Uses of Interface
de.jstacs.motifDiscovery.MotifDiscoverer

Packages that use MotifDiscoverer

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 in de.jstacs.motifDiscovery

Subinterfaces of MotifDiscoverer in de.jstacs.motifDiscovery

Modifier and Type	Interface and Description
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

Modifier and Type	Method and Description
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

Modifier and Type	Method and Description
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

Constructor and Description
SignificantMotifOccurrencesFinder(MotifDiscoverer disc, DataSet bg, double[] weights, double sign) This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a DataSet to determine the siginificance level.
SignificantMotifOccurrencesFinder(MotifDiscoverer disc, SignificantMotifOccurrencesFinder.JoinMethod joiner, DataSet bg, double[] weights, double sign) This constructor creates an instance of SignificantMotifOccurrencesFinder that uses a DataSet 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.sequenceScores.statisticalModels.differentiable

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

Modifier and Type	Class and Description
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 MotifDiscoverer in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

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

Modifier and Type	Class and Description
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 MotifDiscoverer in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif

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

Modifier and Type	Class and Description
class	ExtendedZOOPSDiffSM This class handles mixtures with at least one hidden motif.

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

Classes in de.jstacs.sequenceScores.statisticalModels.trainable.mixture.motif that implement MotifDiscoverer

Modifier and Type	Class and Description
class	HiddenMotifMixture This is the main class that every generative motif discoverer should implement.
class	ZOOPSTrainSM This class enables the user to search for a single motif in a sequence.