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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 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.

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