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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 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 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 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.
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