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

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 are declared.

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

protected void

MotifAnnotationParser.add(String identifier, int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness) Adds the motif with identifier identifier at position position with length length and StrandedLocatedSequenceAnnotationWithLength.Strand strandedness

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.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.

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.