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## Uses of Interface
de.jstacs.motifDiscovery.MutableMotifDiscoverer

Packages that use MutableMotifDiscoverer
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.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.
de.jstacs.scoringFunctions.mix.motifSearch |

Uses of MutableMotifDiscoverer in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery with parameters of type MutableMotifDiscoverer
`static boolean` | `MutableMotifDiscovererToolbox.findModification(int clazz, int motif, MutableMotifDiscoverer mmd, ScoringFunction[] score, Sample[] data, double[][] weights, SFBasedOptimizableFunction opt, DifferentiableFunction neg, byte algo, double linEps, StartDistanceForecaster startDistance, SafeOutputStream out, History hist, int minimalNewLength, boolean maxPos)` This method tries to find a modification, i.e. shifting, shrinking, or expanding a motif, that is promising.
`static void` | `MutableMotifDiscovererToolbox.initMotif(int idx, int[] classIndex, int[] motifIndex, Sample[] s, double[][] seqWeights, boolean[] adjust, MutableMotifDiscoverer[] mmd, int[] len, Sample[] data, double[][] dataWeights)` This method allows to initialize a number of motifs.

Uses of MutableMotifDiscoverer in de.jstacs.scoringFunctions

Classes in de.jstacs.scoringFunctions that implement MutableMotifDiscoverer
`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 `Sequence`s.

Uses of MutableMotifDiscoverer in de.jstacs.scoringFunctions.mix

Classes in de.jstacs.scoringFunctions.mix that implement MutableMotifDiscoverer
`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 MutableMotifDiscoverer in de.jstacs.scoringFunctions.mix.motifSearch

Classes in de.jstacs.scoringFunctions.mix.motifSearch that implement MutableMotifDiscoverer
`class` | `HiddenMotifsMixture` This class handles mixtures with at least one hidden motif.

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