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## 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.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.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.motifDiscovery.MutableMotifDiscovererToolbox.InitMethodForScoringFunction
  Returns an array containing the constants of this enum type, in the order they're 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'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.
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'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 `ScoringFunction`s 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 of a `VariableLengthScoringFunction` that models sequences of arbitrary length.
VariableLengthScoringFunction(AlphabetContainer, int) - Constructor for class de.jstacs.scoringFunctions.VariableLengthScoringFunction
  This is the main constructor that creates an instance of a `VariableLengthScoringFunction` that models sequences of a given length.
VariableLengthScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.VariableLengthScoringFunction
  This is the constructor for the interface `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
  Creates a new `VarianceRatioBurnInTest` instance.
VarianceRatioBurnInTest(StringBuffer) - Constructor for class de.jstacs.models.mixture.gibbssampling.VarianceRatioBurnInTest
  The standard constructor for the `Storable` interface.
vars - Variable in class de.jstacs.classifier.scoringFunctionBased.logPrior.SeparateLogPrior
  The base variances for the parameters of the `ScoringFunction`s 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.

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