Uses of Class
de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength.Strand

Packages that use StrandedLocatedSequenceAnnotationWithLength.Strand

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.models.mixture.motif
de.jstacs.motifDiscovery	This package provides the framework including the interface for any de novo motif discoverer

Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.data.sequences.annotation

Methods in de.jstacs.data.sequences.annotation that return StrandedLocatedSequenceAnnotationWithLength.Strand

static StrandedLocatedSequenceAnnotationWithLength.Strand	StrandedLocatedSequenceAnnotationWithLength.Strand.valueOf(String name) Returns the enum constant of this type with the specified name.
static StrandedLocatedSequenceAnnotationWithLength.Strand[]	StrandedLocatedSequenceAnnotationWithLength.Strand.values() Returns an array containing the constants of this enum type, in the order they're declared.

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

MotifAnnotation(String identifier, int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, Result... additionalAnnotation)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) additionalAnnotation.

StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, Collection<Result> results)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.

StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, Result... results)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.

StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) additionalAnnotations, and sub-annotations.

StrandedLocatedSequenceAnnotationWithLength(String type, String identifier, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) additionalAnnotations, and sub-annotations.

Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.models.mixture.motif

Methods in de.jstacs.models.mixture.motif that return StrandedLocatedSequenceAnnotationWithLength.Strand

StrandedLocatedSequenceAnnotationWithLength.Strand

SingleHiddenMotifMixture.getStrandFor(int component, int motif, Sequence sequence, int startpos)

Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return StrandedLocatedSequenceAnnotationWithLength.Strand

StrandedLocatedSequenceAnnotationWithLength.Strand

MotifDiscoverer.getStrandFor(int component, int motif, Sequence sequence, int startpos) This method returns the strand for a given subsequence if it is consider as site of the motif model in a specific component.