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

Packages that use MotifDiscoverer.KindOfProfile

de.jstacs.models.mixture.motif
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 MotifDiscoverer.KindOfProfile in de.jstacs.models.mixture.motif

Methods in de.jstacs.models.mixture.motif with parameters of type MotifDiscoverer.KindOfProfile

double[]

SingleHiddenMotifMixture.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.motifDiscovery

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

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

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.scoringFunctions

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

double[]	MappingScoringFunction.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)
double[]	IndependentProductScoringFunction.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.scoringFunctions.mix

Methods in de.jstacs.scoringFunctions.mix with parameters of type MotifDiscoverer.KindOfProfile

double[]

MixtureScoringFunction.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile kind)

Uses of MotifDiscoverer.KindOfProfile in de.jstacs.scoringFunctions.mix.motifSearch

Methods in de.jstacs.scoringFunctions.mix.motifSearch with parameters of type MotifDiscoverer.KindOfProfile

double[]

HiddenMotifsMixture.getProfileOfScoresFor(int component, int motif, Sequence sequence, int startpos, MotifDiscoverer.KindOfProfile dist)