Uses of Package
de.jstacs.data.sequences.annotation

Packages that use de.jstacs.data.sequences.annotation

de.jstacs.data	Provides classes for the representation of data.
de.jstacs.data.sequences	Provides classes for representing sequences.
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

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.data

SequenceAnnotation
Class for a general annotation of a Sequence.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.data.sequences

SequenceAnnotation
Class for a general annotation of a Sequence.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.data.sequences.annotation

LocatedSequenceAnnotation
Class for a SequenceAnnotation that has a position on the sequence, e.g for transcription start sites or intron-exon junctions.

LocatedSequenceAnnotationWithLength
Class for a SequenceAnnotation that has a position on the sequence and a length, e.g. for donor splice sites, exons, or genes.

MotifAnnotation
Class for a StrandedLocatedSequenceAnnotationWithLength that is a motif.

SequenceAnnotation
Class for a general annotation of a Sequence.

SinglePositionSequenceAnnotation
Class for some annotations that consist mainly of one position on a sequence.

SinglePositionSequenceAnnotation.Type
The possible types of a SinglePositionSequenceAnnotation.

StrandedLocatedSequenceAnnotationWithLength
Class for a SequenceAnnotation that has a position, a length, and an orientation on the strand of a Sequence.

StrandedLocatedSequenceAnnotationWithLength.Strand
The possible orientations on the strands.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.models.mixture.motif

StrandedLocatedSequenceAnnotationWithLength.Strand
The possible orientations on the strands.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.motifDiscovery

StrandedLocatedSequenceAnnotationWithLength.Strand
The possible orientations on the strands.