Package de.jstacs.motifDiscovery

This package provides the framework including the interface for any de novo motif discoverer.

See:
Description

Interface Summary

MotifDiscoverer	This is the interface that any tool for de-novo motif discovery should implement.
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.
SignificantMotifOccurrencesFinder.JoinMethod	Interface for methods that combine several profiles over the same sequence into one common profile

Class Summary

KMereStatistic	This class enables the user to get some statistics of a DataSet in an easy way.
MotifDiscovererToolBox	This class contains static methods for the MotifDiscoverer.
MotifDiscoveryAssessment	This class enables the user to assess the prediction of motif occurrences
MutableMotifDiscovererToolbox	This class contains some important methods for the initiation and optimization of MutableMotifDiscoverer.
SignificantMotifOccurrencesFinder	This class enables the user to predict motif occurrences given a specific significance level.
SignificantMotifOccurrencesFinder.SumOfProbabilities	Joins several profiles containing log-probabilities into one profile containing the logarithm of the sum of the probabilities of the single profiles.

Enum Summary

MotifDiscoverer.KindOfProfile	This enum can be used to determine which kind of profile should be returned.
MutableMotifDiscovererToolbox.InitMethodForDiffSM	This enum defines some constants for the method MutableMotifDiscovererToolbox.getSortedInitialParameters(DifferentiableSequenceScore[], InitMethodForDiffSM[], DiffSSBasedOptimizableFunction, int, OutputStream, int).
SignificantMotifOccurrencesFinder.RandomSeqType

Package de.jstacs.motifDiscovery Description

This package provides the framework including the interface for any de novo motif discoverer.