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.
 

Class Summary
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.
 

Enum Summary
MotifDiscoverer.KindOfProfile This enum can be used to determine which kind of profile should be returned.
MutableMotifDiscovererToolbox.InitMethodForScoringFunction This enum defines some constants for the method MutableMotifDiscovererToolbox.getSortedInitialParameters(Sample[], ScoringFunction[], InitMethodForScoringFunction[], OptimizableFunction, int, SafeOutputStream).
SignificantMotifOccurrencesFinder.RandomSeqType  
 

Package de.jstacs.motifDiscovery Description

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