Uses of Class
de.jstacs.utils.DoubleList

Packages that use DoubleList

Package	Description
de.jstacs.classifiers.differentiableSequenceScoreBased	Provides the classes for Classifiers that are based on SequenceScores. It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior.
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer.
de.jstacs.sampling	This package contains many classes that can be used while a sampling.
de.jstacs.sequenceScores.differentiable
de.jstacs.sequenceScores.differentiable.logistic
de.jstacs.sequenceScores.statisticalModels.differentiable	Provides all DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels	Provides DifferentiableStatisticalModels that are directed graphical models.
de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous	Provides DifferentiableStatisticalModels that are homogeneous, i.e.
de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models	The package provides different implementations of hidden Markov models based on AbstractHMM.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states	The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions	The package provides all interfaces and classes for transitions used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

Uses of DoubleList in de.jstacs.classifiers.differentiableSequenceScoreBased

Fields in de.jstacs.classifiers.differentiableSequenceScoreBased declared as DoubleList

Modifier and Type	Field and Description
protected DoubleList[][]	DiffSSBasedOptimizableFunction.dList These DoubleLists are used during the parallel computation of the gradient.

Uses of DoubleList in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type DoubleList

Modifier and Type	Method and Description
Pair<double[][],double[]>	SignificantMotifOccurrencesFinder.getPWMAndPosDist(int motif, DataSet data, double[] weights, double[] mean, int addLeft, int addRight, LinkedList<Sequence> bs, DoubleList bsWeight, DoubleList bsScores) Returns the position weight matrix and standard deviation of the position distribution using the given mean.
protected double[][]	SignificantMotifOccurrencesFinder.getPWMAndPositions(int motif, DataSet data, double[] weights, int addLeft, int addRight, int[][] positions, double[][] pvals, double[] mean, double[] sd, LinkedList<Sequence> bs, DoubleList bsWeights, DoubleList bsScores) Returns the Position weight matrix (PWM) of the binding sites of motif motif in the data set data of the MotifDiscoverer of this SignificantMotifOccurrencesFinder and fills with the positions of the binding sites within the sequences of data and the corresponding p-values into the corresponding arrays.

Uses of DoubleList in de.jstacs.sampling

Fields in de.jstacs.sampling declared as DoubleList

Modifier and Type	Field and Description
protected DoubleList[]	AbstractBurnInTest.values This array contains all values that will be set via BurnInTest.setValue(double).

Uses of DoubleList in de.jstacs.sequenceScores.differentiable

Methods in de.jstacs.sequenceScores.differentiable with parameters of type DoubleList

Modifier and Type	Method and Description
double	DifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList partialDer) Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.
double	AbstractDifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer)
double	UniformDiffSS.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)
double	MultiDimensionalSequenceWrapperDiffSS.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	IndependentProductDiffSS.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	DifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer) Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.
double	DifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer) Returns the logarithmic score for a Sequence seq and fills lists with the indices and the partial derivations.
double	AbstractDifferentiableSequenceScore.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)

Uses of DoubleList in de.jstacs.sequenceScores.differentiable.logistic

Methods in de.jstacs.sequenceScores.differentiable.logistic with parameters of type DoubleList

Modifier and Type	Method and Description
double	LogisticDiffSS.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable with parameters of type DoubleList

Modifier and Type	Method and Description
double	VariableLengthDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer)
double	CyclicMarkovModelDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList dList)
abstract double	AbstractVariableLengthDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer)
double	UniformDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)
double	NormalizedDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	MarkovRandomFieldDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	MappingDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	AbstractVariableLengthDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels with parameters of type DoubleList

Modifier and Type	Method and Description
double	BayesianNetworkDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.homogeneous with parameters of type DoubleList

Modifier and Type	Method and Description
double	UniformHomogeneousDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList dList)
double	HomogeneousMMDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList dList)
double	HomogeneousMM0DiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList dList)

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.localMixture with parameters of type DoubleList

Modifier and Type	Method and Description
double	LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

Fields in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture declared as DoubleList

Modifier and Type	Field and Description
protected DoubleList[]	AbstractMixtureDiffSM.dList This array contains some DoubleLists that are used while computing the partial derivation.

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture with parameters of type DoubleList

Modifier and Type	Method and Description
double	VariableLengthMixtureDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, int end, IntList indices, DoubleList partialDer)
double	StrandDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	MixtureDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif with parameters of type DoubleList

Modifier and Type	Method and Description
double	UniformDurationDiffSM.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)
double	SkewNormalLikeDurationDiffSM.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)
abstract double	PositionDiffSM.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values) This method enables the user to get the log-score and the partial derivations without using a sequence object.
double	MixtureDurationDiffSM.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)
double	PositionDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	ExtendedZOOPSDiffSM.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	PositionDiffSM.getLogScoreAndPartialDerivationForInternal(IntList indices, DoubleList partialDer) This method enables the user to get the log-score and the partial derivations without using a sequence object by using the internal iterator.

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models

Fields in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models declared as DoubleList

Modifier and Type	Field and Description
protected DoubleList[]	DifferentiableHigherOrderHMM.partDerState Help array for the derivatives of the parameters of the states
protected DoubleList[]	DifferentiableHigherOrderHMM.partDerTransition Help array for the derivatives of the parameters of the transition

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.models with parameters of type DoubleList

Modifier and Type	Method and Description
double	DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq, int startPos, int endPos, IntList indices, DoubleList partialDer)
double	DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq, int startPos, IntList indices, DoubleList partialDer)
double	DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states with parameters of type DoubleList

Modifier and Type	Method and Description
double	SimpleDifferentiableState.getLogScoreAndPartialDerivation(int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)
double	DifferentiableState.getLogScoreAndPartialDerivation(int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq) This method allows to compute the logarithm of the score and the gradient for the given subsequences.

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions with parameters of type DoubleList

Modifier and Type	Method and Description
double	UniformEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)
double	SilentEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)
double	DifferentiableEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq) Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous with parameters of type DoubleList

Modifier and Type	Method and Description
double	GaussianEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete with parameters of type DoubleList

Modifier and Type	Method and Description
double	PhyloDiscreteEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)
double	AbstractConditionalDiscreteEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions with parameters of type DoubleList

Modifier and Type	Method and Description
double	HigherOrderTransition.getLogScoreAndPartialDerivation(int layer, int index, int childIdx, IntList indices, DoubleList partDer, Sequence sequence, int sequencePosition)
double	DifferentiableTransition.getLogScoreAndPartialDerivation(int layer, int index, int childIdx, IntList indices, DoubleList partDer, Sequence sequence, int sequencePosition) This method allows to compute the logarithm of the score and the gradient for a specific transition.

Uses of DoubleList in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements with parameters of type DoubleList

Modifier and Type	Method and Description
double	TransitionElement.getLogScoreAndPartialDerivation(int childIdx, IntList indices, DoubleList partialDer, Sequence sequence, int sequencePosition) Returns the logarithmic score and fills lists with the indices and the partial derivations.

Uses of DoubleList in de.jstacs.utils

Methods in de.jstacs.utils that return DoubleList

Modifier and Type	Method and Description
DoubleList	DoubleList.clone()

Methods in de.jstacs.utils with parameters of type DoubleList

Modifier and Type	Method and Description
void	DoubleList.addAll(DoubleList list2) This method adds all elements of DoubleList list2 to the current list.