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

Packages that use LocatedSequenceAnnotation

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

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

Subclasses of LocatedSequenceAnnotation in de.jstacs.data.sequences.annotation

class	IntronAnnotation Annotation class for an intron as defined by a donor and an acceptor splice site.
class	LocatedSequenceAnnotationWithLength Class for a SequenceAnnotation that has a position on the sequence and a length, e.g. for donor splice sites, exons or genes.
class	MotifAnnotation Class for a StrandedLocatedSequenceAnnotationWithLength that is a motif.
class	SinglePositionSequenceAnnotation Class for some annotations that consist mainly of one position on a sequence.
class	StrandedLocatedSequenceAnnotationWithLength Class for a SequenceAnnotation that has a position, a length and an orientation on the strand of a Sequence.

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

LocatedSequenceAnnotation(String type, String identifier, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotation)
Creates a new LocatedSequenceAnnotation of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotation and sub-annotations annotations.

LocatedSequenceAnnotationWithLength(String type, String identifier, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations)
Creates a new LocatedSequenceAnnotationWithLength 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.