Package | Description |
---|---|
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 |
Modifier and Type | Method and Description |
---|---|
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.
|
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.
|
Modifier and Type | Class and Description |
---|---|
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. |
Modifier and Type | Class and Description |
---|---|
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 . |
Modifier and Type | Class and Description |
---|---|
class |
ExtendedZOOPSDiffSM
This class handles mixtures with at least one hidden motif.
|