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.mixture.gibbssampling	This package contains many classes that can be used while a Gibbs 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.mixture.gibbssampling

Fields in de.jstacs.models.mixture.gibbssampling 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	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.