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

V

validator - Variable in class de.jstacs.parameters.SimpleParameter

The validator for the parameter values

value - Variable in class de.jstacs.parameters.SimpleParameter

The current value of the parameter

valueOf(String) - Static method in enum de.jstacs.algorithms.alignment.Alignment.AlignmentType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.LearningPrinciple

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction.KindOfParameter

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier.SamplingScheme

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.data.AlphabetContainer.AlphabetContainerType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.data.DataSet.PartitionMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.data.DataSet.WeightedDataSetFactory.SortOperation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.data.DinucleotideProperty.HowCreated

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.data.DinucleotideProperty.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.data.DinucleotideProperty

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength.Strand

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.DataType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.io.RegExFilenameFilter.Directory

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.motifDiscovery.MotifDiscoverer.KindOfProfile

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.motifDiscovery.MutableMotifDiscovererToolbox.InitMethodForDiffSM

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder.RandomSeqType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.parameters.RangeParameter.RangeType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.parameters.RangeParameter.Scale

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.DataSource

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.StrandDiffSM.InitMethod

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.ConstraintManager.Decomposition

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.StructureLearner.LearningType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.StructureLearner.ModelType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory.HMMType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM.Type

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.SamplingHigherOrderHMM.ViterbiComputation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Algorithm

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Parameterization

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.jstacs.utils.ToolBox.TiedRanks

Returns the enum constant of this type with the specified name.

values() - Static method in enum de.jstacs.algorithms.alignment.Alignment.AlignmentType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix.LearningPrinciple

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction.KindOfParameter

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier.SamplingScheme

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.data.AlphabetContainer.AlphabetContainerType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.data.DataSet.PartitionMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.data.DataSet.WeightedDataSetFactory.SortOperation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.data.DinucleotideProperty.HowCreated

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.data.DinucleotideProperty.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.data.DinucleotideProperty

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.data.sequences.annotation.SinglePositionSequenceAnnotation.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength.Strand

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.DataType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.io.RegExFilenameFilter.Directory

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.motifDiscovery.MotifDiscoverer.KindOfProfile

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.motifDiscovery.MutableMotifDiscovererToolbox.InitMethodForDiffSM

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.motifDiscovery.SignificantMotifOccurrencesFinder.RandomSeqType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.parameters.RangeParameter.RangeType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.parameters.RangeParameter.Scale

Returns an array containing the constants of this enum type, in the order they are declared.

values - Variable in class de.jstacs.sampling.AbstractBurnInTest

This array contains all values that will be set via BurnInTest.setValue(double).

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.DataSource

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.StrandDiffSM.InitMethod

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.ConstraintManager.Decomposition

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.StructureLearner.LearningType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.StructureLearner.ModelType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory.HMMType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM.Type

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.SamplingHigherOrderHMM.ViterbiComputation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Algorithm

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Parameterization

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum de.jstacs.utils.ToolBox.TiedRanks

Returns an array containing the constants of this enum type, in the order they are declared.

valuesToString() - Method in class de.jstacs.parameters.MultiSelectionParameter

valuesToString() - Method in interface de.jstacs.parameters.RangeIterator

Returns a String representation of the set of values.

valuesToString() - Method in class de.jstacs.parameters.RangeParameter

VariableLengthDiffSM - Interface in de.jstacs.sequenceScores.statisticalModels.differentiable

This is an interface for all DifferentiableStatisticalModels that allow to score subsequences of arbitrary length.

VariableLengthMixtureDiffSM - Class in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

This class implements a mixture of VariableLengthDiffSM by extending MixtureDiffSM and implementing the methods of VariableLengthDiffSM.

VariableLengthMixtureDiffSM(int, boolean, VariableLengthDiffSM...) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.VariableLengthMixtureDiffSM

This constructor creates a new VariableLengthMixtureDiffSM.

VariableLengthMixtureDiffSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.VariableLengthMixtureDiffSM

This is the constructor for the interface Storable.

VariableLengthWrapperTrainSM - Class in de.jstacs.sequenceScores.statisticalModels.trainable

This class allows to train any TrainableStatisticalModel on DataSets of Sequences with variable length if each individual length is at least SequenceScore.getLength().

VariableLengthWrapperTrainSM(TrainableStatisticalModel) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.VariableLengthWrapperTrainSM

This is the main constructor that creates an instance from any TrainableStatisticalModel.

VariableLengthWrapperTrainSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.VariableLengthWrapperTrainSM

The standard constructor for the interface Storable.

VarianceRatioBurnInTest - Class in de.jstacs.sampling

In this class the Variance-Ratio method of Gelman and Rubin is implemented to test the length of the burn-in phase of a multi-chain Gibbs Sampling (number of chains >2).

VarianceRatioBurnInTest(VarianceRatioBurnInTestParameterSet) - Constructor for class de.jstacs.sampling.VarianceRatioBurnInTest

Creates a new VarianceRatioBurnInTest instance.

VarianceRatioBurnInTest(StringBuffer) - Constructor for class de.jstacs.sampling.VarianceRatioBurnInTest

The standard constructor for the Storable interface.

VarianceRatioBurnInTestParameterSet - Class in de.jstacs.sampling

Class for the parameters of a VarianceRatioBurnInTest.

VarianceRatioBurnInTestParameterSet() - Constructor for class de.jstacs.sampling.VarianceRatioBurnInTestParameterSet

Creates a new VarianceRatioBurnInTestParameterSet with empty parameter values.

VarianceRatioBurnInTestParameterSet(int, double) - Constructor for class de.jstacs.sampling.VarianceRatioBurnInTestParameterSet

Creates a new VarianceRatioBurnInTestParameterSet with pre-defined parameter values.

VarianceRatioBurnInTestParameterSet(StringBuffer) - Constructor for class de.jstacs.sampling.VarianceRatioBurnInTestParameterSet

The standard constructor for the interface Storable.

vars - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateLogPrior

The base variances for the parameters of the DifferentiableSequenceScores of each class, the means of the non-class parameters should be 0.

viterbi(IntList, int, int, double, Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM

This method computes the viterbi score of a given sequence seq.

ViterbiParameterSet - Class in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training

This class implements an ParameterSet for the viterbi training of an AbstractHMM.

ViterbiParameterSet() - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.ViterbiParameterSet

This is the empty constructor that can be used to fill the parameters after creation.

ViterbiParameterSet(int, AbstractTerminationCondition, int) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.ViterbiParameterSet

This constructor can be used to create an instance with specified parameters.

ViterbiParameterSet(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.ViterbiParameterSet

The standard constructor for the interface Storable.

voidEval(CharSequence) - Method in class de.jstacs.utils.REnvironment

Evaluates the String as R commands.