Uses of Interface
de.jstacs.motifDiscovery.MutableMotifDiscoverer

Packages that use MutableMotifDiscoverer

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.mix	Provides ScoringFunctions that are mixtures of other ScoringFunctions.
de.jstacs.scoringFunctions.mix.motifSearch

Uses of MutableMotifDiscoverer in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type MutableMotifDiscoverer

static boolean

MutableMotifDiscovererToolbox.findModification(int clazz, int motif, MutableMotifDiscoverer mmd, ScoringFunction[] score, Sample[] data, double[][] weights, SFBasedOptimizableFunction opt, DifferentiableFunction neg, byte algo, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, History hist, int minimalNewLength, boolean maxPos) This method tries to find a modification, i.e. shifting, shrinking, or expanding a motif, that is promising.

static void

MutableMotifDiscovererToolbox.initMotif(int idx, int[] classIndex, int[] motifIndex, Sample[] s, double[][] seqWeights, boolean[] adjust, MutableMotifDiscoverer[] mmd, int[] len, Sample[] data, double[][] dataWeights) This method allows to initialize a number of motifs.

Uses of MutableMotifDiscoverer in de.jstacs.scoringFunctions

Classes in de.jstacs.scoringFunctions that implement MutableMotifDiscoverer

class	IndependentProductScoringFunction This class enables the user to model parts of a sequence independent of each other.
class	MappingScoringFunction This class implements a NormalizableScoringFunction that works on mapped Sequences.

Uses of MutableMotifDiscoverer in de.jstacs.scoringFunctions.mix

Classes in de.jstacs.scoringFunctions.mix that implement MutableMotifDiscoverer

class	MixtureScoringFunction This class implements a real mixture model.
class	VariableLengthMixtureScoringFunction This class implements a mixture of VariableLengthScoringFunction by extending MixtureScoringFunction and implementing the methods of VariableLengthScoringFunction.

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

Classes in de.jstacs.scoringFunctions.mix.motifSearch that implement MutableMotifDiscoverer

class

HiddenMotifsMixture This class handles mixtures with at least one hidden motif.