Uses of Package
de.jstacs.motifDiscovery

Packages that use de.jstacs.motifDiscovery

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.directedGraphicalModels	Provides ScoringFunctions that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.mix	Provides ScoringFunctions that are mixtures of other ScoringFunctions.
de.jstacs.scoringFunctions.mix.motifSearch

Classes in de.jstacs.motifDiscovery used by de.jstacs.models.mixture.motif

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.

Classes in de.jstacs.motifDiscovery used by de.jstacs.motifDiscovery

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.

MotifDiscovererToolBox
This class contains static methods for the MotifDiscoverer.

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.

MutableMotifDiscovererToolbox.InitMethodForScoringFunction
This enum defines some constants for the method MutableMotifDiscovererToolbox.getSortedInitialParameters(ScoringFunction[], InitMethodForScoringFunction[], SFBasedOptimizableFunction, int, OutputStream, int).

SignificantMotifOccurrencesFinder.JoinMethod
Interface for methods that combine several profiles over the same sequence into one common profile

SignificantMotifOccurrencesFinder.RandomSeqType

Classes in de.jstacs.motifDiscovery used by de.jstacs.scoringFunctions

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.

Mutable
This interface allows to modify a motif model.

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.

Classes in de.jstacs.motifDiscovery used by de.jstacs.scoringFunctions.directedGraphicalModels

Mutable
This interface allows to modify a motif model.

Classes in de.jstacs.motifDiscovery used by de.jstacs.scoringFunctions.mix

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.

Mutable
This interface allows to modify a motif model.

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.

Classes in de.jstacs.motifDiscovery used by de.jstacs.scoringFunctions.mix.motifSearch

MotifDiscoverer
This is the interface that any tool for de-novo motif discovery should implement.

MotifDiscoverer.KindOfProfile
This enum can be used to determine which kind of profile should be returned.

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.