potential values.
SimpleFactorExample() - Constructor for class cc.mallet.grmm.examples.SimpleFactorExample
SimpleFileLineIterator - Class in cc.mallet.pipe.iterator
SimpleFileLineIterator(String) - Constructor for class cc.mallet.pipe.iterator.SimpleFileLineIterator
SimpleFileLineIterator(File) - Constructor for class cc.mallet.pipe.iterator.SimpleFileLineIterator
SimpleGraphExample - Class in cc.mallet.grmm.examples
  Created: Aug 13, 2004
SimpleGraphExample() - Constructor for class cc.mallet.grmm.examples.SimpleGraphExample
SimpleLDA - Class in cc.mallet.topics
  A simple implementation of Latent Dirichlet Allocation using Gibbs sampling.
SimpleLDA(int) - Constructor for class cc.mallet.topics.SimpleLDA
SimpleLDA(int, double, double) - Constructor for class cc.mallet.topics.SimpleLDA
SimpleLDA(int, double, double, Randoms) - Constructor for class cc.mallet.topics.SimpleLDA
SimpleLDA(LabelAlphabet, double, double, Randoms) - Constructor for class cc.mallet.topics.SimpleLDA
SimpleTagger - Class in cc.mallet.fst
  This class's main method trains, tests, or runs a generic CRF-based sequence tagger.
SimpleTagger.SimpleTaggerSentence2FeatureVectorSequence - Class in cc.mallet.fst
  Converts an external encoding of a sequence of elements with binary features to a `FeatureVectorSequence`.
SimpleTagger.SimpleTaggerSentence2FeatureVectorSequence() - Constructor for class cc.mallet.fst.SimpleTagger.SimpleTaggerSentence2FeatureVectorSequence
  Creates a new `SimpleTaggerSentence2FeatureVectorSequence` instance.
SimpleTaggerSentence2StringTokenization - Class in cc.mallet.pipe
  This extends `SimpleTaggerSentence2TokenSequence` to use {Slink StringTokenizations} for use with the extract package.
SimpleTaggerSentence2StringTokenization() - Constructor for class cc.mallet.pipe.SimpleTaggerSentence2StringTokenization
  Creates a new `SimpleTaggerSentence2StringTokenization` instance.
SimpleTaggerSentence2StringTokenization(boolean) - Constructor for class cc.mallet.pipe.SimpleTaggerSentence2StringTokenization
  creates a new `SimpleTaggerSentence2StringTokenization` instance which includes tokens as features iff the supplied argument is true.
SimpleTaggerSentence2TokenSequence - Class in cc.mallet.pipe
  Converts an external encoding of a sequence of elements with binary features to a `TokenSequence`.
SimpleTaggerSentence2TokenSequence() - Constructor for class cc.mallet.pipe.SimpleTaggerSentence2TokenSequence
  Creates a new `SimpleTaggerSentence2TokenSequence` instance.
SimpleTaggerSentence2TokenSequence(boolean) - Constructor for class cc.mallet.pipe.SimpleTaggerSentence2TokenSequence
  creates a new `SimpleTaggerSentence2TokenSequence` instance which includes tokens as features iff the supplied argument is true.
SimpleTokenizer - Class in cc.mallet.pipe
  A simple unicode tokenizer that accepts sequences of letters as tokens.
SimpleTokenizer(int) - Constructor for class cc.mallet.pipe.SimpleTokenizer
SimpleTokenizer(File) - Constructor for class cc.mallet.pipe.SimpleTokenizer
SimpleTokenizer(HashSet<String>) - Constructor for class cc.mallet.pipe.SimpleTokenizer
singleIndex(int[]) - Method in class cc.mallet.grmm.types.AbstractTableFactor
singleIndex() - Method in class cc.mallet.grmm.types.Assignment
  Converts this assignment into a unique integer.
singleIndex(int) - Method in class cc.mallet.grmm.types.Assignment
singleIndex(int[]) - Method in class cc.mallet.grmm.types.CPT
singleIndex(int[]) - Method in interface cc.mallet.grmm.types.DiscreteFactor
singleIndex(int[]) - Method in interface cc.mallet.types.ConstantMatrix
singleIndex(int[]) - Method in class cc.mallet.types.DenseMatrix
singleIndex(int[]) - Method in class cc.mallet.types.DenseVector
singleIndex(int[]) - Method in class cc.mallet.types.Matrix2
  Deprecated.
singleIndex(int[]) - Method in class cc.mallet.types.Matrixn
singleIndex(int[], int[]) - Static method in class cc.mallet.types.Matrixn
singleIndex(int[]) - Method in class cc.mallet.types.SparseMatrixn
singleIndex(int[], int[]) - Static method in class cc.mallet.types.SparseMatrixn
singleIndex(int[]) - Method in class cc.mallet.types.SparseVector
SingleInstanceIterator - Class in cc.mallet.types
SingleInstanceIterator(Instance) - Constructor for class cc.mallet.types.SingleInstanceIterator
singleSize() - Method in class cc.mallet.types.AugmentableFeatureVector
singleSize() - Method in interface cc.mallet.types.ConstantMatrix
singleSize() - Method in class cc.mallet.types.DenseMatrix
singleSize() - Method in class cc.mallet.types.Matrix2
  Deprecated.
singleSize() - Method in class cc.mallet.types.SparseMatrixn
singleSize() - Method in class cc.mallet.types.SparseVector
singleToIndices(int, int[]) - Method in interface cc.mallet.types.ConstantMatrix
singleToIndices(int, int[]) - Method in class cc.mallet.types.DenseMatrix
singleToIndices(int, int[]) - Method in class cc.mallet.types.DenseVector
singleToIndices(int, int[]) - Method in class cc.mallet.types.Matrix2
  Deprecated.
singleToIndices(int, int[]) - Method in class cc.mallet.types.Matrixn
singleToIndices(int, int[], int[]) - Static method in class cc.mallet.types.Matrixn
  Just a utility function for arbitrary-dimensional matrix dereferencing.
singleToIndices(int, int[]) - Method in class cc.mallet.types.SparseMatrixn
singleToIndices(int, int[]) - Method in class cc.mallet.types.SparseVector
singleValue(int) - Method in interface cc.mallet.types.ConstantMatrix
singleValue(int) - Method in class cc.mallet.types.DenseMatrix
singleValue(int) - Method in class cc.mallet.types.Matrix2
  Deprecated.
singleValue(int) - Method in class cc.mallet.types.SparseMatrixn
singleValue(int) - Method in class cc.mallet.types.SparseVector
size() - Method in class cc.mallet.classify.evaluate.Graph.Legend
size(int) - Method in class cc.mallet.cluster.Clustering
size() - Method in class cc.mallet.cluster.Clusterings
size() - Method in class cc.mallet.cluster.evaluate.ClusteringEvaluators
size() - Method in class cc.mallet.extract.DocumentExtraction
size() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
size() - Method in class cc.mallet.fst.Segment
size() - Method in class cc.mallet.grmm.types.Assignment
size() - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
size() - Method in class cc.mallet.grmm.types.BitVarSet
size() - Method in class cc.mallet.grmm.types.HashVarSet
size() - Method in class cc.mallet.grmm.types.ListVarSet
size() - Method in class cc.mallet.grmm.types.Universe
size() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
size() - Method in class cc.mallet.grmm.util.CSIntInt2ObjectMultiMap
size() - Method in class cc.mallet.grmm.util.MIntInt2ObjectMap
size() - Method in class cc.mallet.pipe.Array2FeatureVector
  Current size of the Vocabulary
size() - Method in class cc.mallet.pipe.SerialPipes
size() - Method in class cc.mallet.types.Alphabet
size() - Method in class cc.mallet.types.ArraySequence
size() - Method in class cc.mallet.types.Dirichlet
size() - Method in class cc.mallet.types.FeatureConjunction.List
size() - Method in class cc.mallet.types.FeatureSequence
size() - Method in class cc.mallet.types.FeatureVectorSequence
size() - Method in class cc.mallet.types.Labels
size() - Method in class cc.mallet.types.LabelsSequence
size() - Method in class cc.mallet.types.MultiInstanceList
size() - Method in class cc.mallet.types.Multinomial.Estimator
size() - Method in class cc.mallet.types.Multinomial
size() - Method in class cc.mallet.types.PagedInstanceList
size() - Method in interface cc.mallet.types.Sequence
size() - Method in class cc.mallet.util.CommandOption.List
size() - Method in class cc.mallet.util.PropertyList
size() - Method in class cc.mallet.util.search.MinHeap
size() - Method in interface cc.mallet.util.search.PriorityQueue
  The current size of the queue.
size() - Method in class cc.mallet.util.Univariate
sizeMatches(ConstantMatrix) - Method in class cc.mallet.types.Matrix2
  Deprecated.
sizeMatches(Matrix2) - Method in class cc.mallet.types.Matrix2
  Deprecated.
SkeletonFactor - Class in cc.mallet.grmm.types
  A subclass of Factor in which all operations throw an UnsupportedOperationException.
SkeletonFactor() - Constructor for class cc.mallet.grmm.types.SkeletonFactor
skip - Static variable in class cc.mallet.share.weili.ner.enron.EnronMessage2TokenSequence
SKIP_HEADER - Static variable in class cc.mallet.pipe.CharSequenceReplace
SKIP_HEADER - Static variable in class cc.mallet.pipe.CharSubsequence
SKIP_SGML - Static variable in class cc.mallet.pipe.CharSequenceReplace
skiptestOldCrf() - Method in class cc.mallet.fst.tests.TestCRF
skipToBlankLine - Static variable in class cc.mallet.share.weili.ner.enron.EnronMessage2TokenSequence
SLEEP_TIME - Static variable in class cc.mallet.fst.ThreadedOptimizable
slice(Assignment) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Creates a new potential that is equal to this one, restricted to a given assignment.
slice(Assignment) - Method in class cc.mallet.grmm.types.Assignment
slice(Assignment) - Method in class cc.mallet.grmm.types.BetaFactor
slice(Assignment) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
slice(Assignment) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
slice(Assignment) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
slice(Assignment) - Method in class cc.mallet.grmm.types.ConstantFactor
slice(Assignment) - Method in class cc.mallet.grmm.types.CPT
slice(Assignment) - Method in interface cc.mallet.grmm.types.Factor
slice(Assignment) - Method in class cc.mallet.grmm.types.FactorGraph
slice(Assignment, Map) - Method in class cc.mallet.grmm.types.FactorGraph
slice(Assignment) - Method in class cc.mallet.grmm.types.NormalFactor
slice(Assignment) - Method in class cc.mallet.grmm.types.PottsTableFactor
slice(Assignment) - Method in class cc.mallet.grmm.types.SkeletonFactor
slice(Assignment) - Method in class cc.mallet.grmm.types.UniformFactor
slice(Assignment) - Method in class cc.mallet.grmm.types.UniNormalFactor
slice_general(Variable[], Assignment) - Method in class cc.mallet.grmm.types.AbstractTableFactor
slice_general(Variable[], Assignment) - Method in class cc.mallet.grmm.types.LogTableFactor
slice_general(Variable[], Assignment) - Method in class cc.mallet.grmm.types.TableFactor
slice_onevar(Variable, Assignment) - Method in class cc.mallet.grmm.types.AbstractTableFactor
slice_onevar(Variable, Assignment) - Method in class cc.mallet.grmm.types.LogTableFactor
slice_onevar(Variable, Assignment) - Method in class cc.mallet.grmm.types.TableFactor
  Creates a new potential from another by restricting it to a given assignment.
slice_twovar(Variable, Variable, Assignment) - Method in class cc.mallet.grmm.types.AbstractTableFactor
slice_twovar(Variable, Variable, Assignment) - Method in class cc.mallet.grmm.types.LogTableFactor
slice_twovar(Variable, Variable, Assignment) - Method in class cc.mallet.grmm.types.TableFactor
SliceLabelsSequence - Class in cc.mallet.grmm.util
  * Created: Fri Jan 02 23:27:04 2004
SliceLabelsSequence(int) - Constructor for class cc.mallet.grmm.util.SliceLabelsSequence
sliceLabelsSequence(LabelsSequence, int) - Static method in class cc.mallet.grmm.util.SliceLabelsSequence
sliceLabelsSequence(LabelsSequence, LabelAlphabet, int) - Static method in class cc.mallet.grmm.util.SliceLabelsSequence
slicePipes(int) - Method in class cc.mallet.extract.CRFExtractor
  Transfer some Pipes from the feature pipe to the tokenization pipe.
smoothingOnlyMass - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
smoothingOnlyMass - Variable in class cc.mallet.topics.MarginalProbEstimator
smoothingOnlyMass - Variable in class cc.mallet.topics.WorkerRunnable
solveWithBackSubstitution(double[], double[]) - Static method in class cc.mallet.util.MVNormal
  This method returns x such that L'x = b.
solveWithForwardSubstitution(double[], double[]) - Static method in class cc.mallet.util.MVNormal
  This method returns x such that Lx = b where L is lower triangular
someUnsupportedTrain(ACRF, InstanceList, InstanceList, InstanceList, ACRFEvaluator, int) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
sort() - Method in class cc.mallet.util.Univariate
sortClassifications() - Method in class cc.mallet.classify.evaluate.AccuracyCoverage
  Sort classifications ArrayList by winner's value
sortedUnion(List, List) - Static method in class cc.mallet.util.CollectionUtils
sortIndices() - Method in class cc.mallet.types.AugmentableFeatureVector
sortIndices() - Method in class cc.mallet.types.SparseVector
sortInstances(InstanceList, int[], int) - Static method in class cc.mallet.types.GainRatio
source - Variable in class cc.mallet.types.Instance
SourceLocation2TokenSequence - Class in cc.mallet.pipe
  Read from File or BufferedRead in the data field and produce a TokenSequence.
SourceLocation2TokenSequence(CharSequenceLexer) - Constructor for class cc.mallet.pipe.SourceLocation2TokenSequence
sourceNowHasNext(Iterator<Instance>) - Method in class cc.mallet.types.ChainedInstanceIterator
  Deprecated. The "source" of this iterator sends this message to tell this iterator that, even though source.hasNext() may have returned false before, it would now return true.
spacePipeOutput - Static variable in class cc.mallet.pipe.tests.TestSpacePipe
span(int) - Method in class cc.mallet.extract.Field
Span - Interface in cc.mallet.extract
  A sub-section of a document, either linear or two-dimensional.
SparseMatrixn - Class in cc.mallet.types
  Implementation of Matrix that allows arbitrary number of dimensions.
SparseMatrixn(double[]) - Constructor for class cc.mallet.types.SparseMatrixn
  Create a 1-d dense matrix with the given values.
SparseMatrixn(int[]) - Constructor for class cc.mallet.types.SparseMatrixn
  Create a dense matrix with the given dimensions.
SparseMatrixn(int[], double[]) - Constructor for class cc.mallet.types.SparseMatrixn
SparseMatrixn(int[], int[], double[]) - Constructor for class cc.mallet.types.SparseMatrixn
  Create a sparse matrix with the given dimensions and the given values.
SparseMessageSender - Class in cc.mallet.grmm.inference.gbp
  Created: Jun 1, 2005
SparseMessageSender(double) - Constructor for class cc.mallet.grmm.inference.gbp.SparseMessageSender
SparseVector - Class in cc.mallet.types
  A vector that allocates memory only for non-zero values.
SparseVector(int[], double[], int, int, boolean, boolean, boolean) - Constructor for class cc.mallet.types.SparseVector
  If "indices" is null, the vector will be dense.
SparseVector(double[], boolean) - Constructor for class cc.mallet.types.SparseVector
SparseVector(double[]) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int, double) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int[], double[], boolean, boolean, boolean) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int[], double[]) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int[], double[], boolean) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int[], double[], boolean, boolean) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int[], boolean, boolean, boolean, boolean) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int[], int, int, boolean, boolean, boolean) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int[], boolean, boolean) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int[], boolean) - Constructor for class cc.mallet.types.SparseVector
SparseVector(int[]) - Constructor for class cc.mallet.types.SparseVector
SparseVector() - Constructor for class cc.mallet.types.SparseVector
  An empty vector, with all zero values
SparseVector(Alphabet, PropertyList, boolean, boolean) - Constructor for class cc.mallet.types.SparseVector
SparseVector(Alphabet, PropertyList, boolean) - Constructor for class cc.mallet.types.SparseVector
split() - Method in class cc.mallet.classify.C45.Node
split(FeatureSelection) - Method in class cc.mallet.classify.DecisionTree.Node
split(Random, double[]) - Method in class cc.mallet.types.InstanceList
  Shuffles the elements of this list among several smaller lists.
split(double[]) - Method in class cc.mallet.types.InstanceList
split(double[]) - Method in class cc.mallet.types.MultiInstanceList
split(Random, double[]) - Method in class cc.mallet.types.MultiInstanceList
split(Random, double[]) - Method in class cc.mallet.types.PagedInstanceList
  Shuffles the elements of this list among several smaller lists.
splitInOrder(double[]) - Method in class cc.mallet.types.InstanceList
  Chops this list into several sequential sublists.
splitInOrder(int[]) - Method in class cc.mallet.types.InstanceList
splitInOrder(double[]) - Method in class cc.mallet.types.MultiInstanceList
splitInOrder(int[]) - Method in class cc.mallet.types.MultiInstanceList
splitInTwoByModulo(int) - Method in class cc.mallet.types.InstanceList
  Returns a pair of new lists such that the first list in the pair contains every `m`th element of this list, starting with the first.
splitInTwoByModulo(int) - Method in class cc.mallet.types.MultiInstanceList
splitTree(C45.Node, int) - Method in class cc.mallet.classify.C45Trainer
splitTree(DecisionTree.Node, FeatureSelection, int) - Method in class cc.mallet.classify.DecisionTreeTrainer
sqrt() - Static method in class cc.mallet.grmm.util.Flops
squaredDifference(Dirichlet) - Method in class cc.mallet.types.Dirichlet
  Compute the L2 residual between two dirichlets
startGrowth() - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
startGrowth() - Method in class cc.mallet.types.Alphabet
STARTING_DIRECTORIES - Static variable in class cc.mallet.pipe.iterator.FileIterator
STARTING_DIRECTORIES - Static variable in class cc.mallet.pipe.iterator.FileListIterator
  Use as label names the directories of the given files, optionally removing common prefix of all starting directories
STARTING_DIRECTORIES - Static variable in class cc.mallet.pipe.iterator.UnlabeledFileIterator
  Use as label names the directories specified in the constructor, optionally removing common prefix of all starting directories
state - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice.LatticeNode
stateFilename - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
stateFilename - Variable in class cc.mallet.topics.ParallelTopicModel
stateFilename - Variable in class cc.mallet.topics.PolylingualTopicModel
stateIndexOfString(String) - Method in class cc.mallet.fst.Transducer
  Returns the index of the input state name, returns -1 if name not found.
stateLabelMap - Variable in class cc.mallet.fst.semi_supervised.GECriteria
StateLabelMap - Class in cc.mallet.fst.semi_supervised
  Maps states in the lattice to labels.
StateLabelMap(Alphabet, boolean) - Constructor for class cc.mallet.fst.semi_supervised.StateLabelMap
  Initializes the state and label maps.
states - Variable in class cc.mallet.fst.CRF
stateTopics() - Method in class cc.mallet.topics.MultinomialHMM
stateTransitionMatrix() - Method in class cc.mallet.topics.MultinomialHMM
StatFunctions - Class in cc.mallet.util
StatFunctions() - Constructor for class cc.mallet.util.StatFunctions
stddev(double[]) - Static method in class cc.mallet.types.MatrixOps
  Return the standard deviation
stddev(InstanceList, SparseVector, boolean) - Static method in class cc.mallet.util.VectorStats
  Square root of variance.
stddev(InstanceList) - Static method in class cc.mallet.util.VectorStats
  Square root of unbiased variance.
stddev(InstanceList, boolean) - Static method in class cc.mallet.util.VectorStats
  Square root of variance.
stddev(InstanceList, SparseVector) - Static method in class cc.mallet.util.VectorStats
  Square root of unbiased variance of instances having the given mean
stderr(double[]) - Static method in class cc.mallet.types.MatrixOps
stdev() - Method in class cc.mallet.util.Univariate
StochasticMetaAscent - Class in cc.mallet.optimize
StochasticMetaAscent(Optimizable.ByBatchGradient) - Constructor for class cc.mallet.optimize.StochasticMetaAscent
stop(String) - Method in class cc.mallet.pipe.SimpleTokenizer
stopGrowth() - Method in class cc.mallet.classify.C45.Node
  Saves memory by allowing ilist to be garbage collected (deletes this node's associated instance list)
stopGrowth() - Method in class cc.mallet.classify.DecisionTree.Node
stopGrowth() - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
stopGrowth() - Method in class cc.mallet.types.Alphabet
stoplist - Variable in class cc.mallet.pipe.SimpleTokenizer
stoppingThreshold - Variable in class cc.mallet.cluster.GreedyAgglomerative
  Converged when merge score is below this value.
string2ints(String[], Alphabet) - Static method in class cc.mallet.cluster.tui.Clusterings2Clusterer
StringAddNewLineDelimiter - Class in cc.mallet.pipe
  Pipe that can adds special text between lines to explicitly represent line breaks.
StringAddNewLineDelimiter(String) - Constructor for class cc.mallet.pipe.StringAddNewLineDelimiter
stringArray2FileArray(String[]) - Static method in class cc.mallet.pipe.iterator.FileIterator
stringArray2FileArray(String[]) - Static method in class cc.mallet.pipe.iterator.UnlabeledFileIterator
StringArrayIterator - Class in cc.mallet.pipe.iterator
StringArrayIterator(String[]) - Constructor for class cc.mallet.pipe.iterator.StringArrayIterator
StringEditFeatureVectorSequence - Class in cc.mallet.types
StringEditFeatureVectorSequence(FeatureVector[], String, String) - Constructor for class cc.mallet.types.StringEditFeatureVectorSequence
StringEditFeatureVectorSequence(FeatureVector[], String, String, char) - Constructor for class cc.mallet.types.StringEditFeatureVectorSequence
StringEditFeatureVectorSequence(FeatureVector[], String, String, HashMap) - Constructor for class cc.mallet.types.StringEditFeatureVectorSequence
StringEditFeatureVectorSequence(FeatureVector[], String, String, char, HashMap) - Constructor for class cc.mallet.types.StringEditFeatureVectorSequence
StringEditVector - Class in cc.mallet.types
StringEditVector(String) - Constructor for class cc.mallet.types.StringEditVector
StringEditVector() - Constructor for class cc.mallet.types.StringEditVector
StringKernel - Class in cc.mallet.types
  Computes a similarity metric between two strings, based on counts of common subsequences of characters.
StringKernel(boolean, double, int, boolean) - Constructor for class cc.mallet.types.StringKernel
StringKernel() - Constructor for class cc.mallet.types.StringKernel
StringKernel(boolean, double, int) - Constructor for class cc.mallet.types.StringKernel
StringList2FeatureSequence - Class in cc.mallet.pipe
  Convert a list of strings into a feature sequence
StringList2FeatureSequence(Alphabet) - Constructor for class cc.mallet.pipe.StringList2FeatureSequence
StringList2FeatureSequence() - Constructor for class cc.mallet.pipe.StringList2FeatureSequence
Strings - Class in cc.mallet.util
  Static utility methods for Strings
Strings() - Constructor for class cc.mallet.util.Strings
StringSpan - Class in cc.mallet.extract
  A sub-section of a linear string.
StringSpan(CharSequence, int, int) - Constructor for class cc.mallet.extract.StringSpan
StringTokenization - Class in cc.mallet.extract
StringTokenization(CharSequence) - Constructor for class cc.mallet.extract.StringTokenization
  Create an empty StringTokenization
StringTokenization(CharSequence, CharSequenceLexer) - Constructor for class cc.mallet.extract.StringTokenization
  Creates a tokenization of the given string.
structureMatches(CRF.Factors) - Method in class cc.mallet.fst.CRF.Factors
SUB_TOPIC - Static variable in class cc.mallet.topics.HierarchicalPAM
subAssn(int, int) - Method in class cc.mallet.grmm.types.Assignment
subList(int, int) - Method in class cc.mallet.types.InstanceList
subList(double) - Method in class cc.mallet.types.InstanceList
subList(double) - Method in class cc.mallet.types.MultiInstanceList
subList(int, int) - Method in class cc.mallet.types.MultiInstanceList
subset(Collection, int, Random) - Static method in class cc.mallet.util.CollectionUtils
subset(int[]) - Method in class cc.mallet.util.Univariate
subspan(int, int) - Method in class cc.mallet.extract.DocumentExtraction
subspan(int, int) - Method in class cc.mallet.extract.StringTokenization
subspan(int, int) - Method in interface cc.mallet.extract.Tokenization
  Returns a span formed by concatenating the spans from start to end.
substitute(double, double) - Method in class cc.mallet.types.DenseMatrix
substitute(double[], double, double) - Static method in class cc.mallet.types.MatrixOps
subtractLogProb(double, double) - Static method in class cc.mallet.util.Maths
  Returns the difference of two doubles expressed in log space, that is,
suite() - Static method in class cc.mallet.classify.tests.TestClassifiers
suite() - Static method in class cc.mallet.classify.tests.TestMaxEntTrainer
suite() - Static method in class cc.mallet.classify.tests.TestStaticParameters
suite() - Static method in class cc.mallet.cluster.evaluate.tests.TestClusteringEvaluators
suite() - Static method in class cc.mallet.cluster.iterator.tests.TestIterators
suite() - Static method in class cc.mallet.extract.test.TestDocumentExtraction
suite() - Static method in class cc.mallet.extract.test.TestDocumentViewer
suite() - Static method in class cc.mallet.extract.test.TestLatticeViewer
suite() - Static method in class cc.mallet.extract.test.TestPerDocumentF1Evaluator
suite() - Static method in class cc.mallet.fst.tests.TestCRF
suite() - Static method in class cc.mallet.fst.tests.TestFeatureTransducer
suite() - Static method in class cc.mallet.fst.tests.TestMEMM
suite() - Static method in class cc.mallet.fst.tests.TestSumNegLogProb2
suite() - Static method in class cc.mallet.grmm.test.TestAbstractBeliefPropagation
suite() - Static method in class cc.mallet.grmm.test.TestAssignment
suite() - Static method in class cc.mallet.grmm.test.TestAssignmentIterator
suite() - Static method in class cc.mallet.grmm.test.TestBetaFactor
suite() - Static method in class cc.mallet.grmm.test.TestBitVarSet
suite() - Static method in class cc.mallet.grmm.test.TestDirectedModel
suite() - Static method in class cc.mallet.grmm.test.TestFactorGraph
suite() - Static method in class cc.mallet.grmm.test.TestFactors
suite() - Static method in class cc.mallet.grmm.test.TestGenericAcrfData2TokenSequence
suite() - Static method in class cc.mallet.grmm.test.TestGibbsSampler
suite() - Static method in class cc.mallet.grmm.test.TestHashClique
suite() - Static method in class cc.mallet.grmm.test.TestInference
suite() - Static method in class cc.mallet.grmm.test.TestListVarSet
suite() - Static method in class cc.mallet.grmm.test.TestLogTableFactor
suite() - Static method in class cc.mallet.grmm.test.TestMIntInt2ObjectMap
suite() - Static method in class cc.mallet.grmm.test.TestNormalFactor
suite() - Static method in class cc.mallet.grmm.test.TestPottsFactor
suite() - Static method in class cc.mallet.grmm.test.TestRandomGraphs
suite() - Static method in class cc.mallet.grmm.test.TestTableFactor
suite() - Static method in class cc.mallet.grmm.test.TestTRP
suite() - Static method in class cc.mallet.grmm.test.TestUndirectedModel
suite() - Static method in class cc.mallet.grmm.test.TestUniformFactor
suite() - Static method in class cc.mallet.grmm.test.TestUniNormalFactor
suite() - Static method in class cc.mallet.optimize.tests.TestOptimizable
suite() - Static method in class cc.mallet.optimize.tests.TestOptimizer
suite() - Static method in class cc.mallet.pipe.iterator.tests.TestPatternMatchIterator
suite() - Static method in class cc.mallet.pipe.tests.TestInstancePipe
suite() - Static method in class cc.mallet.pipe.tests.TestIterators
suite() - Static method in class cc.mallet.pipe.tests.TestPipeUtils
suite() - Static method in class cc.mallet.pipe.tests.TestRainbowStyle
suite() - Static method in class cc.mallet.pipe.tests.TestSGML2TokenSequence
suite() - Static method in class cc.mallet.pipe.tests.TestSpacePipe
suite() - Static method in class cc.mallet.pipe.tsf.tests.TestOffsetConjunctions
suite() - Static method in class cc.mallet.pipe.tsf.tests.TestOffsetFeatureConjunctions
suite() - Static method in class cc.mallet.pipe.tsf.tests.TestSequencePrintingPipe
suite() - Static method in class cc.mallet.types.tests.TestAlphabet
suite() - Static method in class cc.mallet.types.tests.TestAugmentableFeatureVector
suite() - Static method in class cc.mallet.types.tests.TestFeatureSequence
suite() - Static method in class cc.mallet.types.tests.TestFeatureVector
suite() - Static method in class cc.mallet.types.tests.TestHashedSparseVector
suite() - Static method in class cc.mallet.types.tests.TestIndexedSparseVector
suite() - Static method in class cc.mallet.types.tests.TestLabelAlphabet
suite() - Static method in class cc.mallet.types.tests.TestLabelsSequence
suite() - Static method in class cc.mallet.types.tests.TestLabelVector
suite() - Static method in class cc.mallet.types.tests.TestMatrix
suite() - Static method in class cc.mallet.types.tests.TestMatrixn
suite() - Static method in class cc.mallet.types.tests.TestMultinomial
suite() - Static method in class cc.mallet.types.tests.TestPagedInstanceList
suite() - Static method in class cc.mallet.types.tests.TestRankedFeatureVector
suite() - Static method in class cc.mallet.types.tests.TestSerializable
suite() - Static method in class cc.mallet.types.tests.TestSparseMatrixn
suite() - Static method in class cc.mallet.types.tests.TestSparseVector
suite() - Static method in class cc.mallet.types.tests.TestToken
suite() - Static method in class cc.mallet.util.tests.TestAStar
suite() - Static method in class cc.mallet.util.tests.TestMaths
suite() - Static method in class cc.mallet.util.tests.TestPriorityQueue
suite() - Static method in class cc.mallet.util.tests.TestPropertyList
suite() - Static method in class cc.mallet.util.tests.TestRandom
suite() - Static method in class cc.mallet.util.tests.TestStrings
sum() - Method in class cc.mallet.grmm.types.AbstractFactor
sum() - Method in class cc.mallet.grmm.types.AbstractTableFactor
sum() - Method in class cc.mallet.grmm.types.CPT
sum() - Method in interface cc.mallet.grmm.types.Factor
  Returns the sum of this potential over all cases.
sum() - Method in class cc.mallet.grmm.types.FactorGraph
sum() - Method in class cc.mallet.grmm.types.LogTableFactor
sum() - Method in class cc.mallet.grmm.types.TableFactor
sum(double[]) - Static method in class cc.mallet.types.DenseVector
sum(double[]) - Static method in class cc.mallet.types.MatrixOps
sum(double[][]) - Static method in class cc.mallet.types.MatrixOps
sum(int[]) - Static method in class cc.mallet.types.MatrixOps
sum(Vector) - Static method in class cc.mallet.types.MatrixOps
sumDuplicateKeyValues(PropertyList) - Static method in class cc.mallet.util.PropertyList
sumDuplicateKeyValues(PropertyList, boolean) - Static method in class cc.mallet.util.PropertyList
sumGradLog(Factor, Variable, Assignment) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
sumGradLog(Factor, Variable, Assignment) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
sumGradLog(Factor, Variable, Assignment) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
sumGradLog(Factor, Variable, Assignment) - Method in interface cc.mallet.grmm.types.ParameterizedFactor
  Computes the expected derivative of the log factor value.
sumGradLog(Factor, Variable, Assignment) - Method in class cc.mallet.grmm.types.PottsTableFactor
SumLattice - Interface in cc.mallet.fst
  Interface to perform forward-backward during training of a transducer.
SumLatticeBeam - Class in cc.mallet.fst
SumLatticeBeam(Transducer, Sequence, Sequence, Transducer.Incrementor) - Constructor for class cc.mallet.fst.SumLatticeBeam
SumLatticeBeam(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean) - Constructor for class cc.mallet.fst.SumLatticeBeam
SumLatticeBeam(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean, LabelAlphabet) - Constructor for class cc.mallet.fst.SumLatticeBeam
SumLatticeBeam(Transducer, Sequence, Sequence, Transducer.Incrementor, LabelAlphabet, int[]) - Constructor for class cc.mallet.fst.SumLatticeBeam
  Create a lattice that constrains its transitions such that the pairs in "constraints" are adhered to.
SumLatticeBeam.Factory - Class in cc.mallet.fst
SumLatticeBeam.Factory(int) - Constructor for class cc.mallet.fst.SumLatticeBeam.Factory
SumLatticeConstrained - Class in cc.mallet.fst
SumLatticeConstrained(Transducer, Sequence, Sequence, Segment, Sequence) - Constructor for class cc.mallet.fst.SumLatticeConstrained
SumLatticeConstrained(Transducer, Sequence, Sequence, Transducer.Incrementor, LabelAlphabet, int[]) - Constructor for class cc.mallet.fst.SumLatticeConstrained
  Create a lattice that constrains its transitions such that the pairs in "constraints" are adhered to.
SumLatticeDefault - Class in cc.mallet.fst
  Default, full dynamic programming implementation of the Forward-Backward "Sum-(Product)-Lattice" algorithm
SumLatticeDefault() - Constructor for class cc.mallet.fst.SumLatticeDefault
SumLatticeDefault(Transducer, Sequence) - Constructor for class cc.mallet.fst.SumLatticeDefault
SumLatticeDefault(Transducer, Sequence, boolean) - Constructor for class cc.mallet.fst.SumLatticeDefault
SumLatticeDefault(Transducer, Sequence, Transducer.Incrementor) - Constructor for class cc.mallet.fst.SumLatticeDefault
SumLatticeDefault(Transducer, Sequence, Sequence) - Constructor for class cc.mallet.fst.SumLatticeDefault
SumLatticeDefault(Transducer, Sequence, Sequence, Transducer.Incrementor) - Constructor for class cc.mallet.fst.SumLatticeDefault
SumLatticeDefault(Transducer, Sequence, Sequence, Transducer.Incrementor, LabelAlphabet) - Constructor for class cc.mallet.fst.SumLatticeDefault
SumLatticeDefault(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean) - Constructor for class cc.mallet.fst.SumLatticeDefault
SumLatticeDefault(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean, LabelAlphabet) - Constructor for class cc.mallet.fst.SumLatticeDefault
SumLatticeDefault.Factory - Class in cc.mallet.fst
SumLatticeDefault.Factory() - Constructor for class cc.mallet.fst.SumLatticeDefault.Factory
SumLatticeDefault.LatticeNode - Class in cc.mallet.fst
sumLatticeExecutor - Variable in class cc.mallet.fst.semi_supervised.CRFOptimizableByGECriteria
SumLatticeFactory - Class in cc.mallet.fst
  Provides factory methods to create inference engine for training a transducer.
SumLatticeFactory() - Constructor for class cc.mallet.fst.SumLatticeFactory
SumLatticeScaling - Class in cc.mallet.fst
SumLatticeScaling() - Constructor for class cc.mallet.fst.SumLatticeScaling
SumLatticeScaling(Transducer, Sequence) - Constructor for class cc.mallet.fst.SumLatticeScaling
SumLatticeScaling(Transducer, Sequence, boolean) - Constructor for class cc.mallet.fst.SumLatticeScaling
SumLatticeScaling(Transducer, Sequence, Transducer.Incrementor) - Constructor for class cc.mallet.fst.SumLatticeScaling
SumLatticeScaling(Transducer, Sequence, Sequence) - Constructor for class cc.mallet.fst.SumLatticeScaling
SumLatticeScaling(Transducer, Sequence, Sequence, Transducer.Incrementor) - Constructor for class cc.mallet.fst.SumLatticeScaling
SumLatticeScaling(Transducer, Sequence, Sequence, Transducer.Incrementor, LabelAlphabet) - Constructor for class cc.mallet.fst.SumLatticeScaling
SumLatticeScaling(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean) - Constructor for class cc.mallet.fst.SumLatticeScaling
SumLatticeScaling(Transducer, Sequence, Sequence, Transducer.Incrementor, boolean, LabelAlphabet) - Constructor for class cc.mallet.fst.SumLatticeScaling
SumLatticeScaling.Factory - Class in cc.mallet.fst
SumLatticeScaling.Factory() - Constructor for class cc.mallet.fst.SumLatticeScaling.Factory
SumLatticeScaling.LatticeNode - Class in cc.mallet.fst
sumLogProb(double, double) - Static method in class cc.mallet.fst.Transducer
  Returns `Math.log(Math.exp(a) + Math.exp(b))`.
sumLogProb(int) - Static method in class cc.mallet.grmm.util.Flops
sumLogProb(double, double) - Static method in class cc.mallet.util.Maths
  Returns the sum of two doubles expressed in log space, that is,
sumLogProb(double[]) - Static method in class cc.mallet.util.Maths
  Sums an array of numbers log(x1)...log(xn).
summary() - Method in class cc.mallet.util.Univariate
sumTypeTopicCounts(WorkerRunnable[]) - Method in class cc.mallet.topics.ParallelTopicModel
SUPER_TOPIC - Static variable in class cc.mallet.topics.HierarchicalPAM
SvmLight2Classify - Class in cc.mallet.classify.tui
  Command line tool for classifying a sequence of instances directly from text input, without creating an instance list.
SvmLight2Classify() - Constructor for class cc.mallet.classify.tui.SvmLight2Classify
SvmLight2FeatureVectorAndLabel - Class in cc.mallet.pipe
  This Pipe converts a line in SVMLight format to a Mallet instance with FeatureVector data and Label target.
SvmLight2FeatureVectorAndLabel() - Constructor for class cc.mallet.pipe.SvmLight2FeatureVectorAndLabel
SvmLight2Vectors - Class in cc.mallet.classify.tui
  Command line import tool for loading a sequence of instances from an SVMLight feature-value pair file, with one instance per line of the input file.
SvmLight2Vectors() - Constructor for class cc.mallet.classify.tui.SvmLight2Vectors

## T

t - Variable in class cc.mallet.fst.CRFTrainerByStochasticGradient
TableFactor - Class in cc.mallet.grmm.types
  Created: Jan 4, 2006
TableFactor(Variable) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(Variable, double[]) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor() - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(BidirectionalIntObjectMap) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(Variable[]) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(Collection) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(Variable[], double[]) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(VarSet, double[]) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(Variable[], Matrix) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(AbstractTableFactor) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(VarSet, Matrix) - Constructor for class cc.mallet.grmm.types.TableFactor
TableFactor(AbstractTableFactor, double[]) - Constructor for class cc.mallet.grmm.types.TableFactor
tanh(double) - Static method in class cc.mallet.util.Maths
target - Variable in class cc.mallet.fst.semi_supervised.GECriterion
target - Variable in class cc.mallet.types.Instance
Target2BIOFormat - Class in cc.mallet.pipe.tsf
  Creates a `LabelSequence` out of a `TokenSequence` that is the target of an `Instance`.
Target2BIOFormat() - Constructor for class cc.mallet.pipe.tsf.Target2BIOFormat
Target2BIOFormat(String) - Constructor for class cc.mallet.pipe.tsf.Target2BIOFormat
Target2FeatureSequence - Class in cc.mallet.pipe
  Convert a token sequence in the target field into a feature sequence in the target field.
Target2FeatureSequence() - Constructor for class cc.mallet.pipe.Target2FeatureSequence
Target2Label - Class in cc.mallet.pipe
  Convert object in the target field into a label in the target field.
Target2Label(Alphabet, LabelAlphabet) - Constructor for class cc.mallet.pipe.Target2Label
Target2Label() - Constructor for class cc.mallet.pipe.Target2Label
Target2Label(LabelAlphabet) - Constructor for class cc.mallet.pipe.Target2Label
Target2LabelSequence - Class in cc.mallet.pipe
  convert a token sequence in the target field into a label sequence in the target field.
Target2LabelSequence() - Constructor for class cc.mallet.pipe.Target2LabelSequence
TARGET_PROPERTY - Static variable in class cc.mallet.types.InstanceList
targetLabelDistribution() - Method in class cc.mallet.types.InstanceList
TargetRememberLastLabel - Class in cc.mallet.pipe
  For each position in the target, remember the last non-background label.
TargetRememberLastLabel() - Constructor for class cc.mallet.pipe.TargetRememberLastLabel
TargetRememberLastLabel(String, boolean) - Constructor for class cc.mallet.pipe.TargetRememberLastLabel
  offset determines how the memory and base sequences will be aligned.
targets - Static variable in class cc.mallet.classify.tui.Vectors2FeatureConstraints
TargetStringToFeatures - Class in cc.mallet.pipe
TargetStringToFeatures() - Constructor for class cc.mallet.pipe.TargetStringToFeatures
temperAlpha(WorkerRunnable[]) - Method in class cc.mallet.topics.ParallelTopicModel
temperingInterval - Variable in class cc.mallet.topics.ParallelTopicModel
test(TransducerTrainer, TransducerEvaluator, InstanceList) - Static method in class cc.mallet.fst.SimpleTagger
  Test a transducer on the given test data, evaluating accuracy with the given evaluator
test(InstanceList, List, String) - Method in class cc.mallet.grmm.learning.ACRFEvaluator
test(ACRF, InstanceList, String) - Method in class cc.mallet.grmm.learning.ACRFEvaluator
test(InstanceList, List, String) - Method in class cc.mallet.grmm.learning.AcrfSerialEvaluator
test(InstanceList, List, String) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.FileEvaluator
test(InstanceList, List, String) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer.LogEvaluator
test(ACRF, InstanceList, ACRFEvaluator) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
test(ACRF, InstanceList, ACRFEvaluator[]) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
test(InstanceList, List, String) - Method in class cc.mallet.grmm.learning.MultiSegmentationEvaluatorACRF
test(Classifier, String[][], String[]) - Static method in class cc.mallet.share.upenn.MaxEntShell
  Test a maxent classifier.
test(Classifier, Iterator<Instance>) - Static method in class cc.mallet.share.upenn.MaxEntShell
  Test a maxent classifier.
test - Variable in class cc.mallet.topics.LDAStream
TestAbstractBeliefPropagation - Class in cc.mallet.grmm.test
  $Id: TestAbstractBeliefPropagation.java,v 1.1 2007/10/22 21:37:40 mccallum Exp $
TestAbstractBeliefPropagation(String) - Constructor for class cc.mallet.grmm.test.TestAbstractBeliefPropagation
testAddAllOrdering() - Method in class cc.mallet.grmm.test.TestBitVarSet
testAddAllOrdering() - Method in class cc.mallet.grmm.test.TestHashClique
testAddAllOrdering() - Method in class cc.mallet.grmm.test.TestListVarSet
testAddAllOrdering2() - Method in class cc.mallet.grmm.test.TestBitVarSet
testAddAllOrdering2() - Method in class cc.mallet.grmm.test.TestHashClique
testAddAllOrdering2() - Method in class cc.mallet.grmm.test.TestListVarSet
testAddAllOrdering3() - Method in class cc.mallet.grmm.test.TestBitVarSet
testAddAllOrdering3() - Method in class cc.mallet.grmm.test.TestHashClique
testAddAllOrdering3() - Method in class cc.mallet.grmm.test.TestListVarSet
testAddOrderNStates() - Method in class cc.mallet.fst.tests.TestCRF
testAddRowMixed() - Method in class cc.mallet.grmm.test.TestAssignment
testAddWithPrefix() - Method in class cc.mallet.types.tests.TestAugmentableFeatureVector
testAllFactorsOf() - Method in class cc.mallet.grmm.test.TestFactorGraph
testAllFactorsOf2() - Method in class cc.mallet.grmm.test.TestFactorGraph
TestAlphabet - Class in cc.mallet.types.tests
  Created: Nov 24, 2004
TestAlphabet(String) - Constructor for class cc.mallet.types.tests.TestAlphabet
testAscending() - Method in class cc.mallet.util.tests.TestPriorityQueue
testAsJava() - Static method in class cc.mallet.util.tests.TestRandom
TestAssignment - Class in cc.mallet.grmm.test
  Created: Aug 11, 2004
TestAssignment(String) - Constructor for class cc.mallet.grmm.test.TestAssignment
  Constructs a test case with the given name.
TestAssignmentIterator - Class in cc.mallet.grmm.test
  Created: Aug 11, 2004
TestAssignmentIterator(String) - Constructor for class cc.mallet.grmm.test.TestAssignmentIterator
  Constructs a test case with the given name.
testAsTable() - Method in class cc.mallet.grmm.test.TestAssignment
testAsTable() - Method in class cc.mallet.grmm.test.TestFactorGraph
testAsTable2() - Method in class cc.mallet.grmm.test.TestFactorGraph
TestAStar - Class in cc.mallet.util.tests
  Created by IntelliJ IDEA.
TestAStar(String) - Constructor for class cc.mallet.util.tests.TestAStar
testAttractiveGraphs() - Method in class cc.mallet.grmm.test.TestRandomGraphs
TestAugmentableFeatureVector - Class in cc.mallet.types.tests
  Created: Dec 30, 2004
TestAugmentableFeatureVector(String) - Constructor for class cc.mallet.types.tests.TestAugmentableFeatureVector
testBadVariable() - Method in class cc.mallet.grmm.test.TestAbstractBeliefPropagation
testBeliefPropagation() - Method in class cc.mallet.grmm.test.TestInference
TestBetaFactor - Class in cc.mallet.grmm.test
  $Id: TestBetaFactor.java,v 1.1 2007/10/22 21:37:41 mccallum Exp $
TestBetaFactor(String) - Constructor for class cc.mallet.grmm.test.TestBetaFactor
testBinaryVector() - Method in class cc.mallet.types.tests.TestHashedSparseVector
testBinaryVector() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testBinaryVector() - Method in class cc.mallet.types.tests.TestSparseVector
TestBitVarSet - Class in cc.mallet.grmm.test
  Created: Aug 22, 2005
TestBitVarSet(String) - Constructor for class cc.mallet.grmm.test.TestBitVarSet
testBpJoint() - Method in class cc.mallet.grmm.test.TestInference
testBpLargeModels() - Method in class cc.mallet.grmm.test.TestInference
testCacheExpanding() - Method in class cc.mallet.grmm.test.TestFactorGraph
testChangePriority() - Method in class cc.mallet.util.tests.TestPriorityQueue
testCholesky() - Static method in class cc.mallet.util.MVNormal
TestClassifiers - Class in cc.mallet.classify.tests
TestClassifiers(String) - Constructor for class cc.mallet.classify.tests.TestClassifiers
testClear() - Method in class cc.mallet.grmm.test.TestFactorGraph
testCloneMatrixZeroed() - Method in class cc.mallet.types.tests.TestHashedSparseVector
testCloneMatrixZeroed() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testCloneMatrixZeroed() - Method in class cc.mallet.types.tests.TestSparseVector
TestClusteringEvaluators - Class in cc.mallet.cluster.evaluate.tests
  Examples drawn from Luo, "On Coreference Resolution Performance Metrics", HLT 2005.
TestClusteringEvaluators(String) - Constructor for class cc.mallet.cluster.evaluate.tests.TestClusteringEvaluators
testConcatenateBadPipes() - Method in class cc.mallet.pipe.tests.TestPipeUtils
testConcatenateNullPipes() - Method in class cc.mallet.pipe.tests.TestPipeUtils
testConcatenatePipes() - Method in class cc.mallet.pipe.tests.TestPipeUtils
testConjugateGradient() - Method in class cc.mallet.optimize.tests.TestOptimizer
testContains() - Method in class cc.mallet.grmm.test.TestListVarSet
testContinousSample() - Method in class cc.mallet.grmm.test.TestFactorGraph
testContinousSample2() - Method in class cc.mallet.grmm.test.TestFactorGraph
testCopyStatesAndWeights() - Method in class cc.mallet.fst.tests.TestCRF
testCorr() - Method in class cc.mallet.grmm.test.TestFactors
testCost() - Method in class cc.mallet.fst.tests.TestCRF
testCostSerialized() - Method in class cc.mallet.fst.tests.TestCRF
testCount() - Static method in class cc.mallet.util.tests.TestStrings
testCptOfVar() - Method in class cc.mallet.grmm.test.TestDirectedModel
TestCRF - Class in cc.mallet.fst.tests
  Tests for CRF training.
TestCRF(String) - Constructor for class cc.mallet.fst.tests.TestCRF
TestCRF.TestCRF2String - Class in cc.mallet.fst.tests
TestCRF.TestCRF2String() - Constructor for class cc.mallet.fst.tests.TestCRF.TestCRF2String
TestCRF.TestCRFTokenSequenceRemoveSpaces - Class in cc.mallet.fst.tests
TestCRF.TestCRFTokenSequenceRemoveSpaces() - Constructor for class cc.mallet.fst.tests.TestCRF.TestCRFTokenSequenceRemoveSpaces
TestCRFPipe - Class in cc.mallet.examples
TestCRFPipe(String) - Constructor for class cc.mallet.examples.TestCRFPipe
testCycleChecking() - Method in class cc.mallet.grmm.test.TestDirectedModel
testDefaultLookupMarginal() - Method in class cc.mallet.grmm.test.TestInference
testDenseFeatureSelection() - Method in class cc.mallet.fst.tests.TestCRF
testDenseSerialization() - Method in class cc.mallet.fst.tests.TestCRF
testDenseSparseVector() - Method in class cc.mallet.types.tests.TestSparseVector
testDenseTrain() - Method in class cc.mallet.fst.tests.TestCRF
testDescending() - Method in class cc.mallet.util.tests.TestPriorityQueue
testDestructiveAssignment() - Method in class cc.mallet.grmm.test.TestInference
testDirectedJt() - Method in class cc.mallet.grmm.test.TestInference
TestDirectedModel - Class in cc.mallet.grmm.test
  Created: Mar 28, 2005
TestDirectedModel(String) - Constructor for class cc.mallet.grmm.test.TestDirectedModel
testDisconnectedModel() - Method in class cc.mallet.grmm.test.TestInference
testDivideByLogSpace() - Method in class cc.mallet.grmm.test.TestLogTableFactor
TestDocumentExtraction - Class in cc.mallet.extract.test
  Created: Oct 12, 2004
TestDocumentExtraction(String) - Constructor for class cc.mallet.extract.test.TestDocumentExtraction
TestDocumentViewer - Class in cc.mallet.extract.test
  Created: Mar 30, 2005
TestDocumentViewer(String) - Constructor for class cc.mallet.extract.test.TestDocumentViewer
testDotProduct() - Method in class cc.mallet.types.tests.TestHashedSparseVector
testDotProduct() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testDotProduct() - Method in class cc.mallet.types.tests.TestSparseVector
testDotProductBinaryToSV() - Method in class cc.mallet.types.tests.TestAugmentableFeatureVector
testDotProductSparseASVToSV() - Method in class cc.mallet.types.tests.TestAugmentableFeatureVector
testDualSpaceViewer() - Method in class cc.mallet.extract.test.TestLatticeViewer
testDuplicateValueFromFeatureSequence() - Method in class cc.mallet.types.tests.TestFeatureVector
testEarlyStopping() - Method in class cc.mallet.grmm.test.TestTRP
testEmbeddedFactorGraph() - Method in class cc.mallet.grmm.test.TestFactorGraph
testEmptyLocations() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testEmptyStringBug() - Method in class cc.mallet.classify.tests.TestNaiveBayes
testEntropy() - Method in class cc.mallet.grmm.test.TestTableFactor
testEntropyLogSpace() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testEqualKeys() - Method in class cc.mallet.util.tests.TestPriorityQueue
testEquals() - Method in class cc.mallet.grmm.test.TestListVarSet
testEqualsHashCode() - Method in class cc.mallet.grmm.test.TestBitVarSet
testEqualsHashCode() - Method in class cc.mallet.grmm.test.TestHashClique
testEqualsHashCode() - Method in class cc.mallet.grmm.test.TestListVarSet
testEstimate() - Method in class cc.mallet.fst.tests.TestFeatureTransducer
testEstimating() - Method in class cc.mallet.types.tests.TestMultinomial
testEvaluators() - Method in class cc.mallet.cluster.evaluate.tests.TestClusteringEvaluators
testEvaluators() - Method in class cc.mallet.cluster.iterator.tests.TestIterators
testExp() - Method in class cc.mallet.grmm.test.TestTableFactor
testExpandToContain() - Method in class cc.mallet.grmm.test.TestTableFactor
testExtendedDotProduct() - Method in class cc.mallet.types.tests.TestSparseVector
testExtractMaxLogSpace() - Method in class cc.mallet.grmm.test.TestLogTableFactor
TestFactorGraph - Class in cc.mallet.grmm.test
  Created: Mar 17, 2005
TestFactorGraph(String) - Constructor for class cc.mallet.grmm.test.TestFactorGraph
testFactorizedJoint() - Method in class cc.mallet.grmm.test.TestInference
testFactorOfSet() - Method in class cc.mallet.grmm.test.TestUndirectedModel
testFactorReplace() - Method in class cc.mallet.grmm.test.TestDirectedModel
TestFactors - Class in cc.mallet.grmm.test
  Created: Mar 28, 2005
TestFactors(String) - Constructor for class cc.mallet.grmm.test.TestFactors
TestFeatureSequence - Class in cc.mallet.types.tests
TestFeatureSequence(String) - Constructor for class cc.mallet.types.tests.TestFeatureSequence
TestFeatureTransducer - Class in cc.mallet.fst.tests
TestFeatureTransducer(String) - Constructor for class cc.mallet.fst.tests.TestFeatureTransducer
TestFeatureVector - Class in cc.mallet.types.tests
TestFeatureVector(String) - Constructor for class cc.mallet.types.tests.TestFeatureVector
testFieldCleaning() - Method in class cc.mallet.extract.test.TestPerDocumentF1Evaluator
testFindVariable() - Method in class cc.mallet.grmm.test.TestInference
testFixedNumLabels() - Method in class cc.mallet.grmm.test.TestGenericAcrfData2TokenSequence
testForwardBackward() - Method in class cc.mallet.fst.tests.TestFeatureTransducer
testFromSerialization() - Method in class cc.mallet.grmm.test.TestGenericAcrfData2TokenSequence
testFrozenWeights() - Method in class cc.mallet.fst.tests.TestCRF
testFrustratedGraphs() - Method in class cc.mallet.grmm.test.TestRandomGraphs
testFrustratedIsGrid() - Method in class cc.mallet.grmm.test.TestRandomGraphs
TestGenericAcrfData2TokenSequence - Class in cc.mallet.grmm.test
  Created: Sep 15, 2005
TestGenericAcrfData2TokenSequence(String) - Constructor for class cc.mallet.grmm.test.TestGenericAcrfData2TokenSequence
testGetBestLabel() - Method in class cc.mallet.types.tests.TestLabelVector
testGetLabelAtRank() - Method in class cc.mallet.types.tests.TestLabelVector
testGetSetParameters() - Method in class cc.mallet.fst.tests.TestCRF
testGetSetParameters() - Method in class cc.mallet.fst.tests.TestMEMM
testGetSetParameters(Optimizable) - Static method in class cc.mallet.optimize.tests.TestOptimizable
  Tests that parameters set by setParameters can be retrieved by getParameters.
TestGibbsSampler - Class in cc.mallet.grmm.test
  $Id: TestGibbsSampler.java,v 1.1 2007/10/22 21:37:41 mccallum Exp $
TestGibbsSampler(String) - Constructor for class cc.mallet.grmm.test.TestGibbsSampler
testGradientAscent() - Method in class cc.mallet.optimize.tests.TestOptimizer
TestHashClique - Class in cc.mallet.grmm.test
  Created: Aug 22, 2005
TestHashClique(String) - Constructor for class cc.mallet.grmm.test.TestHashClique
testHashCodeByHashVarSet() - Method in class cc.mallet.grmm.test.TestListVarSet
TestHashedSparseVector - Class in cc.mallet.types.tests
TestHashedSparseVector(String) - Constructor for class cc.mallet.types.tests.TestHashedSparseVector
testIncrement() - Method in class cc.mallet.fst.tests.TestCRF
testIncrement() - Method in class cc.mallet.fst.tests.TestFeatureTransducer
testIncrement() - Method in class cc.mallet.fst.tests.TestMEMM
testIncrementallyTrained() - Method in class cc.mallet.classify.tests.TestNaiveBayes
testIncrementallyTrainedGrowingAlphabets() - Method in class cc.mallet.classify.tests.TestNaiveBayes
testIncrementValue() - Method in class cc.mallet.types.tests.TestHashedSparseVector
testIncrementValue() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testIncrementValue() - Method in class cc.mallet.types.tests.TestSparseVector
TestIndexedSparseVector - Class in cc.mallet.types.tests
TestIndexedSparseVector(String) - Constructor for class cc.mallet.types.tests.TestIndexedSparseVector
testIndexing1d() - Method in class cc.mallet.types.tests.TestMatrixn
testIndexing1d() - Method in class cc.mallet.types.tests.TestSparseMatrixn
testIndexing2d() - Method in class cc.mallet.types.tests.TestMatrixn
testIndexing2d() - Method in class cc.mallet.types.tests.TestSparseMatrixn
testIndexing3d() - Method in class cc.mallet.types.tests.TestMatrixn
testIndexing3d() - Method in class cc.mallet.types.tests.TestSparseMatrixn
TestInference - Class in cc.mallet.grmm.test
  Torture tests of inference in GRMM.
TestInference(String) - Constructor for class cc.mallet.grmm.test.TestInference
testInfiniteCost() - Method in class cc.mallet.grmm.test.TestInference
testing - Variable in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
testing - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
testInitialAssignment() - Method in class cc.mallet.grmm.test.TestGibbsSampler
testInitialState() - Method in class cc.mallet.fst.tests.TestFeatureTransducer
TestInstanceListWeights - Class in cc.mallet.types.tests
TestInstanceListWeights() - Constructor for class cc.mallet.types.tests.TestInstanceListWeights
TestInstancePipe - Class in cc.mallet.pipe.tests
TestInstancePipe(String) - Constructor for class cc.mallet.pipe.tests.TestInstancePipe
TestInstancePipe.Array2ArrayIterator - Class in cc.mallet.pipe.tests
TestInstancePipe.Array2ArrayIterator() - Constructor for class cc.mallet.pipe.tests.TestInstancePipe.Array2ArrayIterator
testIntersectionOrdering() - Method in class cc.mallet.grmm.test.TestListVarSet
testIntersectionOrderingToBit() - Method in class cc.mallet.grmm.test.TestListVarSet
testIntersectionOrderingToHash() - Method in class cc.mallet.grmm.test.TestListVarSet
TestIterators - Class in cc.mallet.cluster.iterator.tests
TestIterators(String) - Constructor for class cc.mallet.cluster.iterator.tests.TestIterators
TestIterators - Class in cc.mallet.pipe.tests
  Unit Test for PipeInputIterators Created: Thu Feb 26 14:27:15 2004
TestIterators(String) - Constructor for class cc.mallet.pipe.tests.TestIterators
testJointConsistent() - Method in class cc.mallet.grmm.test.TestInference
testJtCaching() - Method in class cc.mallet.grmm.test.TestInference
testJtConsistency() - Method in class cc.mallet.grmm.test.TestInference
testJtConstant() - Method in class cc.mallet.grmm.test.TestInference
testJtViterbi() - Method in class cc.mallet.grmm.test.TestInference
testJunctionTreeConnectedFromRoot() - Method in class cc.mallet.grmm.test.TestInference
TestLabelAlphabet - Class in cc.mallet.types.tests
  Created: Nov 24, 2004
TestLabelAlphabet(String) - Constructor for class cc.mallet.types.tests.TestLabelAlphabet
testLabelsAtEnd() - Method in class cc.mallet.grmm.test.TestGenericAcrfData2TokenSequence
TestLabelsSequence - Class in cc.mallet.types.tests
  Created: Sep 21, 2004
TestLabelsSequence(String) - Constructor for class cc.mallet.types.tests.TestLabelsSequence
TestLabelVector - Class in cc.mallet.types.tests
TestLabelVector(String) - Constructor for class cc.mallet.types.tests.TestLabelVector
TestLatticeViewer - Class in cc.mallet.extract.test
  Created: Oct 31, 2004
TestLatticeViewer(String) - Constructor for class cc.mallet.extract.test.TestLatticeViewer
testLazyAssignment() - Method in class cc.mallet.grmm.test.TestAssignmentIterator
testLinearLBFGS() - Method in class cc.mallet.optimize.tests.TestOptimizer
TestListVarSet - Class in cc.mallet.grmm.test
  Created: Aug 22, 2005
TestListVarSet(String) - Constructor for class cc.mallet.grmm.test.TestListVarSet
testLocation() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testLogBinom() - Method in class cc.mallet.util.tests.TestMaths
testLogErrorRange() - Method in class cc.mallet.grmm.test.TestFactors
testLogMarginalize() - Method in class cc.mallet.grmm.test.TestInference
testLogMultiVarSlice() - Method in class cc.mallet.grmm.test.TestTableFactor
testLogNormalize() - Method in class cc.mallet.grmm.test.TestFactorGraph
testLogNormalize() - Method in class cc.mallet.grmm.test.TestInference
testLogSample() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testLogSample() - Method in class cc.mallet.grmm.test.TestTableFactor
TestLogTableFactor - Class in cc.mallet.grmm.test
  Created: Aug 17, 2004
TestLogTableFactor(String) - Constructor for class cc.mallet.grmm.test.TestLogTableFactor
testLogTableTimesFg() - Method in class cc.mallet.grmm.test.TestFactorGraph
testLogValue() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testLoopyCaching() - Method in class cc.mallet.grmm.test.TestInference
testLoopyConvergence() - Method in class cc.mallet.grmm.test.TestInference
testMarginalize() - Method in class cc.mallet.grmm.test.TestAssignment
testMarginalize() - Method in class cc.mallet.grmm.test.TestFactorGraph
testMarginalize() - Method in class cc.mallet.grmm.test.TestTableFactor
testMarginalizeOut() - Method in class cc.mallet.grmm.test.TestAssignment
testMarginalizeOut() - Method in class cc.mallet.grmm.test.TestTableFactor
testMarginals() - Method in class cc.mallet.grmm.test.TestInference
TestMaths - Class in cc.mallet.util.tests
  Created: Oct 31, 2004
TestMaths(String) - Constructor for class cc.mallet.util.tests.TestMaths
TestMatrix - Class in cc.mallet.types.tests
TestMatrix(String) - Constructor for class cc.mallet.types.tests.TestMatrix
TestMatrixn - Class in cc.mallet.types.tests
  Created: Aug 30, 2004
TestMatrixn(String) - Constructor for class cc.mallet.types.tests.TestMatrixn
testMatrixnSerializable() - Method in class cc.mallet.types.tests.TestMatrixn
TestMaxEntTrainer - Class in cc.mallet.classify.tests
TestMaxEntTrainer(String) - Constructor for class cc.mallet.classify.tests.TestMaxEntTrainer
testMaxLattice() - Method in class cc.mallet.fst.tests.TestCRF
testMaxMarginals() - Method in class cc.mallet.grmm.test.TestInference
testMdlToGraph() - Method in class cc.mallet.grmm.test.TestUndirectedModel
TestMEMM - Class in cc.mallet.fst.tests
  Tests for MEMM training.
TestMEMM(String) - Constructor for class cc.mallet.fst.tests.TestMEMM
TestMEMM.TestMEMM2String - Class in cc.mallet.fst.tests
TestMEMM.TestMEMM2String() - Constructor for class cc.mallet.fst.tests.TestMEMM.TestMEMM2String
TestMEMM.TestMEMMTokenSequenceRemoveSpaces - Class in cc.mallet.fst.tests
TestMEMM.TestMEMMTokenSequenceRemoveSpaces() - Constructor for class cc.mallet.fst.tests.TestMEMM.TestMEMMTokenSequenceRemoveSpaces
TestMIntInt2ObjectMap - Class in cc.mallet.grmm.test
  Created: Dec 14, 2005
TestMIntInt2ObjectMap(String) - Constructor for class cc.mallet.grmm.test.TestMIntInt2ObjectMap
testMix() - Method in class cc.mallet.grmm.test.TestFactors
TestMultinomial - Class in cc.mallet.types.tests
TestMultinomial(String) - Constructor for class cc.mallet.types.tests.TestMultinomial
testMultinomial() - Method in class cc.mallet.types.tests.TestMultinomial
testMultipleEdgePotentials() - Method in class cc.mallet.grmm.test.TestUndirectedModel
  Tests that models can be created that have multiple factors over the same edge, and that potentialOfEdge returns the product in that case.
testMultipleNodePotentials() - Method in class cc.mallet.grmm.test.TestUndirectedModel
  Tests that models can be created that have multiple factors over the same variable, and that potentialOfVertex returns the product in that case.
testMultiply() - Method in class cc.mallet.grmm.test.TestFactorGraph
testMultiply() - Method in class cc.mallet.grmm.test.TestInference
testMultiplyAll() - Method in class cc.mallet.grmm.test.TestTableFactor
testMultiplyBy() - Method in class cc.mallet.grmm.test.TestFactorGraph
testMultiplyByLogSpace() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testMultiplyMultiplyBy() - Method in class cc.mallet.grmm.test.TestTableFactor
testMultiRow() - Method in class cc.mallet.grmm.test.TestAssignment
testMultiTag() - Static method in class cc.mallet.pipe.tsf.tests.TestOffsetFeatureConjunctions
testMultiTagSerialization() - Static method in class cc.mallet.pipe.tsf.tests.TestOffsetFeatureConjunctions
testMultiVarSlice() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testMultiVarSlice() - Method in class cc.mallet.grmm.test.TestTableFactor
testMutualInfo1() - Method in class cc.mallet.grmm.test.TestFactors
testMutualInfo2() - Method in class cc.mallet.grmm.test.TestFactors
TestNaiveBayes - Class in cc.mallet.classify.tests
TestNaiveBayes(String) - Constructor for class cc.mallet.classify.tests.TestNaiveBayes
testNestedToXML() - Method in class cc.mallet.extract.test.TestDocumentExtraction
testNestedXMLTokenizationFilter() - Method in class cc.mallet.extract.test.TestDocumentExtraction
testNewFeatures() - Method in class cc.mallet.classify.tests.TestClassifiers
testNewPutSizeFreeze() - Method in class cc.mallet.types.tests.TestFeatureSequence
testNonTrained() - Method in class cc.mallet.classify.tests.TestNaiveBayes
TestNormalFactor - Class in cc.mallet.grmm.test
  $Id: TestNormalFactor.java,v 1.1 2007/10/22 21:37:41 mccallum Exp $
TestNormalFactor(String) - Constructor for class cc.mallet.grmm.test.TestNormalFactor
testNormalize() - Method in class cc.mallet.grmm.test.TestFactorGraph
testNormalizeAsCpt() - Method in class cc.mallet.grmm.test.TestFactors
testNormalizeAsCptLogSpace() - Method in class cc.mallet.grmm.test.TestFactors
testNotFound() - Method in class cc.mallet.types.tests.TestAlphabet
testNoTokenText() - Method in class cc.mallet.grmm.test.TestGenericAcrfData2TokenSequence
testNumVariables() - Method in class cc.mallet.grmm.test.TestFactorGraph
TestOffsetConjunctions - Class in cc.mallet.pipe.tsf.tests
TestOffsetConjunctions(String) - Constructor for class cc.mallet.pipe.tsf.tests.TestOffsetConjunctions
TestOffsetFeatureConjunctions - Class in cc.mallet.pipe.tsf.tests
  $Id: TestOffsetFeatureConjunctions.java,v 1.1 2007/10/22 21:37:57 mccallum Exp $
TestOffsetFeatureConjunctions(String) - Constructor for class cc.mallet.pipe.tsf.tests.TestOffsetFeatureConjunctions
testOne() - Method in class cc.mallet.pipe.iterator.tests.TestPatternMatchIterator
testOne() - Method in class cc.mallet.pipe.tests.TestInstancePipe
testOne() - Method in class cc.mallet.pipe.tests.TestSGML2TokenSequence
testOne() - Method in class cc.mallet.pipe.tsf.tests.TestOffsetConjunctions
testOne() - Method in class cc.mallet.types.tests.TestToken
testOne() - Method in class cc.mallet.util.tests.TestPropertyList
testOneFromSerialized() - Method in class cc.mallet.pipe.tests.TestInstancePipe
testOneVarSlice() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testOneVarSlice() - Method in class cc.mallet.grmm.test.TestTableFactor
TestOptimizable - Class in cc.mallet.optimize.tests
  Contains static methods for testing subclasses of Maximizable and Maximizable.ByGradient.
TestOptimizable(String) - Constructor for class cc.mallet.optimize.tests.TestOptimizable
TestOptimizer - Class in cc.mallet.optimize.tests
  Unit Test for class TestMaximizer.java Created: Mon Apr 26 19:54:25 2004
TestOptimizer(String) - Constructor for class cc.mallet.optimize.tests.TestOptimizer
testOrthantWiseLBFGSWithL1() - Method in class cc.mallet.optimize.tests.TestOptimizer
testOrthantWiseLBFGSWithoutL1() - Method in class cc.mallet.optimize.tests.TestOptimizer
testOutputToDot() - Method in class cc.mallet.grmm.test.TestUndirectedModel
TestPagedInstanceList - Class in cc.mallet.types.tests
  Created: Apr 19, 2005
TestPagedInstanceList(String) - Constructor for class cc.mallet.types.tests.TestPagedInstanceList
testParameterSetting() - Method in class cc.mallet.classify.tests.TestStaticParameters
testParenGroupIterator() - Method in class cc.mallet.pipe.tests.TestIterators
TestPatternMatchIterator - Class in cc.mallet.pipe.iterator.tests
TestPatternMatchIterator(String) - Constructor for class cc.mallet.pipe.iterator.tests.TestPatternMatchIterator
testPbinom() - Method in class cc.mallet.util.tests.TestMaths
testPerDocEval() - Method in class cc.mallet.extract.test.TestPerDocumentF1Evaluator
TestPerDocumentF1Evaluator - Class in cc.mallet.extract.test
  Created: Nov 18, 2004
TestPerDocumentF1Evaluator(String) - Constructor for class cc.mallet.extract.test.TestPerDocumentF1Evaluator
testPerFieldEval() - Method in class cc.mallet.extract.test.TestPerDocumentF1Evaluator
testPipesAreStupid() - Method in class cc.mallet.pipe.tests.TestPipeUtils
TestPipeUtils - Class in cc.mallet.pipe.tests
  Created: Aug 28, 2005
TestPipeUtils(String) - Constructor for class cc.mallet.pipe.tests.TestPipeUtils
testPlusEquals() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testPlusEquals() - Method in class cc.mallet.grmm.test.TestTableFactor
testPlusEquals() - Method in class cc.mallet.types.tests.TestHashedSparseVector
testPlusEquals() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testPlusEquals() - Method in class cc.mallet.types.tests.TestSparseVector
testPlusEqualsAfterClone() - Method in class cc.mallet.types.tests.TestHashedSparseVector
testPlusEqualsFromSaved() - Method in class cc.mallet.types.tests.TestHashedSparseVector
testPotentialConnections() - Method in class cc.mallet.grmm.test.TestUndirectedModel
TestPottsFactor - Class in cc.mallet.grmm.test
  $Id: TestPottsFactor.java,v 1.1 2007/10/22 21:37:41 mccallum Exp $
TestPottsFactor(String) - Constructor for class cc.mallet.grmm.test.TestPottsFactor
testPrint() - Method in class cc.mallet.fst.tests.TestCRF
testPrint() - Method in class cc.mallet.types.tests.TestSparseVector
testPrinting() - Static method in class cc.mallet.pipe.tsf.tests.TestSequencePrintingPipe
TestPriorityQueue - Class in cc.mallet.util.tests
  Created by IntelliJ IDEA.
TestPriorityQueue(String) - Constructor for class cc.mallet.util.tests.TestPriorityQueue
TestPropertyList - Class in cc.mallet.util.tests
TestPropertyList(String) - Constructor for class cc.mallet.util.tests.TestPropertyList
testPunctuationIgnoringEvaluator() - Method in class cc.mallet.extract.test.TestPerDocumentF1Evaluator
testQuery() - Method in class cc.mallet.grmm.test.TestInference
TestRainbowStyle - Class in cc.mallet.pipe.tests
TestRainbowStyle(String) - Constructor for class cc.mallet.pipe.tests.TestRainbowStyle
TestRandom - Class in cc.mallet.util.tests
  Created: Jan 19, 2005
TestRandom(String) - Constructor for class cc.mallet.util.tests.TestRandom
TestRandomGraphs - Class in cc.mallet.grmm.test
  Created: Mar 26, 2005
TestRandomGraphs(String) - Constructor for class cc.mallet.grmm.test.TestRandomGraphs
testRandomMaximizable() - Method in class cc.mallet.classify.tests.TestMaxEntTrainer
testRandomTrained() - Method in class cc.mallet.classify.tests.TestClassifiers
testRandomTrained() - Method in class cc.mallet.classify.tests.TestNaiveBayes
testRandomTrained() - Method in class cc.mallet.types.tests.TestPagedInstanceList
TestRankedFeatureVector - Class in cc.mallet.types.tests
TestRankedFeatureVector(String) - Constructor for class cc.mallet.types.tests.TestRankedFeatureVector
testReadResolve() - Method in class cc.mallet.types.tests.TestAlphabet
testReadResolve() - Method in class cc.mallet.types.tests.TestLabelAlphabet
  Tests how serializing labels separately can lead to big losses.
testRecenter() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testRecenter2() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testRedundantDomains() - Method in class cc.mallet.grmm.test.TestFactorGraph
testRemove() - Method in class cc.mallet.grmm.test.TestFactorGraph
testRepulsiveGraphs() - Method in class cc.mallet.grmm.test.TestRandomGraphs
testRetainMass() - Method in class cc.mallet.grmm.test.TestFactors
testReverse() - Method in class cc.mallet.grmm.test.TestMIntInt2ObjectMap
testReverse() - Method in class cc.mallet.util.tests.TestPriorityQueue
testSample() - Method in class cc.mallet.grmm.test.TestBetaFactor
testSample() - Method in class cc.mallet.grmm.test.TestNormalFactor
testSample() - Method in class cc.mallet.grmm.test.TestTableFactor
testSample() - Method in class cc.mallet.grmm.test.TestUniformFactor
testSample() - Method in class cc.mallet.grmm.test.TestUniNormalFactor
testSample2() - Method in class cc.mallet.grmm.test.TestBetaFactor
testScale() - Method in class cc.mallet.grmm.test.TestAssignment
testScaleMarginalize() - Method in class cc.mallet.grmm.test.TestAssignment
TestSequencePrintingPipe - Class in cc.mallet.pipe.tsf.tests
  Created: Jul 8, 2005
TestSequencePrintingPipe(String) - Constructor for class cc.mallet.pipe.tsf.tests.TestSequencePrintingPipe
testSerializable() - Method in class cc.mallet.grmm.test.TestInference
testSerializable() - Method in class cc.mallet.grmm.test.TestMIntInt2ObjectMap
testSerializable() - Method in class cc.mallet.types.tests.TestHashedSparseVector
testSerializable() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testSerializable() - Method in class cc.mallet.types.tests.TestLabelsSequence
TestSerializable - Class in cc.mallet.types.tests
  Static utility for testing serializable classes in MALLET.
TestSerializable(String) - Constructor for class cc.mallet.types.tests.TestSerializable
testSerializable2() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testSerialization() - Method in class cc.mallet.fst.tests.TestCRF
testSerialization() - Method in class cc.mallet.grmm.test.TestAssignment
testSerialization() - Method in class cc.mallet.grmm.test.TestListVarSet
testSetGetParameters() - Method in class cc.mallet.classify.tests.TestMaxEntTrainer
testSetRankOrder() - Method in class cc.mallet.types.tests.TestRankedFeatureVector
testSetRow() - Method in class cc.mallet.grmm.test.TestAssignment
testSetRowFromAssn() - Method in class cc.mallet.grmm.test.TestAssignment
testSetValue() - Method in class cc.mallet.grmm.test.TestAssignment
testSetValue() - Method in class cc.mallet.types.tests.TestHashedSparseVector
testSetValue() - Method in class cc.mallet.types.tests.TestIndexedSparseVector
testSetValue() - Method in class cc.mallet.types.tests.TestSparseVector
testSetValueDup() - Method in class cc.mallet.grmm.test.TestAssignment
testSetValueExpand() - Method in class cc.mallet.grmm.test.TestAssignment
TestSGML2TokenSequence - Class in cc.mallet.pipe.tests
TestSGML2TokenSequence(String) - Constructor for class cc.mallet.pipe.tests.TestSGML2TokenSequence
TestSGML2TokenSequence.Array2ArrayIterator - Class in cc.mallet.pipe.tests
TestSGML2TokenSequence.Array2ArrayIterator() - Constructor for class cc.mallet.pipe.tests.TestSGML2TokenSequence.Array2ArrayIterator
testSimple() - Method in class cc.mallet.grmm.test.TestAssignment
testSimpleModel() - Method in class cc.mallet.grmm.test.TestDirectedModel
testSingletonGraph() - Method in class cc.mallet.grmm.test.TestInference
testSingleValueFromFeatureSequence() - Method in class cc.mallet.types.tests.TestFeatureVector
testSizeFromFeatureSequence() - Method in class cc.mallet.types.tests.TestFeatureVector
testSlice() - Method in class cc.mallet.grmm.test.TestPottsFactor
testSliceInFg() - Method in class cc.mallet.grmm.test.TestBetaFactor
testSliceInFg() - Method in class cc.mallet.grmm.test.TestUniformFactor
testSmall() - Method in class cc.mallet.util.tests.TestAStar
testSpaceMaximizable() - Method in class cc.mallet.fst.tests.TestMEMM
TestSpacePipe - Class in cc.mallet.pipe.tests
  Unit Test for class TestSpacePipe.java Created: Thu Feb 26 14:56:55 2004
TestSpacePipe(String) - Constructor for class cc.mallet.pipe.tests.TestSpacePipe
testSpacePipe() - Method in class cc.mallet.pipe.tests.TestSpacePipe
testSpaceSerializable() - Method in class cc.mallet.fst.tests.TestMEMM
testSpaceViewer() - Method in class cc.mallet.extract.test.TestDocumentViewer
testSpaceViewer() - Method in class cc.mallet.extract.test.TestLatticeViewer
testSparseDivide() - Method in class cc.mallet.grmm.test.TestTableFactor
testSparseDivideLogSpace() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testSparseExtractMax() - Method in class cc.mallet.grmm.test.TestTableFactor
testSparseMarginalize() - Method in class cc.mallet.grmm.test.TestTableFactor
testSparseMarginalizeLogSpace() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testSparseMatrixN() - Method in class cc.mallet.grmm.test.TestAssignmentIterator
TestSparseMatrixn - Class in cc.mallet.types.tests
  Created: Aug 30, 2004
TestSparseMatrixn(String) - Constructor for class cc.mallet.types.tests.TestSparseMatrixn
testSparseMatrixnSerializable() - Method in class cc.mallet.types.tests.TestSparseMatrixn
testSparseMultiply() - Method in class cc.mallet.grmm.test.TestTableFactor
testSparseMultiplyLogSpace() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testSparseNormalizeAsCpt() - Method in class cc.mallet.grmm.test.TestFactors
testSparseValueAndLogValue() - Method in class cc.mallet.grmm.test.TestLogTableFactor
TestSparseVector - Class in cc.mallet.types.tests
TestSparseVector(String) - Constructor for class cc.mallet.types.tests.TestSparseVector
testStartState() - Method in class cc.mallet.fst.tests.TestCRF
testStateAddWeights() - Method in class cc.mallet.fst.tests.TestCRF
TestStaticParameters - Class in cc.mallet.classify.tests
TestStaticParameters() - Constructor for class cc.mallet.classify.tests.TestStaticParameters
TestStaticParameters.Factory - Class in cc.mallet.classify.tests
TestStaticParameters.Factory() - Constructor for class cc.mallet.classify.tests.TestStaticParameters.Factory
TestStrings - Class in cc.mallet.util.tests
  Created: Jan 19, 2005
TestStrings(String) - Constructor for class cc.mallet.util.tests.TestStrings
testStringTrained() - Method in class cc.mallet.classify.tests.TestNaiveBayes
testSubtractLogProb() - Method in class cc.mallet.util.tests.TestMaths
testSum(double, double) - Method in class cc.mallet.fst.tests.TestSumNegLogProb2
testSum() - Method in class cc.mallet.grmm.test.TestAssignmentIterator
testSum() - Method in class cc.mallet.grmm.test.TestFactorGraph
testSumGradLog() - Method in class cc.mallet.grmm.test.TestPottsFactor
testSumGradLog2() - Method in class cc.mallet.grmm.test.TestPottsFactor
testSumLattice() - Method in class cc.mallet.fst.tests.TestCRF
testSumLatticeImplementations() - Method in class cc.mallet.fst.tests.TestCRF
testSumLogProb() - Method in class cc.mallet.fst.tests.TestCRF
testSumLogProb() - Method in class cc.mallet.grmm.test.TestInference
testSumLogProb() - Method in class cc.mallet.util.tests.TestMaths
TestSumNegLogProb2 - Class in cc.mallet.fst.tests
TestSumNegLogProb2(String) - Constructor for class cc.mallet.fst.tests.TestSumNegLogProb2
testSymmetricConcentration(int, int, int) - Static method in class cc.mallet.types.Dirichlet
TestTableFactor - Class in cc.mallet.grmm.test
  Created: Aug 17, 2004
TestTableFactor(String) - Constructor for class cc.mallet.grmm.test.TestTableFactor
testTableTimesFg() - Method in class cc.mallet.grmm.test.TestFactorGraph
testTblTblPlusEquals() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testTblTblPlusEquals() - Method in class cc.mallet.grmm.test.TestTableFactor
testTestSerializable() - Method in class cc.mallet.types.tests.TestSerializable
testTestValueAndGradient() - Method in class cc.mallet.optimize.tests.TestOptimizable
testThree() - Method in class cc.mallet.pipe.tests.TestRainbowStyle
testThreeNodeModel() - Method in class cc.mallet.grmm.test.TestUndirectedModel
testTimesEquals() - Method in class cc.mallet.types.tests.TestMatrix
testTimesTableFactor() - Method in class cc.mallet.grmm.test.TestLogTableFactor
TestToken - Class in cc.mallet.types.tests
TestToken(String) - Constructor for class cc.mallet.types.tests.TestToken
testTokenAccuracy() - Method in class cc.mallet.fst.tests.TestCRF
testToStdout() - Method in class cc.mallet.extract.test.TestPerDocumentF1Evaluator
testToXml() - Method in class cc.mallet.extract.test.TestDocumentExtraction
testToXmlBIO() - Method in class cc.mallet.extract.test.TestDocumentExtraction
testTrain() - Method in class cc.mallet.fst.tests.TestCRF
testTrainedMaximizable() - Method in class cc.mallet.classify.tests.TestMaxEntTrainer
testTrainStochasticGradient() - Method in class cc.mallet.fst.tests.TestCRF
testTreeViterbi() - Method in class cc.mallet.grmm.test.TestInference
testTrp() - Method in class cc.mallet.grmm.test.TestInference
TestTRP - Class in cc.mallet.grmm.test
  $Id: TestTRP.java,v 1.1 2007/10/22 21:37:40 mccallum Exp $
TestTRP(String) - Constructor for class cc.mallet.grmm.test.TestTRP
testTrpJoint() - Method in class cc.mallet.grmm.test.TestInference
testTrpLargeModels() - Method in class cc.mallet.grmm.test.TestInference
testTrpNonDestructivity() - Method in class cc.mallet.grmm.test.TestInference
  Tests that running TRP doesn't inadvertantly change potentials in the original graph.
testTrpOnTrees() - Method in class cc.mallet.grmm.test.TestInference
testTrpReuse() - Method in class cc.mallet.grmm.test.TestInference
testTrpTreeList() - Method in class cc.mallet.grmm.test.TestInference
testTrpViterbiEquiv() - Method in class cc.mallet.grmm.test.TestInference
testTrpViterbiEquiv2() - Method in class cc.mallet.grmm.test.TestInference
testTwo() - Method in class cc.mallet.fst.tests.TestSumNegLogProb2
testTwo() - Method in class cc.mallet.pipe.tests.TestInstancePipe
testTwo() - Method in class cc.mallet.types.tests.TestToken
testTwoVarSlice() - Method in class cc.mallet.grmm.test.TestLogTableFactor
testTwoVarSlice() - Method in class cc.mallet.grmm.test.TestTableFactor
testUndirectedCaches() - Method in class cc.mallet.grmm.test.TestUndirectedModel
testUndirectedCachesAfterRemove() - Method in class cc.mallet.grmm.test.TestUndirectedModel
testUndirectedIndices() - Method in class cc.mallet.grmm.test.TestInference
TestUndirectedModel - Class in cc.mallet.grmm.test
  Created: Mar 17, 2005
TestUndirectedModel(String) - Constructor for class cc.mallet.grmm.test.TestUndirectedModel
TestUniformFactor - Class in cc.mallet.grmm.test
  $Id: TestUniformFactor.java,v 1.1 2007/10/22 21:37:41 mccallum Exp $
TestUniformFactor(String) - Constructor for class cc.mallet.grmm.test.TestUniformFactor
testUniformGrid() - Method in class cc.mallet.grmm.test.TestRandomGraphs
testUniformGridWithObservations() - Method in class cc.mallet.grmm.test.TestRandomGraphs
testUniformJoint() - Method in class cc.mallet.grmm.test.TestInference
TestUniNormalFactor - Class in cc.mallet.grmm.test
  $Id: TestUniNormalFactor.java,v 1.1 2007/10/22 21:37:41 mccallum Exp $
TestUniNormalFactor(String) - Constructor for class cc.mallet.grmm.test.TestUniNormalFactor
testUnion() - Method in class cc.mallet.grmm.test.TestAssignment
testValue() - Method in class cc.mallet.grmm.test.TestBetaFactor
testValue() - Method in class cc.mallet.grmm.test.TestFactorGraph
testValue() - Method in class cc.mallet.grmm.test.TestUniNormalFactor
testValue() - Method in class cc.mallet.types.tests.TestLabelVector
testValueAndGradient(Optimizable.ByGradientValue) - Static method in class cc.mallet.optimize.tests.TestOptimizable
  Tests that getValue and getValueGradient are consistent.
testValueAndGradientCurrentParameters(Optimizable.ByGradientValue) - Static method in class cc.mallet.optimize.tests.TestOptimizable
  Tests that the value and gradient function are consistent at the current parameters.
testValueAndGradientInDirection(Optimizable.ByGradientValue, double[]) - Static method in class cc.mallet.optimize.tests.TestOptimizable
testValueAndGradientRandomParameters(Optimizable.ByGradientValue, Random) - Static method in class cc.mallet.optimize.tests.TestOptimizable
  Tests that getValue and getValueGradient are consistent at a random parameter setting.
testValueGradient() - Method in class cc.mallet.fst.tests.TestCRF
testVarSet() - Method in class cc.mallet.grmm.test.TestBetaFactor
testVarSet() - Method in class cc.mallet.grmm.test.TestUniformFactor
testVarSet() - Method in class cc.mallet.grmm.test.TestUniNormalFactor
testViterbi() - Method in class cc.mallet.fst.tests.TestFeatureTransducer
testXis() - Method in class cc.mallet.fst.tests.TestCRF
Text2Classify - Class in cc.mallet.classify.tui
  Command line tool for classifying a sequence of instances directly from text input, without creating an instance list.
Text2Classify() - Constructor for class cc.mallet.classify.tui.Text2Classify
Text2Clusterings - Class in cc.mallet.cluster.tui
Text2Clusterings() - Constructor for class cc.mallet.cluster.tui.Text2Clusterings
Text2Vectors - Class in cc.mallet.classify.tui
  Convert document files into vectors (a persistent instance list).
Text2Vectors() - Constructor for class cc.mallet.classify.tui.Text2Vectors
THashMultiMap - Class in cc.mallet.grmm.util
  Version of THashMap where every key is mapped to a list of objects.
THashMultiMap() - Constructor for class cc.mallet.grmm.util.THashMultiMap
THashMultiMap(int) - Constructor for class cc.mallet.grmm.util.THashMultiMap
ThreadedOptimizable - Class in cc.mallet.fst
  An adaptor for optimizables based on batch values/gradients.
ThreadedOptimizable(Optimizable.ByCombiningBatchGradient, InstanceList, int, CacheStaleIndicator) - Constructor for class cc.mallet.fst.ThreadedOptimizable
  Initializes the optimizable and starts new threads.
tick() - Method in class cc.mallet.grmm.util.Flops.Watch
tick(String) - Method in class cc.mallet.grmm.util.Flops.Watch
tick(String) - Method in class cc.mallet.util.Timing
  Print to System.out how much time has passed, resetting this Timing's start time to the current time.
timeMarginalization() - Method in class cc.mallet.grmm.test.TestInference
timesEquals(double) - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Multiplies a constant by all values in the table.
timesEquals(double) - Method in class cc.mallet.grmm.types.LogTableFactor
timesEquals(double) - Method in class cc.mallet.grmm.types.TableFactor
timesEquals(double) - Method in class cc.mallet.types.DenseMatrix
timesEquals(double[], double[]) - Static method in class cc.mallet.types.DenseMatrix
timesEquals(double) - Method in interface cc.mallet.types.Matrix
timesEquals(double[], double) - Static method in class cc.mallet.types.MatrixOps
  Multiplies every element in an array by a scalar.
timesEquals(double[], double[]) - Static method in class cc.mallet.types.MatrixOps
timesEquals(double[][], double) - Static method in class cc.mallet.types.MatrixOps
timesEquals(double) - Method in class cc.mallet.types.SparseMatrixn
timesEquals(double) - Method in class cc.mallet.types.SparseVector
  Scale all elements by the same factor.
timesEqualsSparse(SparseVector) - Method in class cc.mallet.types.SparseVector
  For each index i that is present in this vector, set this[i] *= v[i].
timesEqualsSparse(SparseVector, double) - Method in class cc.mallet.types.SparseVector
  For each index i that is present in this vector, set this[i] *= factor * v[i].
timesEqualsSparseZero(SparseVector, double) - Method in class cc.mallet.types.SparseVector
  For each index i that is present in this vector, set this[i] *= factor * v[i].
Timing - Class in cc.mallet.util
  A class for timing things.
Timing() - Constructor for class cc.mallet.util.Timing
tmpls - Variable in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
to() - Method in class cc.mallet.grmm.inference.MessageArray.Iterator
toArray() - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
toArray(Object[]) - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
  Returns an array containing all the entries in the Alphabet.
toArray(Object[]) - Method in class cc.mallet.grmm.types.HashVarSet
  Returns the variables in this clique as an array.
toArray() - Method in class cc.mallet.grmm.types.HashVarSet
  Returns the variables in this clique as an array.
toArray() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
toArray(Object[]) - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
toArray() - Method in class cc.mallet.types.Alphabet
toArray(Object[]) - Method in class cc.mallet.types.Alphabet
  Returns an array containing all the entries in the Alphabet.
toArray() - Method in class cc.mallet.types.Matrixn
  Returns a one-dimensional array representation of the matrix.
toArray() - Method in class cc.mallet.types.MultiInstanceList
toArray(T[]) - Method in class cc.mallet.types.MultiInstanceList
toArray() - Method in class cc.mallet.types.SparseMatrixn
  Returns a one-dimensional array representation of the matrix.
toArray() - Method in class cc.mallet.util.search.MinHeap
toArray() - Method in interface cc.mallet.util.search.PriorityQueue
  Returns any array containing all of the elements in the queue.
toArrayList() - Method in class cc.mallet.pipe.iterator.SegmentIterator
toDoubleArray(int) - Method in class cc.mallet.grmm.types.Assignment
toDoubleArray(ArrayList) - Static method in class cc.mallet.util.ArrayListUtils
toFeatureIndexSequence() - Method in class cc.mallet.types.FeatureSequence
toFeatureSequence(Alphabet) - Method in class cc.mallet.types.TokenSequence
toFeatureVector() - Method in class cc.mallet.types.AugmentableFeatureVector
toFeatureVector() - Method in class cc.mallet.types.FeatureCounter
toFeatureVector(Alphabet, boolean) - Method in interface cc.mallet.types.PropertyHolder
toFeatureVector(Alphabet, boolean) - Method in class cc.mallet.types.Token
toFeatureVector(Alphabet) - Method in class cc.mallet.types.TokenSequence
toFile(String) - Method in class cc.mallet.types.Dirichlet
  Write the parameters alpha_i to the specified file, one per line
toInstance() - Method in class cc.mallet.classify.Classification
toIntArray(ArrayList) - Static method in class cc.mallet.util.ArrayListUtils
Token - Class in cc.mallet.types
  A representation of a piece of text, usually a single word, to which we can attach properties.
Token(String) - Constructor for class cc.mallet.types.Token
Token2FeatureVector - Class in cc.mallet.pipe
  convert the property list on a token into a feature vector
Token2FeatureVector(Alphabet, boolean, boolean) - Constructor for class cc.mallet.pipe.Token2FeatureVector
Token2FeatureVector(Alphabet) - Constructor for class cc.mallet.pipe.Token2FeatureVector
Token2FeatureVector(boolean, boolean) - Constructor for class cc.mallet.pipe.Token2FeatureVector
Token2FeatureVector() - Constructor for class cc.mallet.pipe.Token2FeatureVector
tokenAccuracy(Sequence, PrintWriter) - Method in class cc.mallet.fst.MaxLatticeDefault
TokenAccuracyEvaluator - Class in cc.mallet.fst
  Evaluates a transducer model based on predictions of individual tokens.
TokenAccuracyEvaluator(InstanceList[], String[]) - Constructor for class cc.mallet.fst.TokenAccuracyEvaluator
TokenAccuracyEvaluator(InstanceList, String) - Constructor for class cc.mallet.fst.TokenAccuracyEvaluator
TokenAccuracyEvaluator(InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.fst.TokenAccuracyEvaluator
TokenAccuracyEvaluator(InstanceList, String, InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.fst.TokenAccuracyEvaluator
TokenFirstPosition - Class in cc.mallet.pipe.tsf
TokenFirstPosition(String) - Constructor for class cc.mallet.pipe.tsf.TokenFirstPosition
TokenFirstPosition() - Constructor for class cc.mallet.pipe.tsf.TokenFirstPosition
Tokenization - Interface in cc.mallet.extract
TokenizationFilter - Interface in cc.mallet.extract
  Created: Nov 12, 2004
TokenSequence - Class in cc.mallet.types
  A representation of a piece of text, usually a single word, to which we can attach properties.
TokenSequence(Collection<Token>) - Constructor for class cc.mallet.types.TokenSequence
TokenSequence() - Constructor for class cc.mallet.types.TokenSequence
TokenSequence(int) - Constructor for class cc.mallet.types.TokenSequence
TokenSequence(Token[]) - Constructor for class cc.mallet.types.TokenSequence
TokenSequence(Object[]) - Constructor for class cc.mallet.types.TokenSequence
TokenSequence2FeatureSequence - Class in cc.mallet.pipe
  Convert the token sequence in the data field each instance to a feature sequence.
TokenSequence2FeatureSequence(Alphabet) - Constructor for class cc.mallet.pipe.TokenSequence2FeatureSequence
TokenSequence2FeatureSequence() - Constructor for class cc.mallet.pipe.TokenSequence2FeatureSequence
TokenSequence2FeatureSequenceWithBigrams - Class in cc.mallet.pipe
  Convert the token sequence in the data field of each instance to a feature sequence that preserves bigram information.
TokenSequence2FeatureSequenceWithBigrams(Alphabet, Alphabet) - Constructor for class cc.mallet.pipe.TokenSequence2FeatureSequenceWithBigrams
TokenSequence2FeatureSequenceWithBigrams(Alphabet) - Constructor for class cc.mallet.pipe.TokenSequence2FeatureSequenceWithBigrams
TokenSequence2FeatureSequenceWithBigrams() - Constructor for class cc.mallet.pipe.TokenSequence2FeatureSequenceWithBigrams
TokenSequence2FeatureVectorSequence - Class in cc.mallet.pipe
  Convert the token sequence in the data field of each instance to a feature vector sequence.
TokenSequence2FeatureVectorSequence(Alphabet, boolean, boolean) - Constructor for class cc.mallet.pipe.TokenSequence2FeatureVectorSequence
TokenSequence2FeatureVectorSequence(Alphabet) - Constructor for class cc.mallet.pipe.TokenSequence2FeatureVectorSequence
TokenSequence2FeatureVectorSequence(boolean, boolean) - Constructor for class cc.mallet.pipe.TokenSequence2FeatureVectorSequence
TokenSequence2FeatureVectorSequence() - Constructor for class cc.mallet.pipe.TokenSequence2FeatureVectorSequence
TokenSequence2TokenInstances - Class in cc.mallet.pipe
TokenSequence2TokenInstances() - Constructor for class cc.mallet.pipe.TokenSequence2TokenInstances
TokenSequence2Tokenization - Class in cc.mallet.extract.pipe
  Heuristically converts a simple token sequence into a Tokenization that can be used with all the extract package goodies.
TokenSequence2Tokenization() - Constructor for class cc.mallet.extract.pipe.TokenSequence2Tokenization
TokenSequenceDocHeader - Class in cc.mallet.share.mccallum.ner
TokenSequenceDocHeader() - Constructor for class cc.mallet.share.mccallum.ner.TokenSequenceDocHeader
TokenSequenceLowercase - Class in cc.mallet.pipe
  Convert the text in each token in the token sequence in the data field to lower case.
TokenSequenceLowercase() - Constructor for class cc.mallet.pipe.TokenSequenceLowercase
TokenSequenceMatchDataAndTarget - Class in cc.mallet.pipe
  Run a regular expression over the text of each token; replace the text with the substring matching one regex group; create a target TokenSequence from the text matching another regex group.
TokenSequenceMatchDataAndTarget(Pattern, int, int) - Constructor for class cc.mallet.pipe.TokenSequenceMatchDataAndTarget
TokenSequenceMatchDataAndTarget(String, int, int) - Constructor for class cc.mallet.pipe.TokenSequenceMatchDataAndTarget
TokenSequenceNGrams - Class in cc.mallet.pipe
  Convert the token sequence in the data field to a token sequence of ngrams.
TokenSequenceNGrams(int[]) - Constructor for class cc.mallet.pipe.TokenSequenceNGrams
TokenSequenceParseFeatureString - Class in cc.mallet.pipe
  Convert the string in each field `Token.text` to a list of Strings (space delimited).
TokenSequenceParseFeatureString(boolean, boolean, String) - Constructor for class cc.mallet.pipe.TokenSequenceParseFeatureString
TokenSequenceParseFeatureString(boolean, boolean) - Constructor for class cc.mallet.pipe.TokenSequenceParseFeatureString
TokenSequenceParseFeatureString(boolean) - Constructor for class cc.mallet.pipe.TokenSequenceParseFeatureString
TokenSequenceRemoveNonAlpha - Class in cc.mallet.pipe
  Remove tokens that contain non-alphabetic characters.
TokenSequenceRemoveNonAlpha(boolean) - Constructor for class cc.mallet.pipe.TokenSequenceRemoveNonAlpha
TokenSequenceRemoveNonAlpha() - Constructor for class cc.mallet.pipe.TokenSequenceRemoveNonAlpha
TokenSequenceRemoveStopwords - Class in cc.mallet.pipe
  Remove tokens from the token sequence in the data field whose text is in the stopword list.
TokenSequenceRemoveStopwords(boolean, boolean) - Constructor for class cc.mallet.pipe.TokenSequenceRemoveStopwords
TokenSequenceRemoveStopwords(boolean) - Constructor for class cc.mallet.pipe.TokenSequenceRemoveStopwords
TokenSequenceRemoveStopwords() - Constructor for class cc.mallet.pipe.TokenSequenceRemoveStopwords
TokenSequenceRemoveStopwords(File, String, boolean, boolean, boolean) - Constructor for class cc.mallet.pipe.TokenSequenceRemoveStopwords
  Load a stoplist from a file.
tokensPerTopic - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
tokensPerTopic - Variable in class cc.mallet.topics.MarginalProbEstimator
tokensPerTopic - Variable in class cc.mallet.topics.NPTopicModel
tokensPerTopic - Variable in class cc.mallet.topics.ParallelTopicModel
tokensPerTopic - Variable in class cc.mallet.topics.SimpleLDA
tokensPerTopic - Variable in class cc.mallet.topics.TopicInferencer
tokensPerTopic - Variable in class cc.mallet.topics.WorkerRunnable
TokenText - Class in cc.mallet.pipe.tsf
TokenText(String, Pattern) - Constructor for class cc.mallet.pipe.tsf.TokenText
TokenText(String) - Constructor for class cc.mallet.pipe.tsf.TokenText
TokenText() - Constructor for class cc.mallet.pipe.tsf.TokenText
TokenTextCharNGrams - Class in cc.mallet.pipe.tsf
TokenTextCharNGrams(String, int[], boolean) - Constructor for class cc.mallet.pipe.tsf.TokenTextCharNGrams
TokenTextCharNGrams(String, int[]) - Constructor for class cc.mallet.pipe.tsf.TokenTextCharNGrams
TokenTextCharNGrams() - Constructor for class cc.mallet.pipe.tsf.TokenTextCharNGrams
TokenTextCharPrefix - Class in cc.mallet.pipe.tsf
TokenTextCharPrefix(String, int) - Constructor for class cc.mallet.pipe.tsf.TokenTextCharPrefix
TokenTextCharPrefix() - Constructor for class cc.mallet.pipe.tsf.TokenTextCharPrefix
TokenTextCharSuffix - Class in cc.mallet.pipe.tsf
TokenTextCharSuffix(String, int) - Constructor for class cc.mallet.pipe.tsf.TokenTextCharSuffix
TokenTextCharSuffix() - Constructor for class cc.mallet.pipe.tsf.TokenTextCharSuffix
TokenTextNGrams - Class in cc.mallet.pipe.tsf
TokenTextNGrams(String, int[]) - Constructor for class cc.mallet.pipe.tsf.TokenTextNGrams
TokenTextNGrams() - Constructor for class cc.mallet.pipe.tsf.TokenTextNGrams
tokPipe - Variable in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
toLabelsSequence(Assignment) - Method in class cc.mallet.grmm.util.LabelsAssignment
toLabelVector() - Method in class cc.mallet.types.Label
toLabelVector() - Method in interface cc.mallet.types.Labeling
toLabelVector() - Method in class cc.mallet.types.LabelVector
toLogValueArray() - Method in class cc.mallet.grmm.types.AbstractTableFactor
toMessagesIterator(int) - Method in class cc.mallet.grmm.inference.MessageArray
TopicalNGrams - Class in cc.mallet.topics
  Like Latent Dirichlet Allocation, but with integrated phrase discovery.
TopicalNGrams(int) - Constructor for class cc.mallet.topics.TopicalNGrams
TopicalNGrams(int, double, double, double, double, double, double) - Constructor for class cc.mallet.topics.TopicalNGrams
topicAlphabet - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
topicAlphabet - Variable in class cc.mallet.topics.NPTopicModel
topicAlphabet - Variable in class cc.mallet.topics.ParallelTopicModel
topicAlphabet - Variable in class cc.mallet.topics.PolylingualTopicModel
topicAlphabet - Variable in class cc.mallet.topics.SimpleLDA
TopicAssignment - Class in cc.mallet.topics
  This class combines a sequence of observed features with a sequence of hidden "labels".
TopicAssignment(Instance, LabelSequence) - Constructor for class cc.mallet.topics.TopicAssignment
topicBits - Variable in class cc.mallet.topics.MarginalProbEstimator
topicBits - Variable in class cc.mallet.topics.ParallelTopicModel
topicBits - Variable in class cc.mallet.topics.PolylingualTopicModel
topicBits - Variable in class cc.mallet.topics.TopicInferencer
topicBits - Variable in class cc.mallet.topics.WorkerRunnable
topicDistribution - Variable in class cc.mallet.topics.LDAHyper.Topication
  Deprecated.
topicDistribution - Variable in class cc.mallet.topics.PolylingualTopicModel.TopicAssignment
topicDistribution - Variable in class cc.mallet.topics.TopicAssignment
topicDocCounts - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
topicDocCounts - Variable in class cc.mallet.topics.ParallelTopicModel
topicDocCounts - Variable in class cc.mallet.topics.PolylingualTopicModel
topicDocCounts - Variable in class cc.mallet.topics.WorkerRunnable
TopicInferencer - Class in cc.mallet.topics
TopicInferencer(int[][], int[], Alphabet, double[], double, double) - Constructor for class cc.mallet.topics.TopicInferencer
topicLabelMutualInformation() - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
topicMask - Variable in class cc.mallet.topics.MarginalProbEstimator
topicMask - Variable in class cc.mallet.topics.ParallelTopicModel
topicMask - Variable in class cc.mallet.topics.PolylingualTopicModel
topicMask - Variable in class cc.mallet.topics.TopicInferencer
topicMask - Variable in class cc.mallet.topics.WorkerRunnable
topicPhraseXMLReport(PrintWriter, int) - Method in class cc.mallet.topics.ParallelTopicModel
topicSequence - Variable in class cc.mallet.topics.LDAHyper.Topication
  Deprecated.
topicSequence - Variable in class cc.mallet.topics.TopicAssignment
topicSequences - Variable in class cc.mallet.topics.PolylingualTopicModel.TopicAssignment
TopicTrain - Class in cc.mallet.topics.tui
TopicTrain() - Constructor for class cc.mallet.topics.tui.TopicTrain
topicXMLReport(PrintWriter, int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
topicXMLReport(PrintWriter, int) - Method in class cc.mallet.topics.ParallelTopicModel
topicXMLReportPhrases(PrintStream, int) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
topWords(int) - Method in class cc.mallet.topics.NPTopicModel
topWords(int) - Method in class cc.mallet.topics.SimpleLDA
toRankedFeatureVector() - Method in class cc.mallet.types.FeatureCounter
toSimpFile(String, int, boolean) - Method in class cc.mallet.types.FeatureVector
toSizesArray(Variable[]) - Static method in class cc.mallet.grmm.inference.Utils
toSortedFeatureIndexSequence() - Method in class cc.mallet.types.FeatureSequence
toSparseVector() - Method in class cc.mallet.types.AugmentableFeatureVector
toString() - Method in class cc.mallet.classify.ClassifierTrainer.Factory
toString() - Method in class cc.mallet.classify.evaluate.ConfusionMatrix
toString() - Method in class cc.mallet.classify.MaxEntTrainer
  Like the other version of `trainWithFeatureInduction`, but allows some default options to be changed.
toString() - Method in class cc.mallet.classify.MCMaxEntTrainer
toString() - Method in class cc.mallet.classify.NaiveBayesEMTrainer
toString() - Method in class cc.mallet.classify.NaiveBayesTrainer
  Create a NaiveBayes classifier from a set of training data and the previous state of the trainer.
toString() - Method in class cc.mallet.classify.RankMaxEntTrainer
  Like the other version of `trainWithFeatureInduction`, but allows some default options to be changed.
toString() - Method in class cc.mallet.cluster.Clustering
toString() - Method in class cc.mallet.cluster.GreedyAgglomerative
toString() - Method in class cc.mallet.cluster.GreedyAgglomerativeByDensity
toString() - Method in class cc.mallet.cluster.neighbor_evaluator.AgglomerativeNeighbor
toString() - Method in class cc.mallet.cluster.neighbor_evaluator.ClassifyingNeighborEvaluator
toString() - Method in class cc.mallet.cluster.neighbor_evaluator.MedoidEvaluator
toString() - Method in class cc.mallet.cluster.neighbor_evaluator.Neighbor
toString() - Method in class cc.mallet.cluster.neighbor_evaluator.PairwiseEvaluator
toString() - Method in class cc.mallet.cluster.neighbor_evaluator.RankingNeighborEvaluator
toString() - Method in class cc.mallet.cluster.Record
toString(boolean) - Method in class cc.mallet.cluster.Record
toString() - Method in class cc.mallet.cluster.util.PairwiseMatrix
toString() - Method in class cc.mallet.extract.Field
toString() - Method in class cc.mallet.extract.LabeledSpan
toString() - Method in class cc.mallet.extract.StringSpan
toString() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator.EntityConfidence
toString() - Method in class cc.mallet.fst.confidence.ConfidenceEvaluator
toString() - Method in class cc.mallet.fst.Segment
toString() - Method in class cc.mallet.grmm.inference.SamplingInferencer
toString() - Method in class cc.mallet.grmm.learning.ACRF.BigramTemplate
toString() - Method in class cc.mallet.grmm.learning.ACRF.PairwiseFactorTemplate
toString() - Method in class cc.mallet.grmm.learning.ACRF.UnigramTemplate
toString() - Method in class cc.mallet.grmm.types.AbstractTableFactor
toString() - Method in class cc.mallet.grmm.types.BetaFactor
toString() - Method in class cc.mallet.grmm.types.BidirectionalIntObjectMap
  Return String representation of all Alphabet entries, each separated by a newline.
toString() - Method in class cc.mallet.grmm.types.BitVarSet
toString() - Method in class cc.mallet.grmm.types.ConstantFactor
toString() - Method in class cc.mallet.grmm.types.CPT
toString() - Method in class cc.mallet.grmm.types.FactorGraph
toString() - Method in class cc.mallet.grmm.types.HashVarSet
toString() - Method in class cc.mallet.grmm.types.ListVarSet
toString() - Method in class cc.mallet.grmm.types.NormalFactor
toString() - Method in class cc.mallet.grmm.types.UniformFactor
toString() - Method in class cc.mallet.grmm.types.UniNormalFactor
toString() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
toString() - Method in class cc.mallet.grmm.types.Variable
toString() - Method in class cc.mallet.pipe.SelectiveSGML2TokenSequence
toString() - Method in class cc.mallet.pipe.SerialPipes
toString() - Method in class cc.mallet.types.Alphabet
  Return String representation of all Alphabet entries, each separated by a newline.
toString() - Method in class cc.mallet.types.ArraySequence
toString() - Method in class cc.mallet.types.FeatureSequence
toString() - Method in class cc.mallet.types.FeatureVector
toString(boolean) - Method in class cc.mallet.types.FeatureVector
toString() - Method in class cc.mallet.types.FeatureVectorSequence
toString() - Method in class cc.mallet.types.Label
toString() - Method in class cc.mallet.types.Labels
toString() - Method in class cc.mallet.types.LabelsSequence
toString() - Method in class cc.mallet.types.Matrix2
  Deprecated.
toString(Object) - Static method in class cc.mallet.types.MatrixOps
  Print a space-separated array of elements
toString() - Method in class cc.mallet.types.MultiInstanceList
toString() - Method in class cc.mallet.types.ROCData
toString() - Method in class cc.mallet.types.SparseVector
toString(boolean) - Method in class cc.mallet.types.SparseVector
toString() - Method in class cc.mallet.types.StringEditFeatureVectorSequence
toString() - Method in class cc.mallet.types.Token
toString() - Method in class cc.mallet.types.TokenSequence
toString(int[]) - Static method in class cc.mallet.util.ArrayUtils
toString(double[]) - Static method in class cc.mallet.util.ArrayUtils
toString(Object[]) - Static method in class cc.mallet.util.ArrayUtils
toString() - Method in class cc.mallet.util.search.SearchNode
toStringShort() - Method in class cc.mallet.types.TokenSequence
toStringWithFeatureNames() - Method in class cc.mallet.types.Token
totalCount - Variable in class cc.mallet.cluster.iterator.PairSampleIterator
totalDocTopics - Variable in class cc.mallet.topics.NPTopicModel
totalElapsedTime() - Method in class cc.mallet.util.Timing
  Returns the number of milliseconds since this object was created.
totalFlopsElapsed() - Method in class cc.mallet.grmm.util.Flops.Watch
totalNanos - Variable in class cc.mallet.pipe.StringList2FeatureSequence
totalTokens - Variable in class cc.mallet.topics.ParallelTopicModel
toValueArray() - Method in class cc.mallet.grmm.types.AbstractTableFactor
toValueArray() - Method in class cc.mallet.grmm.types.CPT
toValueArray() - Method in interface cc.mallet.grmm.types.DiscreteFactor
toVariableArray() - Method in class cc.mallet.grmm.types.BitVarSet
toVariableArray() - Method in class cc.mallet.grmm.types.HashVarSet
toVariableArray() - Method in class cc.mallet.grmm.types.ListVarSet
toVariableArray() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
toVariableArray() - Method in interface cc.mallet.grmm.types.VarSet
  Returns the variables in this clique as an array, that should not be modified.
toXmlDocument() - Method in class cc.mallet.extract.DocumentExtraction
toXmlDocument(String, Namespace) - Method in class cc.mallet.extract.DocumentExtraction
toXmlString() - Method in class cc.mallet.extract.DocumentExtraction
train(InstanceList) - Method in class cc.mallet.classify.AdaBoostM2Trainer
  Boosting method that resamples instances using their weights
train(InstanceList) - Method in class cc.mallet.classify.AdaBoostTrainer
  Boosting method that resamples instances using their weights
train(InstanceList) - Method in class cc.mallet.classify.BaggingTrainer
train(InstanceList) - Method in class cc.mallet.classify.BalancedWinnowTrainer
  Trains the classifier on the instance list, updating class weight vectors as appropriate
train(InstanceList) - Method in class cc.mallet.classify.C45Trainer
train(InstanceList) - Method in class cc.mallet.classify.ClassifierEnsembleTrainer
train(InstanceList, Labeler, int) - Method in interface cc.mallet.classify.ClassifierTrainer.ByActiveLearning
train(InstanceList, int) - Method in interface cc.mallet.classify.ClassifierTrainer.ByOptimization
train(InstanceList) - Method in class cc.mallet.classify.ClassifierTrainer
train(InstanceList) - Method in class cc.mallet.classify.ConfidencePredictingClassifierTrainer
train(InstanceList) - Method in class cc.mallet.classify.DecisionTreeTrainer
train(InstanceList) - Method in class cc.mallet.classify.FeatureSelectingClassifierTrainer
train(InstanceList) - Method in class cc.mallet.classify.MaxEntGETrainer
train(InstanceList, int) - Method in class cc.mallet.classify.MaxEntGETrainer
train(InstanceList) - Method in class cc.mallet.classify.MaxEntTrainer
train(InstanceList, int) - Method in class cc.mallet.classify.MaxEntTrainer
train(InstanceList) - Method in class cc.mallet.classify.MCMaxEntTrainer
train(InstanceList) - Method in class cc.mallet.classify.NaiveBayesEMTrainer
train(InstanceList) - Method in class cc.mallet.classify.NaiveBayesTrainer
  Create a NaiveBayes classifier from a set of training data.
train(InstanceList) - Method in class cc.mallet.classify.RankMaxEntTrainer
train(InstanceList) - Method in class cc.mallet.classify.WinnowTrainer
  Trains winnow on the instance list, updating `weights` according to errors
train(InstanceList, int) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
train(InstanceList, int, double[]) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
  Train a CRF on various-sized subsets of the data.
train(InstanceList, int) - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
train(InstanceList, int, int) - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
train(InstanceList, int) - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
train(InstanceList, int, double[]) - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
  Train a CRF on various-sized subsets of the data.
train(InstanceList, int) - Method in class cc.mallet.fst.CRFTrainerByValueGradients
  Trains a CRF until convergence or specified number of iterations, whichever is earlier.
train(InstanceList, int, double[]) - Method in class cc.mallet.fst.CRFTrainerByValueGradients
  Train a CRF on various-sized subsets of the data.
train(InstanceList) - Method in class cc.mallet.fst.HMM
  Trains a HMM without validation and evaluation.
train(InstanceList, InstanceList, InstanceList) - Method in class cc.mallet.fst.HMM
  Trains a HMM with `evaluator` set to null.
train(InstanceList, InstanceList, InstanceList, TransducerEvaluator) - Method in class cc.mallet.fst.HMM
train(InstanceList, int) - Method in class cc.mallet.fst.HMMTrainerByLikelihood
train(InstanceList, InstanceList, int) - Method in class cc.mallet.fst.HMMTrainerByLikelihood
train(InstanceList) - Method in class cc.mallet.fst.MEMMTrainer
  Trains a MEMM until convergence.
train(InstanceList, int) - Method in class cc.mallet.fst.MEMMTrainer
  Trains a MEMM for specified number of iterations or until convergence whichever occurs first; returns true if training converged within specified iterations.
train(InstanceList, InstanceList, InstanceList, TransducerEvaluator, int, int, double[]) - Method in class cc.mallet.fst.MEMMTrainer
  Not implemented yet.
train(InstanceList) - Method in class cc.mallet.fst.NoopTransducerTrainer
train(InstanceList, int) - Method in class cc.mallet.fst.NoopTransducerTrainer
train(InstanceList, int) - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByEntropyRegularization
train(InstanceList, InstanceList, int) - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByEntropyRegularization
  Performs CRF training with label likelihood and entropy regularization.
train(InstanceList, int) - Method in class cc.mallet.fst.semi_supervised.CRFTrainerByGE
train(InstanceList, int) - Method in class cc.mallet.fst.ShallowTransducerTrainer
  Deprecated.
train(InstanceList, InstanceList, TransducerEvaluator, int[], String, String, String, boolean, int, double, CRF) - Static method in class cc.mallet.fst.SimpleTagger
  Create and train a CRF model from the given training data, optionally testing it on the given test data.
train(InstanceList) - Method in class cc.mallet.fst.TransducerTrainer
train(InstanceList, int) - Method in class cc.mallet.fst.TransducerTrainer
  Train the transducer associated with this TransducerTrainer.
train(ACRF, InstanceList) - Method in interface cc.mallet.grmm.learning.ACRFTrainer
train(ACRF, InstanceList, int) - Method in interface cc.mallet.grmm.learning.ACRFTrainer
train(ACRF, InstanceList, ACRFEvaluator, int) - Method in interface cc.mallet.grmm.learning.ACRFTrainer
train(ACRF, InstanceList, InstanceList, InstanceList, int) - Method in interface cc.mallet.grmm.learning.ACRFTrainer
train(ACRF, InstanceList, InstanceList, InstanceList, ACRFEvaluator, int) - Method in interface cc.mallet.grmm.learning.ACRFTrainer
train(ACRF, InstanceList, InstanceList, InstanceList, ACRFEvaluator, int, Optimizable.ByGradientValue) - Method in interface cc.mallet.grmm.learning.ACRFTrainer
train(ACRF, InstanceList) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
train(ACRF, InstanceList, int) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
train(ACRF, InstanceList, ACRFEvaluator, int) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
train(ACRF, InstanceList, InstanceList, InstanceList, int) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
train(ACRF, InstanceList, InstanceList, InstanceList, ACRFEvaluator, int) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
train(ACRF, InstanceList, InstanceList, InstanceList, ACRFEvaluator, int, Optimizable.ByGradientValue) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
train(ACRF, InstanceList, InstanceList, InstanceList, ACRFEvaluator, double[], int) - Method in class cc.mallet.grmm.learning.DefaultAcrfTrainer
train(String[][], String[], double, File) - Static method in class cc.mallet.share.upenn.MaxEntShell
  Train a maxent classifier.
train(Iterator<Instance>, double, File) - Static method in class cc.mallet.share.upenn.MaxEntShell
  Train a maxent classifier.
trainAcrf() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
  Trains a new ACRF object with the given settings.
trainClassifier(InstanceList, String, String) - Method in class cc.mallet.fst.confidence.MaxEntConfidenceEstimator
trainClassifier(InstanceList, String, String) - Method in class cc.mallet.fst.confidence.MaxEntSequenceConfidenceEstimator
  Train underlying classifier on `ilist`.
TrainCRF - Class in cc.mallet.examples
TrainCRF(String, String) - Constructor for class cc.mallet.examples.TrainCRF
trainExtractor() - Method in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
TrainHMM - Class in cc.mallet.examples
TrainHMM(String, String) - Constructor for class cc.mallet.examples.TrainHMM
trainIncremental(InstanceList) - Method in interface cc.mallet.classify.ClassifierTrainer.ByIncrements
trainIncremental(Instance) - Method in interface cc.mallet.classify.ClassifierTrainer.ByInstanceIncrements
trainIncremental(InstanceList) - Method in class cc.mallet.classify.NaiveBayesTrainer
trainIncremental(Instance) - Method in class cc.mallet.classify.NaiveBayesTrainer
trainIncremental(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
trainIncremental(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
trainIncremental(Instance) - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
trainIncremental(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByThreadedLabelLikelihood
trainIncremental(InstanceList) - Method in class cc.mallet.fst.CRFTrainerByValueGradients
  Trains a CRF until convergence.
trainIncremental(InstanceList) - Method in class cc.mallet.fst.TransducerTrainer.ByIncrements
trainIncremental(Instance) - Method in class cc.mallet.fst.TransducerTrainer.ByInstanceIncrements
trainIncrementalLikelihood(Instance) - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
  Adjust the parameters by default learning rate according to the gradient of this single Instance, and return the true label sequence likelihood.
trainIncrementalLikelihood(Instance, double) - Method in class cc.mallet.fst.CRFTrainerByStochasticGradient
  Adjust the parameters by learning rate according to the gradient of this single Instance, and return the true label sequence likelihood.
training - Variable in class cc.mallet.grmm.learning.extract.ACRFExtractorTrainer
trainingSet - Variable in class cc.mallet.fst.CRFOptimizableByBatchLabelLikelihood
trainingSet - Variable in class cc.mallet.fst.CRFOptimizableByLabelLikelihood
trainingSet - Variable in class cc.mallet.fst.ThreadedOptimizable
  Data
trainWithFeatureInduction(InstanceList, InstanceList, InstanceList, TransducerEvaluator, int, int, int, int, double, boolean, double[]) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
trainWithFeatureInduction(InstanceList, InstanceList, InstanceList, TransducerEvaluator, int, int, int, int, double, boolean, double[], String) - Method in class cc.mallet.fst.CRFTrainerByLabelLikelihood
  Train a CRF using feature induction to generate conjunctions of features.
trainWithFeatureInduction(InstanceList, InstanceList, InstanceList, TransducerEvaluator, int, int, int, int, double, boolean, double[], String) - Method in class cc.mallet.fst.MEMMTrainer
  Not implemented yet.
transduce(Instance) - Method in class cc.mallet.fst.Transducer
  Take input sequence from instance.data and put the output sequence in instance.data.
transduce(Sequence) - Method in class cc.mallet.fst.Transducer
  Converts the given sequence into another sequence according to this transducer.
transducer - Variable in class cc.mallet.fst.semi_supervised.EntropyLattice
transducer - Variable in class cc.mallet.fst.semi_supervised.GELattice
transducer - Variable in class cc.mallet.fst.ShallowTransducerTrainer
  Deprecated.
Transducer - Class in cc.mallet.fst
  A base class for all sequence models, analogous to `classify.Classifier`.
Transducer() - Constructor for class cc.mallet.fst.Transducer
  Initializes default sum-product and max-product inference engines.
Transducer(Pipe, Pipe) - Constructor for class cc.mallet.fst.Transducer
Transducer.Incrementor - Interface in cc.mallet.fst
  Methods to be called by inference methods to indicate partial counts of sufficient statistics.
Transducer.State - Class in cc.mallet.fst
  An abstract class used to represent the states of the transducer.
Transducer.State() - Constructor for class cc.mallet.fst.Transducer.State
Transducer.TransitionIterator - Class in cc.mallet.fst
  An abstract class to iterate over the states of the transducer.
Transducer.TransitionIterator() - Constructor for class cc.mallet.fst.Transducer.TransitionIterator
TransducerConfidenceEstimator - Class in cc.mallet.fst.confidence
  Abstract class that estimates the confidence of a `Segment` extracted by a `Transducer`.
TransducerConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.TransducerConfidenceEstimator
TransducerCorrector - Interface in cc.mallet.fst.confidence
  Interface for transducerCorrectors, which correct a subset of the `Segment`s produced by a `Transducer`.
TransducerEvaluator - Class in cc.mallet.fst
  An abstract class to evaluate a transducer model.
TransducerEvaluator() - Constructor for class cc.mallet.fst.TransducerEvaluator
TransducerEvaluator(InstanceList[], String[]) - Constructor for class cc.mallet.fst.TransducerEvaluator
TransducerExtractionConfidenceEstimator - Class in cc.mallet.extract
  Estimates the confidence in the labeling of a LabeledSpan using a TransducerConfidenceEstimator.
TransducerExtractionConfidenceEstimator(TransducerConfidenceEstimator, Object[], Object[], Pipe) - Constructor for class cc.mallet.extract.TransducerExtractionConfidenceEstimator
TransducerSequenceConfidenceEstimator - Class in cc.mallet.fst.confidence
  Abstract class that estimates the confidence of a `Sequence` extracted by a `Transducer`.Note that this is different from `TransducerConfidenceEstimator`, which estimates the confidence for a single `Segment`.
TransducerSequenceConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.TransducerSequenceConfidenceEstimator
TransducerTrainer - Class in cc.mallet.fst
  An abstract class to train and evaluate a transducer model.
TransducerTrainer() - Constructor for class cc.mallet.fst.TransducerTrainer
TransducerTrainer.ByIncrements - Class in cc.mallet.fst
TransducerTrainer.ByIncrements() - Constructor for class cc.mallet.fst.TransducerTrainer.ByIncrements
TransducerTrainer.ByInstanceIncrements - Class in cc.mallet.fst
TransducerTrainer.ByInstanceIncrements() - Constructor for class cc.mallet.fst.TransducerTrainer.ByInstanceIncrements
TransducerTrainer.ByOptimization - Interface in cc.mallet.fst
transformedToken(String) - Method in class cc.mallet.share.weili.ner.WordTransformation
transGradientCache - Variable in class cc.mallet.fst.semi_supervised.GELattice
transitionIterator(Sequence, int, Sequence, int) - Method in class cc.mallet.fst.CRF.State
transitionIterator(FeatureVector, String) - Method in class cc.mallet.fst.CRF.State
transitionIterator(Sequence, int, Sequence, int) - Method in class cc.mallet.fst.FeatureTransducer.State
transitionIterator(Sequence, int) - Method in class cc.mallet.fst.FeatureTransducer.State
transitionIterator(Object) - Method in class cc.mallet.fst.FeatureTransducer.State
transitionIterator(int) - Method in class cc.mallet.fst.FeatureTransducer.State
transitionIterator() - Method in class cc.mallet.fst.FeatureTransducer.State
transitionIterator(Sequence, int, Sequence, int) - Method in class cc.mallet.fst.HMM.State
transitionIterator(Sequence, int, Sequence, int) - Method in class cc.mallet.fst.MEMM.State
transitionIterator(Sequence, int, Sequence, int) - Method in class cc.mallet.fst.Transducer.State
transitionIterator(Sequence, int) - Method in class cc.mallet.fst.Transducer.State
transitionIterator() - Method in class cc.mallet.fst.Transducer.State
transpose() - Method in class cc.mallet.types.Matrix2
  Deprecated.
Tree - Class in cc.mallet.grmm.types
  Class for arbitrary trees, based on implementation in OpenJGraph.
Tree() - Constructor for class cc.mallet.grmm.types.Tree
treeAlgs - Variable in class cc.mallet.grmm.test.TestInference
TreeBP - Class in cc.mallet.grmm.inference
  Implements the tree-based schedule of belief propagation for exact inference in trees.
TreeBP() - Constructor for class cc.mallet.grmm.inference.TreeBP
Trial - Class in cc.mallet.classify
  Stores the results of classifying a collection of Instances, and provides many methods for evaluating the results.
Trial(Classifier, InstanceList) - Constructor for class cc.mallet.classify.Trial
TrieLexiconMembership - Class in cc.mallet.pipe.tsf
TrieLexiconMembership(String, Reader, boolean) - Constructor for class cc.mallet.pipe.tsf.TrieLexiconMembership
TrieLexiconMembership(String, Reader, boolean, boolean, String) - Constructor for class cc.mallet.pipe.tsf.TrieLexiconMembership
TrieLexiconMembership(String, File, boolean) - Constructor for class cc.mallet.pipe.tsf.TrieLexiconMembership
TrieLexiconMembership(String, File, boolean, boolean, String) - Constructor for class cc.mallet.pipe.tsf.TrieLexiconMembership
TrieLexiconMembership(File, boolean) - Constructor for class cc.mallet.pipe.tsf.TrieLexiconMembership
TrieLexiconMembership(File) - Constructor for class cc.mallet.pipe.tsf.TrieLexiconMembership
trigamma(double) - Static method in class cc.mallet.types.Dirichlet
trimToSize() - Method in class cc.mallet.types.MultiInstanceList
TRP - Class in cc.mallet.grmm.inference
  Implementation of Wainwright's TRP schedule for loopy BP in general graphical models.
TRP() - Constructor for class cc.mallet.grmm.inference.TRP
TRP(TRP.TreeFactory) - Constructor for class cc.mallet.grmm.inference.TRP
TRP(TRP.TerminationCondition) - Constructor for class cc.mallet.grmm.inference.TRP
TRP(TRP.TreeFactory, TRP.TerminationCondition) - Constructor for class cc.mallet.grmm.inference.TRP
TRP.AlmostRandomTreeFactory - Class in cc.mallet.grmm.inference
  Always adds edges that have not been touched, after that adds random edges.
TRP.AlmostRandomTreeFactory() - Constructor for class cc.mallet.grmm.inference.TRP.AlmostRandomTreeFactory
TRP.ConvergenceTerminator - Class in cc.mallet.grmm.inference
TRP.ConvergenceTerminator() - Constructor for class cc.mallet.grmm.inference.TRP.ConvergenceTerminator
TRP.ConvergenceTerminator(double) - Constructor for class cc.mallet.grmm.inference.TRP.ConvergenceTerminator
TRP.DefaultConvergenceTerminator - Class in cc.mallet.grmm.inference
TRP.DefaultConvergenceTerminator() - Constructor for class cc.mallet.grmm.inference.TRP.DefaultConvergenceTerminator
TRP.DefaultConvergenceTerminator(double, int) - Constructor for class cc.mallet.grmm.inference.TRP.DefaultConvergenceTerminator
TRP.IterationTerminator - Class in cc.mallet.grmm.inference
TRP.IterationTerminator(int) - Constructor for class cc.mallet.grmm.inference.TRP.IterationTerminator
TRP.TerminationCondition - Interface in cc.mallet.grmm.inference
TRP.TreeFactory - Interface in cc.mallet.grmm.inference
  Interface for tree-generation strategies for TRP.
TRP.TreeListFactory - Class in cc.mallet.grmm.inference
  Generates spanning trees cyclically from a predefined collection.
TRP.TreeListFactory(List) - Constructor for class cc.mallet.grmm.inference.TRP.TreeListFactory
TRP.TreeListFactory(Tree[]) - Constructor for class cc.mallet.grmm.inference.TRP.TreeListFactory
TRUE_NEGATIVE - Static variable in class cc.mallet.types.ROCData
TRUE_POSITIVE - Static variable in class cc.mallet.types.ROCData
trueCounts - Variable in class cc.mallet.grmm.learning.DefaultAcrfTrainer.TestResults
TUI - Class in cc.mallet.share.mccallum.ner
TUI() - Constructor for class cc.mallet.share.mccallum.ner.TUI
TUI - Class in cc.mallet.share.weili.ner.enron
TUI() - Constructor for class cc.mallet.share.weili.ner.enron.TUI
twoNorm() - Method in class cc.mallet.types.AugmentableFeatureVector
twoNorm() - Method in interface cc.mallet.types.ConstantMatrix
twoNorm() - Method in class cc.mallet.types.DenseMatrix
twoNorm(double[]) - Static method in class cc.mallet.types.MatrixOps
twoNorm() - Method in class cc.mallet.types.SparseMatrixn
twoNorm() - Method in class cc.mallet.types.SparseVector
twoNormalize() - Method in class cc.mallet.types.DenseMatrix
twoNormalize() - Method in interface cc.mallet.types.Matrix
twoNormalize(double[]) - Static method in class cc.mallet.types.MatrixOps
twoNormalize() - Method in class cc.mallet.types.SparseMatrixn
twoNormSquared() - Method in class cc.mallet.types.Matrix2
  Deprecated.
twoNormSquared(double[]) - Static method in class cc.mallet.types.MatrixOps
typeTopicCounts - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
typeTopicCounts - Variable in class cc.mallet.topics.MarginalProbEstimator
typeTopicCounts - Variable in class cc.mallet.topics.NPTopicModel
typeTopicCounts - Variable in class cc.mallet.topics.ParallelTopicModel
typeTopicCounts - Variable in class cc.mallet.topics.SimpleLDA
typeTopicCounts - Variable in class cc.mallet.topics.TopicInferencer
typeTopicCounts - Variable in class cc.mallet.topics.WorkerRunnable

## U

UndirectedGrid - Class in cc.mallet.grmm.types
  A grid-shaped undirected graphical model.
UndirectedGrid(int, int, int) - Constructor for class cc.mallet.grmm.types.UndirectedGrid
  Creates an undirected grid and its associated Variable objects.
UndirectedModel - Class in cc.mallet.grmm.types
  Class for pairwise undirected graphical models, also known as pairwise Markov random fields.
UndirectedModel() - Constructor for class cc.mallet.grmm.types.UndirectedModel
UndirectedModel(Variable[]) - Constructor for class cc.mallet.grmm.types.UndirectedModel
UndirectedModel(int) - Constructor for class cc.mallet.grmm.types.UndirectedModel
unfreezeWeights(String) - Method in class cc.mallet.fst.CRF
  Unfreezes a set of weights.
unhideAllLabels() - Method in class cc.mallet.types.InstanceList
UNICODE_LETTERS - Static variable in class cc.mallet.util.CharSequenceLexer
UniformFactor - Class in cc.mallet.grmm.types
  $Id: UniformFactor.java,v 1.1 2007/10/22 21:37:44 mccallum Exp $
UniformFactor(Variable, double, double) - Constructor for class cc.mallet.grmm.types.UniformFactor
UniformFactor(Variable, double, double, double) - Constructor for class cc.mallet.grmm.types.UniformFactor
UniNormalFactor - Class in cc.mallet.grmm.types
  Univariate Gaussian factor.
UniNormalFactor(Variable, double, double) - Constructor for class cc.mallet.grmm.types.UniNormalFactor
union(Assignment, Assignment) - Static method in class cc.mallet.grmm.types.Assignment
  Returns the union of two Assignments.
union(Collection, Collection) - Static method in class cc.mallet.util.CollectionUtils
uniqueFile(File, String, String) - Static method in class cc.mallet.util.FileUtils
  Creates a file, making sure that its name is unique.
Univariate - Class in cc.mallet.util
Univariate(double[]) - Constructor for class cc.mallet.util.Univariate
Universe - Class in cc.mallet.grmm.types
  A global mapping between variables and indices.
Universe() - Constructor for class cc.mallet.grmm.types.Universe
UnlabeledFileIterator - Class in cc.mallet.pipe.iterator
  An iterator that generates instances from an initial directory or set of directories.
UnlabeledFileIterator(File[], FileFilter) - Constructor for class cc.mallet.pipe.iterator.UnlabeledFileIterator
  Construct a FileIterator that will supply filenames within initial directories as instances
UnlabeledFileIterator(String[], FileFilter) - Constructor for class cc.mallet.pipe.iterator.UnlabeledFileIterator
UnlabeledFileIterator(File, FileFilter) - Constructor for class cc.mallet.pipe.iterator.UnlabeledFileIterator
UnlabeledFileIterator(File) - Constructor for class cc.mallet.pipe.iterator.UnlabeledFileIterator
UnlabeledFileIterator(File[]) - Constructor for class cc.mallet.pipe.iterator.UnlabeledFileIterator
UnlabeledFileIterator(String) - Constructor for class cc.mallet.pipe.iterator.UnlabeledFileIterator
UnlabeledFileIterator(String, FileFilter) - Constructor for class cc.mallet.pipe.iterator.UnlabeledFileIterator
unLock() - Method in class cc.mallet.types.Instance
UnmodifiableVarSet - Class in cc.mallet.grmm.types
  Created: Dec 15, 2005
UnmodifiableVarSet(VarSet) - Constructor for class cc.mallet.grmm.types.UnmodifiableVarSet
unnormalizedMarginal(FactorGraph, Variable) - Method in class cc.mallet.grmm.inference.VariableElimination
  The bulk of the variable-elimination algorithm.
unroll(Instance) - Method in class cc.mallet.grmm.learning.ACRF
unrolledVarSetIterator() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
unrollStructureOnly(Instance) - Method in class cc.mallet.grmm.learning.ACRF
updateScoreMatrix(Clustering, int, int) - Method in class cc.mallet.cluster.GreedyAgglomerative
  Resets the values of clusters that have been merged.
uriStringToFilename(String) - Static method in class cc.mallet.util.UriUtils
  Convert a string-representation of a URI into a string that could be a filename.
UriUtils - Class in cc.mallet.util
UriUtils() - Constructor for class cc.mallet.util.UriUtils
USE_DEFAULT_ENGLISH_STOPLIST - Static variable in class cc.mallet.pipe.SimpleTokenizer
USE_EMPTY_STOPLIST - Static variable in class cc.mallet.pipe.SimpleTokenizer
useCaching - Variable in class cc.mallet.grmm.inference.AbstractBeliefPropagation
useGaussianPrior() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelDistribution
useGaussianPrior() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
useHyperbolicPrior() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
useNoPrior() - Method in class cc.mallet.classify.MaxEntOptimizableByLabelLikelihood
  In some cases a prior term is implemented in the optimizer, (eg orthant-wise L-BFGS), so we occasionally want to only calculate the log likelihood.
usingSymmetricAlpha - Variable in class cc.mallet.topics.ParallelTopicModel
Utils - Class in cc.mallet.grmm.inference
  A bunch of static utilities useful for dealing with Inferencers.
Utils() - Constructor for class cc.mallet.grmm.inference.Utils
UU_ENCODED_LINE - Static variable in class cc.mallet.pipe.CharSequenceRemoveUUEncodedBlocks
  Given a string, remove lines that begin with M and are 61 characters long.

## V

validationSet - Variable in class cc.mallet.classify.ClassifierTrainer
value(String) - Method in class cc.mallet.cluster.Record
value(int) - Method in class cc.mallet.cluster.Record
value(int) - Method in class cc.mallet.extract.Field
value(Assignment) - Method in class cc.mallet.grmm.types.AbstractFactor
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.AbstractFactor
value(Assignment) - Method in class cc.mallet.grmm.types.AbstractTableFactor
value(Assignment) - Method in class cc.mallet.grmm.types.BetaFactor
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.BinaryUnaryFactor
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.BoltzmannPairFactor
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.BoltzmannUnaryFactor
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.ConstantFactor
value(Assignment) - Method in class cc.mallet.grmm.types.CPT
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.CPT
value(int) - Method in class cc.mallet.grmm.types.CPT
value(int) - Method in interface cc.mallet.grmm.types.DiscreteFactor
value(Assignment) - Method in interface cc.mallet.grmm.types.Factor
  Returns the value of the local function for a given assignment.
value(AssignmentIterator) - Method in interface cc.mallet.grmm.types.Factor
  Returns the probability of an assignment to these variables.
value(Assignment) - Method in class cc.mallet.grmm.types.FactorGraph
  FACTOR IMPLEMENTATION
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.FactorGraph
value(Assignment) - Method in class cc.mallet.grmm.types.LogTableFactor
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.LogTableFactor
value(int) - Method in class cc.mallet.grmm.types.LogTableFactor
value(Assignment) - Method in class cc.mallet.grmm.types.NormalFactor
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.PottsTableFactor
value(Assignment) - Method in class cc.mallet.grmm.types.TableFactor
value(int) - Method in class cc.mallet.grmm.types.TableFactor
value(AssignmentIterator) - Method in class cc.mallet.grmm.types.TableFactor
value(Assignment) - Method in class cc.mallet.grmm.types.UniformFactor
value(Assignment) - Method in class cc.mallet.grmm.types.UniNormalFactor
value(int) - Method in class cc.mallet.types.AugmentableFeatureVector
value(int[]) - Method in interface cc.mallet.types.ConstantMatrix
value(int[]) - Method in class cc.mallet.types.DenseMatrix
value(int[]) - Method in class cc.mallet.types.DenseVector
value(int) - Method in class cc.mallet.types.DenseVector
value(Object) - Method in class cc.mallet.types.FeatureVector
value(Label) - Method in class cc.mallet.types.Label
value(int) - Method in class cc.mallet.types.Label
value(Label) - Method in interface cc.mallet.types.Labeling
value(int) - Method in interface cc.mallet.types.Labeling
value(Label) - Method in class cc.mallet.types.LabelVector
value(int, int) - Method in class cc.mallet.types.Matrix2
  Deprecated.
value(int[]) - Method in class cc.mallet.types.Matrix2
  Deprecated.
value(int[]) - Method in class cc.mallet.types.Matrixn
value(int[]) - Method in class cc.mallet.types.SparseMatrixn
value(int[]) - Method in class cc.mallet.types.SparseVector
value(int) - Method in class cc.mallet.types.SparseVector
value(int) - Method in interface cc.mallet.types.Vector
  Deprecated.
value - Variable in class cc.mallet.util.CommandOption.Boolean
value() - Method in class cc.mallet.util.CommandOption.Boolean
value - Variable in class cc.mallet.util.CommandOption.Double
value() - Method in class cc.mallet.util.CommandOption.Double
value - Variable in class cc.mallet.util.CommandOption.DoubleArray
value() - Method in class cc.mallet.util.CommandOption.DoubleArray
value - Variable in class cc.mallet.util.CommandOption.File
value() - Method in class cc.mallet.util.CommandOption.File
value - Variable in class cc.mallet.util.CommandOption.Integer
value() - Method in class cc.mallet.util.CommandOption.Integer
value - Variable in class cc.mallet.util.CommandOption.IntegerArray
value() - Method in class cc.mallet.util.CommandOption.IntegerArray
value - Variable in class cc.mallet.util.CommandOption.Object
value() - Method in class cc.mallet.util.CommandOption.Object
value() - Method in class cc.mallet.util.CommandOption.ObjectFromBean
value - Variable in class cc.mallet.util.CommandOption.Set
value() - Method in class cc.mallet.util.CommandOption.Set
value - Variable in class cc.mallet.util.CommandOption.SpacedStrings
value() - Method in class cc.mallet.util.CommandOption.SpacedStrings
value - Variable in class cc.mallet.util.CommandOption.String
value() - Method in class cc.mallet.util.CommandOption.String
valueAlphabet() - Method in class cc.mallet.cluster.Record
valueAtLocation(int) - Method in class cc.mallet.grmm.types.CPT
valueAtLocation(int) - Method in interface cc.mallet.grmm.types.DiscreteFactor
valueAtLocation(int) - Method in class cc.mallet.grmm.types.LogTableFactor
valueAtLocation(int) - Method in class cc.mallet.grmm.types.TableFactor
valueAtLocation(int) - Method in class cc.mallet.types.AugmentableFeatureVector
valueAtLocation(int) - Method in interface cc.mallet.types.ConstantMatrix
valueAtLocation(int) - Method in class cc.mallet.types.DenseMatrix
valueAtLocation(int) - Method in class cc.mallet.types.Label
valueAtLocation(int) - Method in interface cc.mallet.types.Labeling
valueAtLocation(int) - Method in class cc.mallet.types.SparseMatrixn
valueAtLocation(int) - Method in class cc.mallet.types.SparseVector
valueOfCorrectLabel() - Method in class cc.mallet.classify.Classification
values(String) - Method in class cc.mallet.cluster.Record
values(int) - Method in class cc.mallet.cluster.Record
values - Variable in class cc.mallet.types.SparseVector
valueToString() - Method in class cc.mallet.util.CommandOption.Boolean
valueToString() - Method in class cc.mallet.util.CommandOption.Double
valueToString() - Method in class cc.mallet.util.CommandOption.DoubleArray
valueToString() - Method in class cc.mallet.util.CommandOption.File
valueToString() - Method in class cc.mallet.util.CommandOption.Integer
valueToString() - Method in class cc.mallet.util.CommandOption.IntegerArray
valueToString() - Method in class cc.mallet.util.CommandOption.Object
valueToString() - Method in class cc.mallet.util.CommandOption.ObjectFromBean
valueToString() - Method in class cc.mallet.util.CommandOption.Set
valueToString() - Method in class cc.mallet.util.CommandOption.SpacedStrings
valueToString() - Method in class cc.mallet.util.CommandOption.String
valueToString() - Method in class cc.mallet.util.CommandOption
varDimensions() - Method in class cc.mallet.grmm.learning.ACRF.UnrolledVarSet
Variable - Class in cc.mallet.grmm.types
  Class for a discrete random variable in a graphical model.
Variable(LabelAlphabet) - Constructor for class cc.mallet.grmm.types.Variable
  Creates a new variable with the given outcomes.
Variable(Universe, LabelAlphabet) - Constructor for class cc.mallet.grmm.types.Variable
Variable(int) - Constructor for class cc.mallet.grmm.types.Variable
Variable(Universe, int) - Constructor for class cc.mallet.grmm.types.Variable
VariableElimination - Class in cc.mallet.grmm.inference
  The variable elimination algorithm for inference in graphical models.
VariableElimination() - Constructor for class cc.mallet.grmm.inference.VariableElimination
variablesIterator() - Method in class cc.mallet.grmm.types.FactorGraph
variablesSet() - Method in class cc.mallet.grmm.types.FactorGraph
variance(double[]) - Static method in class cc.mallet.types.MatrixOps
  Return the variance
variance() - Method in class cc.mallet.util.Univariate
variance(InstanceList, boolean) - Static method in class cc.mallet.util.VectorStats
  Returns a `SparseVector` whose entries (taken from the union of those in the instances) are the variance of those in the `InstanceList`.
variance(InstanceList, SparseVector, boolean) - Static method in class cc.mallet.util.VectorStats
  Returns a `SparseVector` whose entries (taken from the mean argument) are the variance of those in the `InstanceList`.
variance(InstanceList) - Static method in class cc.mallet.util.VectorStats
  Returns unbiased variance
variance(InstanceList, SparseVector) - Static method in class cc.mallet.util.VectorStats
  Returns unbiased variance of instances having the given mean.
varOfIndex(int, int) - Method in class cc.mallet.grmm.learning.ACRF.UnrolledGraph
varOfIndex(int, int) - Method in class cc.mallet.grmm.util.LabelsAssignment
vars - Variable in class cc.mallet.grmm.types.AbstractFactor
varSet() - Method in class cc.mallet.grmm.types.AbstractFactor
varSet() - Method in class cc.mallet.grmm.types.AbstractTableFactor
  Returns set of variables in this potential.
varSet() - Method in class cc.mallet.grmm.types.CPT
varSet() - Method in interface cc.mallet.grmm.types.Factor
  Returns set of variables in this potential.
varSet() - Method in class cc.mallet.grmm.types.FactorGraph
VarSet - Interface in cc.mallet.grmm.types
  Interface for classes that maintain a set of variables in a specified order.
varSetIterator() - Method in class cc.mallet.grmm.types.FactorGraph
  Returns an iterator of all the VarSets in the graph over which factors are defined.
Vector - Interface in cc.mallet.types
  Deprecated.
vectorAdd(SparseVector, double) - Method in class cc.mallet.types.SparseVector
Vectors2Classify - Class in cc.mallet.classify.tui
  Classify documents, run trials, print statistics from a vector file.
Vectors2Classify() - Constructor for class cc.mallet.classify.tui.Vectors2Classify
Vectors2FeatureConstraints - Class in cc.mallet.classify.tui
  Create "feature constraints" from data for use in GE training.
Vectors2FeatureConstraints() - Constructor for class cc.mallet.classify.tui.Vectors2FeatureConstraints
Vectors2Info - Class in cc.mallet.classify.tui
  Diagnostic facilities for a vector file.
Vectors2Info() - Constructor for class cc.mallet.classify.tui.Vectors2Info
Vectors2Topics - Class in cc.mallet.topics.tui
  Perform topic analysis in the style of LDA and its variants.
Vectors2Topics() - Constructor for class cc.mallet.topics.tui.Vectors2Topics
Vectors2Vectors - Class in cc.mallet.classify.tui
  A command-line tool for manipulating InstanceLists.
Vectors2Vectors() - Constructor for class cc.mallet.classify.tui.Vectors2Vectors
vectorsFile - Static variable in class cc.mallet.classify.tui.Vectors2FeatureConstraints
VectorStats - Class in cc.mallet.util
VectorStats() - Constructor for class cc.mallet.util.VectorStats
vertices() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
viewDualResults(File, Extraction, CRFExtractor, Extraction, CRFExtractor) - Static method in class cc.mallet.extract.LatticeViewer
ViterbiConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of an entire sequence by the probability of the Viterbi path normalized by the probabliity of the entire lattice.
ViterbiConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.ViterbiConfidenceEstimator
ViterbiRatioConfidenceEstimator - Class in cc.mallet.fst.confidence
  Estimates the confidence of an entire sequence by the ration of the probabilities of the first and second best Viterbi paths.
ViterbiRatioConfidenceEstimator(Transducer) - Constructor for class cc.mallet.fst.confidence.ViterbiRatioConfidenceEstimator
ViterbiWriter - Class in cc.mallet.fst
  Prints the input instances along with the features and the true and predicted labels to a file.
ViterbiWriter(String, InstanceList[], String[]) - Constructor for class cc.mallet.fst.ViterbiWriter
ViterbiWriter(String, InstanceList, String) - Constructor for class cc.mallet.fst.ViterbiWriter
ViterbiWriter(String, InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.fst.ViterbiWriter
ViterbiWriter(String, InstanceList, String, InstanceList, String, InstanceList, String) - Constructor for class cc.mallet.fst.ViterbiWriter
vocabularySizes - Variable in class cc.mallet.topics.PolylingualTopicModel

## W

wasInvoked() - Method in class cc.mallet.util.CommandOption
  Return true is this CommandOption was matched by one of the processed arguments.
weight - Variable in class cc.mallet.fst.semi_supervised.GECriterion
weight() - Method in class cc.mallet.grmm.types.BitVarSet
weight() - Method in class cc.mallet.grmm.types.HashVarSet
weight() - Method in class cc.mallet.grmm.types.ListVarSet
weight() - Method in class cc.mallet.grmm.types.UnmodifiableVarSet
weight() - Method in interface cc.mallet.grmm.types.VarSet
  Returns the number of assignments of this clique.
weight - Variable in class cc.mallet.types.SequencePairAlignment
weightAlphabet - Variable in class cc.mallet.fst.CRF.Factors
weights - Variable in class cc.mallet.fst.CRF.Factors
weights - Variable in class cc.mallet.fst.CRF.TransitionIterator
weights - Variable in class cc.mallet.grmm.learning.ACRF.Template
weightsFrozen - Variable in class cc.mallet.fst.CRF.Factors
weightsStructureChanged() - Method in class cc.mallet.fst.CRF
  This method should be called whenever the CRFs weights (parameters) have their structure/arity/number changed.
weightsStructureChangeStamp - Variable in class cc.mallet.fst.CRF
weightsValueChanged() - Method in class cc.mallet.fst.CRF
  This method should be called whenever the CRFs weights (parameters) are changed.
weightsValueChangeStamp - Variable in class cc.mallet.fst.CRF
Winnow - Class in cc.mallet.classify
  Classification methods of Winnow2 algorithm.
Winnow(Pipe, double[][], double, int, int) - Constructor for class cc.mallet.classify.Winnow
  Passes along data pipe and weights from `WinnowTrainer`
WinnowTrainer - Class in cc.mallet.classify
  An implementation of the training methods of a Winnow2 on-line classifier.
WinnowTrainer() - Constructor for class cc.mallet.classify.WinnowTrainer
  Default constructor.
WinnowTrainer(double, double) - Constructor for class cc.mallet.classify.WinnowTrainer
  Sets alpha and beta and default value for theta
WinnowTrainer(double, double, double) - Constructor for class cc.mallet.classify.WinnowTrainer
  Sets alpha, beta, and nfactor
wordsPerTopic - Variable in class cc.mallet.topics.LDAHyper
  Deprecated.
wordsPerTopic - Variable in class cc.mallet.topics.NPTopicModel
wordsPerTopic - Variable in class cc.mallet.topics.ParallelTopicModel
wordsPerTopic - Variable in class cc.mallet.topics.PolylingualTopicModel
wordsPerTopic - Variable in class cc.mallet.topics.SimpleLDA
WordTransformation - Class in cc.mallet.share.weili.ner
WordTransformation() - Constructor for class cc.mallet.share.weili.ner.WordTransformation
WordTransformation(boolean, boolean, boolean) - Constructor for class cc.mallet.share.weili.ner.WordTransformation
WorkerRunnable - Class in cc.mallet.topics
  A parallel topic model runnable task.
WorkerRunnable(int, double[], double, double, Randoms, ArrayList<TopicAssignment>, int[][], int[], int, int) - Constructor for class cc.mallet.topics.WorkerRunnable
write(File) - Method in class cc.mallet.fst.CRF
write(File) - Method in class cc.mallet.fst.HMM
write(File) - Method in class cc.mallet.share.weili.ner.enron.EnronMessage2TokenSequence
write(File) - Method in class cc.mallet.topics.LDA
  Deprecated.
write(File) - Method in class cc.mallet.topics.LDAHyper
  Deprecated.
write(File) - Method in class cc.mallet.topics.ParallelTopicModel
write(File) - Method in class cc.mallet.topics.SimpleLDA
write(File) - Method in class cc.mallet.topics.TopicalNGrams
writeCommonWords(File, int) - Method in class cc.mallet.pipe.FeatureCountPipe
  List the most common words, for addition to a stop file
writeExtraction(File, Extraction) - Static method in class cc.mallet.extract.DocumentViewer
  Writes several HTML files describing a given extraction.
writeGzippedObject(File, Serializable) - Static method in class cc.mallet.util.FileUtils
  Writes a serialized version of obj to a given file, compressing it using gzip.
writeInferredDistributions(InstanceList, File, int, int, int, double, int) - Method in class cc.mallet.topics.TopicInferencer
  Infer topics for the provided instances and write distributions to the provided file.
writeInstanceList(SimpleTokenizer) - Static method in class cc.mallet.util.BulkLoader
writeObject(File, Serializable) - Static method in class cc.mallet.util.FileUtils
  Serializes an object to a file, masking out annoying exceptions.
writeParameters(File) - Method in class cc.mallet.topics.DMRTopicModel
writePrunedWords(File, int) - Method in class cc.mallet.pipe.FeatureCountPipe
  Writes a list of features that do not occur at or above the specified cutoff to the pruned file, one per line.
writeWeightsText(Writer) - Method in class cc.mallet.grmm.learning.ACRF

## Z

zero() - Method in class cc.mallet.fst.CRF.Factors

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