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 
de.jstacs.scoringFunctions Provides ScoringFunctions that can be used in a ScoreClassifier
de.jstacs.scoringFunctions.mix Provides ScoringFunctions that are mixtures of other ScoringFunctions. 
de.jstacs.scoringFunctions.mix.motifSearch   
 

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

Methods in de.jstacs.data.sequences.annotation that return StrandedLocatedSequenceAnnotationWithLength.Strand
 StrandedLocatedSequenceAnnotationWithLength.Strand StrandedLocatedSequenceAnnotationWithLength.getStrandedness()
          Returns the strandedness, i.e the orientation of this annotation.
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 MotifAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results 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) given as a Collection of Results results.
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) given as an array of Results results.
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, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations annotations.
StrandedLocatedSequenceAnnotationWithLength(String type, String identifier, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations)
          Creates a new StrandedLocatedSequenceAnnotationWithLength of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations 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 considered as site of the motif model in a specific component.
 

Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.scoringFunctions
 

Methods in de.jstacs.scoringFunctions that return StrandedLocatedSequenceAnnotationWithLength.Strand
 StrandedLocatedSequenceAnnotationWithLength.Strand NormalizedScoringFunction.getStrand(Sequence seq, int startPos)
          This method return the preferred StrandedLocatedSequenceAnnotationWithLength.Strand for a Sequence beginning at startPos.
 StrandedLocatedSequenceAnnotationWithLength.Strand IndependentProductScoringFunction.getStrandFor(int component, int motif, Sequence sequence, int startpos)
           
 

Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.scoringFunctions.mix
 

Methods in de.jstacs.scoringFunctions.mix that return StrandedLocatedSequenceAnnotationWithLength.Strand
 StrandedLocatedSequenceAnnotationWithLength.Strand StrandScoringFunction.getStrand(Sequence seq, int startPos)
          This method returns the preferred StrandedLocatedSequenceAnnotationWithLength.Strand for a given subsequence.
 

Uses of StrandedLocatedSequenceAnnotationWithLength.Strand in de.jstacs.scoringFunctions.mix.motifSearch
 

Methods in de.jstacs.scoringFunctions.mix.motifSearch that return StrandedLocatedSequenceAnnotationWithLength.Strand
 StrandedLocatedSequenceAnnotationWithLength.Strand HiddenMotifsMixture.getStrandFor(int component, int motif, Sequence sequence, int startpos)