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   
 

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.