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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.sequenceScores.statisticalModels.differentiable | Provides all `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif |

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, DifferentiableSequenceScore[] score, DataSet[] data, double[][] weights, DiffSSBasedOptimizableFunction 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, DataSet[] s, double[][] seqWeights, boolean[] adjust, MutableMotifDiscoverer[] mmd, int[] len, DataSet[] data, double[][] dataWeights)` This method allows to initialize a number of motifs.

Uses of MutableMotifDiscoverer in de.jstacs.sequenceScores.statisticalModels.differentiable

Classes in de.jstacs.sequenceScores.statisticalModels.differentiable that implement MutableMotifDiscoverer
`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 `Sequence`s.

Uses of MutableMotifDiscoverer in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture

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

Classes in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif that implement MutableMotifDiscoverer
`class` | `ExtendedZOOPSDiffSM` This class handles mixtures with at least one hidden motif.

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