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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.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 `NormalizableScoringFunction`s that allow to score subsequences of arbitrary length.
VariableLengthWrapperModel - Class in de.jstacs.models
  This class allows to train any `Model` on `Sample`s of `Sequence`s 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 `ScoringFunction`s 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.

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