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Packages that use MutableMotifDiscoverer | |
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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 |
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Methods in de.jstacs.motifDiscovery with parameters of type MutableMotifDiscoverer | |
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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 |
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Classes in de.jstacs.sequenceScores.statisticalModels.differentiable that implement MutableMotifDiscoverer | |
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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 |
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Classes in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture that implement MutableMotifDiscoverer | |
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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 |
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Classes in de.jstacs.sequenceScores.statisticalModels.differentiable.mixture.motif that implement MutableMotifDiscoverer | |
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class |
ExtendedZOOPSDiffSM
This class handles mixtures with at least one hidden motif. |
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