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

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.algorithms.alignment.cost.Costs.Direction

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

valueOf(String) - Static method in enum de.jstacs.classifier.MeasureParameters.Measure

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

valueOf(String) - Static method in enum de.jstacs.classifier.scoringFunctionBased.gendismix.LearningPrinciple

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

valueOf(String) - Static method in enum de.jstacs.classifier.scoringFunctionBased.OptimizableFunction.KindOfParameter

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

valueOf(String) - Static method in enum de.jstacs.classifier.scoringFunctionBased.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.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.Sample.PartitionMethod

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

valueOf(String) - Static method in enum de.jstacs.data.Sample.WeightedSampleFactory.SortOperation

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.models.discrete.inhomogeneous.StructureLearner.LearningType

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

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

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

valueOf(String) - Static method in enum de.jstacs.models.hmm.HMMFactory.HMMType

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

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

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

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

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

valueOf(String) - Static method in enum de.jstacs.models.mixture.AbstractMixtureModel.Algorithm

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

valueOf(String) - Static method in enum de.jstacs.models.mixture.AbstractMixtureModel.Parameterization

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.InitMethodForScoringFunction

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.scoringFunctions.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.scoringFunctions.mix.StrandScoringFunction.InitMethod

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.algorithms.alignment.cost.Costs.Direction

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

values() - Static method in enum de.jstacs.classifier.MeasureParameters.Measure

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

values() - Static method in enum de.jstacs.classifier.scoringFunctionBased.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.classifier.scoringFunctionBased.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.classifier.scoringFunctionBased.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.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.Sample.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.Sample.WeightedSampleFactory.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.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.models.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.models.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.models.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.models.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.models.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.models.mixture.AbstractMixtureModel.Algorithm

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

values() - Static method in enum de.jstacs.models.mixture.AbstractMixtureModel.Parameterization

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.InitMethodForScoringFunction

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.scoringFunctions.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.scoringFunctions.mix.StrandScoringFunction.InitMethod

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

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

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

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

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

VariableLengthMixtureScoringFunction - Class in de.jstacs.scoringFunctions.mix

This class implements a mixture of VariableLengthScoringFunction by extending MixtureScoringFunction and implementing the methods of VariableLengthScoringFunction.

VariableLengthMixtureScoringFunction(int, boolean, VariableLengthScoringFunction...) - Constructor for class de.jstacs.scoringFunctions.mix.VariableLengthMixtureScoringFunction

This constructor creates a new VariableLengthMixtureScoringFunction.

VariableLengthMixtureScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.mix.VariableLengthMixtureScoringFunction

This is the constructor for the interface Storable.

VariableLengthScoringFunction - Interface in de.jstacs.scoringFunctions

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

VariableLengthWrapperModel - Class in de.jstacs.models

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

VariableLengthWrapperModel(Model) - Constructor for class de.jstacs.models.VariableLengthWrapperModel

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

VariableLengthWrapperModel(StringBuffer) - Constructor for class de.jstacs.models.VariableLengthWrapperModel

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.classifier.scoringFunctionBased.logPrior.SeparateLogPrior

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

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

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

ViterbiParameterSet - Class in de.jstacs.models.hmm.training

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

ViterbiParameterSet() - Constructor for class de.jstacs.models.hmm.training.ViterbiParameterSet

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

ViterbiParameterSet(int, AbstractTerminationCondition) - Constructor for class de.jstacs.models.hmm.training.ViterbiParameterSet

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

ViterbiParameterSet(StringBuffer) - Constructor for class de.jstacs.models.hmm.training.ViterbiParameterSet

The standard constructor for the interface Storable.

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

Evaluates the String as R commands.