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.sequenceScores.statisticalModels.differentiable	Provides all DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

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, DifferentiableSequenceScore[] score, DataSet[] data, double[][] weights, DiffSSBasedOptimizableFunction 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, DataSet[] s, double[][] seqWeights, boolean[] adjust, MutableMotifDiscoverer[] mmd, int[] len, DataSet[] data, double[][] dataWeights) This method allows to initialize a number of motifs.

Uses of MutableMotifDiscoverer in de.jstacs.sequenceScores.statisticalModels.differentiable

Classes in de.jstacs.sequenceScores.statisticalModels.differentiable that implement MutableMotifDiscoverer

class	IndependentProductDiffSM This class enables the user to model parts of a sequence independent of each other.
class	MappingDiffSM This class implements a DifferentiableStatisticalModel that works on mapped Sequences.

Uses of MutableMotifDiscoverer in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

Classes in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture that implement MutableMotifDiscoverer

class	MixtureDiffSM This class implements a real mixture model.
class	VariableLengthMixtureDiffSM This class implements a mixture of VariableLengthDiffSM by extending MixtureDiffSM and implementing the methods of VariableLengthDiffSM.

Uses of MutableMotifDiscoverer in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Classes in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif that implement MutableMotifDiscoverer

class

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