Uses of Class
de.jstacs.utils.IntList

Packages that use IntList

de.jstacs.classifier.scoringFunctionBased	Provides the classes for Classifiers that are based on ScoringFunctions.
de.jstacs.models.hmm	The package provides all interfaces and classes for a hidden Markov model (HMM).
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.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer
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 IntList in de.jstacs.classifier.scoringFunctionBased

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

protected IntList[][]

SFBasedOptimizableFunction.iList These IntLists are used during the parallel computation of the gradient.

Uses of IntList in de.jstacs.models.hmm

Methods in de.jstacs.models.hmm that return types with arguments of type IntList

abstract Pair<IntList,Double>	AbstractHMM.getViterbiPathFor(int startPos, int endPos, Sequence seq)
Pair<IntList,Double>	AbstractHMM.getViterbiPathFor(Sequence seq)

Methods in de.jstacs.models.hmm with parameters of type IntList

abstract double

AbstractHMM.getLogProbForPath(IntList path, int startPos, Sequence seq)

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

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

protected IntList[]	DifferentiableHigherOrderHMM.indicesState Help array for the indexes of the parameters of the states
protected IntList[]	DifferentiableHigherOrderHMM.indicesTransition Help array for the indexes of the parameters of the transition
protected IntList	HigherOrderHMM.stateList Helper variable = only for internal use.

Methods in de.jstacs.models.hmm.models that return types with arguments of type IntList

Pair<IntList,Double>	SamplingHigherOrderHMM.getViterbiPath(int startPos, int endPos, Sequence seq, SamplingHigherOrderHMM.ViterbiComputation compute) This method returns a viterbi path that is the optimum for the choosen ViterbiComputation method
Pair<IntList,Double>	SamplingHigherOrderHMM.getViterbiPathFor(int startPos, int endPos, Sequence seq)
Pair<IntList,Double>	HigherOrderHMM.getViterbiPathFor(int startPos, int endPos, Sequence seq)

Methods in de.jstacs.models.hmm.models with parameters of type IntList

double	SamplingHigherOrderHMM.getLogProbForPath(IntList path, int startPos, Sequence seq)
double	HigherOrderHMM.getLogProbForPath(IntList path, int startPos, Sequence seq)
double	DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq, int startPos, IntList indices, DoubleList partialDer)
double	DifferentiableHigherOrderHMM.getLogScoreAndPartialDerivation(Sequence seq, IntList indices, DoubleList partialDer)
void	HigherOrderHMM.samplePath(IntList path, int startPos, int endPos, Sequence seq) This method samples a valid path for the given sequence seq using the internal parameters.
protected double	HigherOrderHMM.viterbi(IntList path, int startPos, int endPos, double weight, Sequence seq) This method computes the viterbi score of a given sequence seq.

Uses of IntList in de.jstacs.models.hmm.states

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

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 IntList in de.jstacs.models.hmm.states.emissions

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

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 IntList in de.jstacs.models.hmm.states.emissions.continuous

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

double

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

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

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

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 IntList in de.jstacs.models.hmm.transitions

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

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 IntList in de.jstacs.models.hmm.transitions.elements

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

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 IntList in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return IntList

IntList

SignificantMotifOccurrencesFinder.getStartPositions(int startPos, Sample data, int motifIndex, int addMax) This method returns a list of start positions of binding sites.

Uses of IntList in de.jstacs.scoringFunctions

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

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 IntList in de.jstacs.scoringFunctions.directedGraphicalModels

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

double

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

Uses of IntList in de.jstacs.scoringFunctions.homogeneous

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

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 IntList in de.jstacs.scoringFunctions.mix

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

protected IntList[]

AbstractMixtureScoringFunction.iList This array contains some IntLists that are used while computing the partial derivation.

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

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 IntList in de.jstacs.scoringFunctions.mix.motifSearch

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

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 IntList in de.jstacs.utils

Methods in de.jstacs.utils that return IntList

IntList

IntList.clone()