Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
 PREV LETTER   NEXT LETTER FRAMES    NO FRAMES    All Classes
A B C D E F G H I J K L M N O P Q R S T U V W X Z

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.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.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.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.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.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.
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.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.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
This array contains all values that will be set via BurnInTest.setValue(double).
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.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.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.
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
This is an interface for all DifferentiableStatisticalModels that allow to score subsequences of arbitrary length.
VariableLengthMixtureDiffSM - Class in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture
This class implements a mixture of VariableLengthDiffSM by extending MixtureDiffSM and implementing the methods of VariableLengthDiffSM.
VariableLengthMixtureDiffSM(int, boolean, VariableLengthDiffSM...) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.VariableLengthMixtureDiffSM
This constructor creates a new 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
This class allows to train any TrainableStatisticalModel on DataSets of Sequences with variable length if each individual length is at least SequenceScore.getLength().
VariableLengthWrapperTrainSM(TrainableStatisticalModel) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.VariableLengthWrapperTrainSM
This is the main constructor that creates an instance from any TrainableStatisticalModel.
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
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.classifiers.differentiableSequenceScoreBased.logPrior.SeparateLogPrior
The base variances for the parameters of the DifferentiableSequenceScores of each class, the means of the non-class parameters should be 0.
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
This class implements an ParameterSet for the viterbi training of an AbstractHMM.
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(String) - Method in class de.jstacs.utils.REnvironment
Evaluates the String as R commands.
Overview  Package  Class  Use  Tree  Deprecated   Index  Help 
 PREV LETTER   NEXT LETTER FRAMES    NO FRAMES    All Classes
A B C D E F G H I J K L M N O P Q R S T U V W X Z