Uses of Class
de.jstacs.motifDiscovery.MotifDiscoverer.KindOfProfile

Packages that use MotifDiscoverer.KindOfProfile

Package	Description
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
de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return MotifDiscoverer.KindOfProfile

Modifier and Type	Method and Description
static MotifDiscoverer.KindOfProfile	MotifDiscoverer.KindOfProfile.valueOf(String name) Returns the enum constant of this type with the specified name.
static MotifDiscoverer.KindOfProfile[]	MotifDiscoverer.KindOfProfile.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in de.jstacs.motifDiscovery with parameters of type MotifDiscoverer.KindOfProfile

Modifier and Type	Method and Description
double[]	MotifDiscoverer.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind) Returns the profile of the scores for component component and motif motif at all possible start positions of the motif in the sequence sequence beginning at startpos.
static ImageResult	MotifDiscovererToolBox.plot(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, MotifDiscoverer.KindOfProfile kind) This method creates a simple plot of the profile of scores for a sequence and a start position.
static ImageResult	MotifDiscovererToolBox.plotAndAnnotate(MotifDiscoverer motifDisc, int component, int motif, Sequence sequence, int startpos, REnvironment r, int width, int height, double yMin, double yMax, double threshold, MotifDiscoverer.KindOfProfile kind) This method creates a plot of the profile of scores for a sequence and a start position and annotates bindings sites in the plot that have a higher score than threshold.

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.sequenceScores.statisticalModels.differentiable

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable with parameters of type MotifDiscoverer.KindOfProfile

Modifier and Type	Method and Description
double[]	MappingDiffSM.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)
double[]	IndependentProductDiffSM.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture with parameters of type MotifDiscoverer.KindOfProfile

Modifier and Type	Method and Description
double[]	MixtureDiffSM.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif with parameters of type MotifDiscoverer.KindOfProfile

Modifier and Type	Method and Description
double[]	ExtendedZOOPSDiffSM.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif

Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif with parameters of type MotifDiscoverer.KindOfProfile

Modifier and Type	Method and Description
double[]	ZOOPSTrainSM.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)