Uses of Class
de.jstacs.data.sequences.annotation.MotifAnnotation

Packages that use MotifAnnotation

Package	Description
de.jstacs.data.sequences.annotation	Provides the facilities to annotate Sequences using a number of pre-defined annotation types, or additional implementations of the SequenceAnnotation class.
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer.

Uses of MotifAnnotation in de.jstacs.data.sequences.annotation

Constructors in de.jstacs.data.sequences.annotation with parameters of type MotifAnnotation

Constructor and Description
CisRegulatoryModuleAnnotation(String identifier, MotifAnnotation[] motifs, Result... additionalAnnotation) Creates a new CisRegulatoryModuleAnnotation from a set of motifs and possibly additional annotations.

Uses of MotifAnnotation in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return MotifAnnotation

Modifier and Type	Method and Description
MotifAnnotation[]	SignificantMotifOccurrencesFinder.findSignificantMotifOccurrences(int motif, Sequence seq, int start) This method finds the significant motif occurrences in the sequence.
MotifAnnotation[]	SignificantMotifOccurrencesFinder.findSignificantMotifOccurrences(int motif, Sequence seq, int addMax, int start) This method finds the significant motif occurrences in the sequence.