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U

UniformBorderWrapper(PFMComparator.PFMDistance) - Constructor for class de.jstacs.utils.PFMComparator.UniformBorderWrapper

Creates a new PFMComparator.UniformBorderWrapper for a given PFMComparator.PFMDistance.

UniformDiffSM - Class in de.jstacs.sequenceScores.statisticalModels.differentiable

This DifferentiableStatisticalModel does nothing.

UniformDiffSM(AlphabetContainer, int, double) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.UniformDiffSM

This is the main constructor that creates an instance of a UniformDiffSM that models each sequence uniformly.

UniformDiffSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.UniformDiffSM

This is the constructor for the interface Storable.

UniformDiffSS - Class in de.jstacs.sequenceScores.differentiable

This DifferentiableSequenceScore does nothing.

UniformDiffSS(AlphabetContainer, int) - Constructor for class de.jstacs.sequenceScores.differentiable.UniformDiffSS

This is the main constructor that creates an instance of a UniformDiffSS that models each sequence uniformly.

UniformDiffSS(StringBuffer) - Constructor for class de.jstacs.sequenceScores.differentiable.UniformDiffSS

This is the constructor for the interface Storable.

UniformDurationDiffSM - Class in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

This scoring function implements a uniform distribution for positions.

UniformDurationDiffSM(int, int) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.UniformDurationDiffSM

This is the main constructor that creates an instance for the given interval.

UniformDurationDiffSM(int, int, double) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.UniformDurationDiffSM

This is the main constructor that creates an instance for the given interval and given ESS.

UniformDurationDiffSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif.UniformDurationDiffSM

This is the constructor for Storable.

UniformEmission - Class in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

This class implements a simple uniform emission.

UniformEmission(AlphabetContainer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.UniformEmission

The main constructor for a UniformEmission.

UniformEmission(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.UniformEmission

The standard constructor for the interface Storable.

UniformHomogeneousDiffSM - Class in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous

This scoring function does nothing.

UniformHomogeneousDiffSM(AlphabetContainer, double) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.UniformHomogeneousDiffSM

This is the main constructor that creates an instance of a UniformHomogeneousDiffSM that models each sequence uniformly.

UniformHomogeneousDiffSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous.UniformHomogeneousDiffSM

This is the constructor for Storable.

UniformPositionPrior - Class in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior

This prior implements a uniform distribution for the start position.

UniformPositionPrior() - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.UniformPositionPrior

This empty constructor creates an instance with motif length -1.

UniformPositionPrior(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif.positionprior.UniformPositionPrior

The standard constructor for the interface Storable.

UniformTrainSM - Class in de.jstacs.sequenceScores.statisticalModels.trainable

This class represents a uniform model.

UniformTrainSM(AlphabetContainer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.UniformTrainSM

Creates a new UniformTrainSM using a given AlphabetContainer.

UniformTrainSM(StringBuffer) - Constructor for class de.jstacs.sequenceScores.statisticalModels.trainable.UniformTrainSM

The standard constructor for the interface Storable.

union(int, int) - Method in class de.jstacs.algorithms.graphs.UnionFind

This method unions the tree that includes the node k1 with the tree that includes node k2.

union(DataSet[], boolean[]) - Static method in class de.jstacs.data.DataSet

This method unites all DataSets of the array s regarding the array in.

union(DataSet...) - Static method in class de.jstacs.data.DataSet

Unites all DataSets of the array s.

union(DataSet[], double[][], boolean[]) - Static method in class de.jstacs.data.DataSet

This method unites all DataSets of the array s regarding the array in and sets the element length in the united DataSet to subsequenceLength.

union(double[][]) - Static method in class de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.structureLearning.measures.Measure

Linearizes the arrays in the two-dimensional array ar to form a new, one-dimensional array.

UnionFind - Class in de.jstacs.algorithms.graphs

This class implements an Union-Find-algorithm with path contraction.

UnionFind(int) - Constructor for class de.jstacs.algorithms.graphs.UnionFind

Creates a new Union-Find data structure with size nodes.

UNKNOWN - Static variable in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.LogPrior

Sometimes the method Function.getDimensionOfScope() can not return a value.

UNKNOWN - Static variable in interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore

Indicates that the number of parameters of this DifferentiableSequenceScore is not known (yet).

unset() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateGaussianLogPrior

unset() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateLaplaceLogPrior

unset() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateLogPrior

Resets all internally pre-computed values, e.g.

unzip(String) - Static method in class de.jstacs.utils.Compression

De-compressed the original String from the supplied (Base64) compressed String.

usedPositions - Variable in class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint

The used positions.

useOnlyFreeParameter() - Method in class de.jstacs.classifiers.differentiableSequenceScoreBased.ScoreClassifierParameterSet

This method indicates if only the free parameters shall be used.

userSelected - Variable in class de.jstacs.parameters.AbstractSelectionParameter

true if the user has selected an item

UserTime - Class in de.jstacs.utils

This is an implementation of Time that uses a native method.

UserTime() - Constructor for class de.jstacs.utils.UserTime

USUALLY - Static variable in class de.jstacs.io.AbstractStringExtractor

The usual comment character is "#".

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