A B C D E F G H I 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.Costs.Direction

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

valueOf(String) - Static method in enum de.jstacs.algorithms.optimization.Optimizer.TerminationCondition

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.OptimizableFunction.KindOfParameter

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.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.io.SubstringFilenameFilter.PartOfName

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.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.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.

values() - Static method in enum de.jstacs.algorithms.Alignment.Costs.Direction

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

values() - Static method in enum de.jstacs.algorithms.optimization.Optimizer.TerminationCondition

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

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

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

values() - Static method in enum de.jstacs.io.SubstringFilenameFilter.PartOfName

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

values - Variable in class de.jstacs.models.mixture.gibbssampling.AbstractBurnInTest

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

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

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

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're 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

VariableLengthScoringFunction - Class in de.jstacs.scoringFunctions

This is the main class for all ScoringFunctions that allow to score subsequences of arbitrary length.

VariableLengthScoringFunction(AlphabetContainer) - Constructor for class de.jstacs.scoringFunctions.VariableLengthScoringFunction

This is the main constructor that creates an instance that models sequence s of arbitrary length.

VariableLengthScoringFunction(AlphabetContainer, int) - Constructor for class de.jstacs.scoringFunctions.VariableLengthScoringFunction

This is the main constructor that creates an instance that models sequence s of a given length.

VariableLengthScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.VariableLengthScoringFunction

This is the constructor for Storable.

VarianceRatioBurnInTest - Class in de.jstacs.models.mixture.gibbssampling

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(int) - Constructor for class de.jstacs.models.mixture.gibbssampling.VarianceRatioBurnInTest

Constructor for initialization of the VarianceRatioBurnInTest given a fixed threshold value of 1.2.

VarianceRatioBurnInTest(int, double) - Constructor for class de.jstacs.models.mixture.gibbssampling.VarianceRatioBurnInTest

Constructor for initialization of the VarianceRatioBurnInTest.

VarianceRatioBurnInTest(StringBuffer) - Constructor for class de.jstacs.models.mixture.gibbssampling.VarianceRatioBurnInTest

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

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

Evaluates the String as R commands.