Uses of Class
de.jstacs.utils.DoubleList

Packages that use DoubleList

de.jstacs.classifier.scoringFunctionBased	Provides the classes for Classifiers that are based on ScoringFunctions.
de.jstacs.models.hmm.models	The package provides different implementations of hidden Markov models based on AbstractHMM
de.jstacs.models.hmm.states	The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.models.hmm.states.emissions
de.jstacs.models.hmm.states.emissions.continuous
de.jstacs.models.hmm.states.emissions.discrete
de.jstacs.models.hmm.transitions	The package provides all interfaces and classes for transitions used in hidden Markov models.
de.jstacs.models.hmm.transitions.elements
de.jstacs.sampling	This package contains many classes that can be used while a sampling.
de.jstacs.scoringFunctions	Provides ScoringFunctions that can be used in a ScoreClassifier.
de.jstacs.scoringFunctions.directedGraphicalModels	Provides ScoringFunctions that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.homogeneous	Provides ScoringFunctions that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix	Provides ScoringFunctions that are mixtures of other ScoringFunctions.
de.jstacs.scoringFunctions.mix.motifSearch
de.jstacs.utils	This package contains a bundle of useful classes and interfaces like ...

Uses of DoubleList in de.jstacs.classifier.scoringFunctionBased

Fields in de.jstacs.classifier.scoringFunctionBased declared as DoubleList

protected DoubleList[][]

SFBasedOptimizableFunction.dList These DoubleLists are used during the parallel computation of the gradient.

Uses of DoubleList in de.jstacs.models.hmm.models

Fields in de.jstacs.models.hmm.models declared as DoubleList

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.models.hmm.models with parameters of type DoubleList

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.models.hmm.states

Methods in de.jstacs.models.hmm.states with parameters of type DoubleList

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.models.hmm.states.emissions

Methods in de.jstacs.models.hmm.states.emissions with parameters of type DoubleList

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.models.hmm.states.emissions.continuous

Methods in de.jstacs.models.hmm.states.emissions.continuous with parameters of type DoubleList

double

GaussianEmission.getLogProbAndPartialDerivationFor(boolean forward, int startPos, int endPos, IntList indices, DoubleList partDer, Sequence seq)

Uses of DoubleList in de.jstacs.models.hmm.states.emissions.discrete

Methods in de.jstacs.models.hmm.states.emissions.discrete with parameters of type DoubleList

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.models.hmm.transitions

Methods in de.jstacs.models.hmm.transitions with parameters of type DoubleList

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.models.hmm.transitions.elements

Methods in de.jstacs.models.hmm.transitions.elements with parameters of type DoubleList

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.sampling

Fields in de.jstacs.sampling declared as DoubleList

protected DoubleList[]

AbstractBurnInTest.values This array contains all values that will be set via BurnInTest.setValue(double).

Uses of DoubleList in de.jstacs.scoringFunctions

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

double	VariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList) This method computes the logarithm of the score and the partial derivations for a given subsequence.
double	CMMScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)
double	UniformScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)
double	ScoringFunction.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	NormalizedScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	MRFScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	MappingScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	IndependentProductScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	AbstractVariableLengthScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)
double	ScoringFunction.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	AbstractNormalizableScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)

Uses of DoubleList in de.jstacs.scoringFunctions.directedGraphicalModels

Methods in de.jstacs.scoringFunctions.directedGraphicalModels with parameters of type DoubleList

double

BayesianNetworkScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)

Uses of DoubleList in de.jstacs.scoringFunctions.homogeneous

Methods in de.jstacs.scoringFunctions.homogeneous with parameters of type DoubleList

double	UniformHomogeneousScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)
double	HMMScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)
double	HMM0ScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList dList)

Uses of DoubleList in de.jstacs.scoringFunctions.mix

Fields in de.jstacs.scoringFunctions.mix declared as DoubleList

protected DoubleList[]

AbstractMixtureScoringFunction.dList This array contains some DoubleLists that are used while computing the partial derivation.

Methods in de.jstacs.scoringFunctions.mix with parameters of type DoubleList

double	VariableLengthMixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList partialDer)
double	StrandScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	MixtureScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)

Uses of DoubleList in de.jstacs.scoringFunctions.mix.motifSearch

Methods in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type DoubleList

double	UniformDurationScoringFunction.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)
double	SkewNormalLikeScoringFunction.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)
abstract double	PositionScoringFunction.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	MixtureDuration.getLogScoreAndPartialDerivation(IntList indices, DoubleList partialDer, int... values)
double	PositionScoringFunction.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	HiddenMotifsMixture.getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)
double	PositionScoringFunction.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.utils

Methods in de.jstacs.utils that return DoubleList

DoubleList

DoubleList.clone()

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

void	DoubleList.addAll(DoubleList list2) This method adds all elements of DoubleList list2 to the current list.