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## 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 `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.directedGraphicalModels | Provides `ScoringFunction`s that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.
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
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.

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