Uses of Interface
de.jstacs.motifDiscovery.MotifDiscoverer

Packages that use MotifDiscoverer

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 in de.jstacs.models.mixture.motif

Classes in de.jstacs.models.mixture.motif that implement MotifDiscoverer

class	HiddenMotifMixture This is the main class that every generative motif discoverer should implement.
class	SingleHiddenMotifMixture This class enables the user to search for a single motif in a sequence.

Uses of MotifDiscoverer in de.jstacs.motifDiscovery

Subinterfaces of MotifDiscoverer in de.jstacs.motifDiscovery

interface

MutableMotifDiscoverer This is the interface that any tool for de-novo motif discovery should implement that allows any modify-operations like shift, shrink and expand.

Methods in de.jstacs.motifDiscovery that return MotifDiscoverer

MotifDiscoverer	MotifDiscoverer.clone() This method returns a deep clone of the instance.
MotifDiscoverer	SignificantMotifOccurrencesFinder.getMotifDiscoverer() This method returns a clone of the internally used MotifDiscoverer.

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

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.

Constructors in de.jstacs.motifDiscovery with parameters of type MotifDiscoverer

SignificantMotifOccurrencesFinder(MotifDiscoverer disc, Sample bg, double[] weights, double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a Sample to determine the siginificance level.

SignificantMotifOccurrencesFinder(MotifDiscoverer disc, SignificantMotifOccurrencesFinder.JoinMethod joiner, Sample bg, double[] weights, double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a Sample to determine the siginificance level.

SignificantMotifOccurrencesFinder(MotifDiscoverer disc, SignificantMotifOccurrencesFinder.RandomSeqType type, boolean oneHistogram, int numSequences, double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses the given SignificantMotifOccurrencesFinder.RandomSeqType to determine the siginificance level.

SignificantMotifOccurrencesFinder(MotifDiscoverer disc, SignificantMotifOccurrencesFinder.RandomSeqType type, SignificantMotifOccurrencesFinder.JoinMethod joiner, boolean oneHistogram, int numSequences, double sign)
This constructor creates an instance of SignificantMotifOccurrencesFinder that uses the given SignificantMotifOccurrencesFinder.RandomSeqType to determine the siginificance level.

Uses of MotifDiscoverer in de.jstacs.scoringFunctions

Classes in de.jstacs.scoringFunctions that implement MotifDiscoverer

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 MotifDiscoverer in de.jstacs.scoringFunctions.mix

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

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 MotifDiscoverer in de.jstacs.scoringFunctions.mix.motifSearch

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

class

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