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.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   
 

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.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 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.