- 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.classifiers.differentiableSequenceScoreBased.gendismix.LearningPrinciple
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.classifiers.differentiableSequenceScoreBased.OptimizableFunction.KindOfParameter
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.classifiers.differentiableSequenceScoreBased.sampling.SamplingScoreBasedClassifier.SamplingScheme
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.classifiers.performanceMeasures.CorrelationCoefficient.Method
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.clustering.hierachical.Hclust.Linkage
-
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.DataSet.PartitionMethod
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.data.DataSet.WeightedDataSetFactory.SortOperation
-
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.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.RegExFilenameFilter.Directory
-
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.InitMethodForDiffSM
-
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.sequenceScores.statisticalModels.differentiable.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.sequenceScores.statisticalModels.differentiable.localMixture.LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder.PriorType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.StrandDiffSM.InitMethod
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.ConstraintManager.Decomposition
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.StructureLearner.LearningType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.StructureLearner.ModelType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.hmm.HMMFactory.HMMType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.SamplingHigherOrderHMM.ViterbiComputation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Algorithm
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Parameterization
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.utils.graphics.GraphicsAdaptorFactory.OutputFormat
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum de.jstacs.utils.ToolBox.TiedRanks
-
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.classifiers.differentiableSequenceScoreBased.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.classifiers.differentiableSequenceScoreBased.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.classifiers.differentiableSequenceScoreBased.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.classifiers.performanceMeasures.CorrelationCoefficient.Method
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum de.jstacs.clustering.hierachical.Hclust.Linkage
-
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.DataSet.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.DataSet.WeightedDataSetFactory.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.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.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.io.RegExFilenameFilter.Directory
-
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.InitMethodForDiffSM
-
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
-
- values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.differentiable.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.sequenceScores.statisticalModels.differentiable.localMixture.LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder.PriorType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.StrandDiffSM.InitMethod
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.discrete.ConstraintManager.Decomposition
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.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.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Algorithm
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum de.jstacs.sequenceScores.statisticalModels.trainable.mixture.AbstractMixtureTrainSM.Parameterization
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum de.jstacs.utils.graphics.GraphicsAdaptorFactory.OutputFormat
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum de.jstacs.utils.ToolBox.TiedRanks
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- valuesToString() - Method in class de.jstacs.parameters.MultiSelectionParameter
-
- 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
-
- VariableLengthDiffSM - Interface in de.jstacs.sequenceScores.statisticalModels.differentiable
-
- VariableLengthMixtureDiffSM - Class in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture
-
- VariableLengthMixtureDiffSM(int, boolean, VariableLengthDiffSM...) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.VariableLengthMixtureDiffSM
-
- VariableLengthMixtureDiffSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.VariableLengthMixtureDiffSM
-
This is the constructor for the interface
Storable
.
- VariableLengthWrapperTrainSM - Class in de.jstacs.sequenceScores.statisticalModels.trainable
-
- VariableLengthWrapperTrainSM(TrainableStatisticalModel) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.VariableLengthWrapperTrainSM
-
- VariableLengthWrapperTrainSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.VariableLengthWrapperTrainSM
-
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
-
- VarianceRatioBurnInTest(StringBuffer) - Constructor for class de.jstacs.sampling.VarianceRatioBurnInTest
-
The standard constructor for the
Storable
interface.
- VarianceRatioBurnInTestParameterSet - Class in de.jstacs.sampling
-
- VarianceRatioBurnInTestParameterSet() - Constructor for class de.jstacs.sampling.VarianceRatioBurnInTestParameterSet
-
- VarianceRatioBurnInTestParameterSet(int, double) - Constructor for class de.jstacs.sampling.VarianceRatioBurnInTestParameterSet
-
- VarianceRatioBurnInTestParameterSet(StringBuffer) - Constructor for class de.jstacs.sampling.VarianceRatioBurnInTestParameterSet
-
The standard constructor for the interface
Storable
.
- vars - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateLogPrior
-
The base variances for the parameters of the
DifferentiableSequenceScore
s of
each class, the means of the non-class parameters should be 0.
- vars2 - Variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateGaussianLogPrior
-
The variances
- viterbi(IntList, int, int, double, Sequence) - Method in class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models.HigherOrderHMM
-
This method computes the viterbi score of a given sequence seq
.
- ViterbiParameterSet - Class in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training
-
- ViterbiParameterSet() - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.ViterbiParameterSet
-
This is the empty constructor that can be used to fill the parameters after creation.
- ViterbiParameterSet(int, AbstractTerminationCondition, int) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.ViterbiParameterSet
-
This constructor can be used to create an instance with specified parameters.
- ViterbiParameterSet(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.training.ViterbiParameterSet
-
The standard constructor for the interface
Storable
.
- voidEval(CharSequence) - Method in class de.jstacs.utils.REnvironment
-
Evaluates the
String
as R commands.