Package 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

See:
Description

Class Summary

CisRegulatoryModuleAnnotation	Annotation for a cis-regulatory module as defined by a set of MotifAnnotations of the motifs in the module.
IntronAnnotation	Annotation class for an intron as defined by a donor and an acceptor splice site.
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.
StrandedLocatedSequenceAnnotationWithLength	Class for a SequenceAnnotation that has a position, a length, and an orientation on the strand of a Sequence.

Enum Summary

SinglePositionSequenceAnnotation.Type	The possible types of a SinglePositionSequenceAnnotation.
StrandedLocatedSequenceAnnotationWithLength.Strand	The possible orientations on the strands.

Package de.jstacs.data.sequences.annotation Description

Provides the facilities to annotate Sequences using a number of pre-defined annotation types, or additional implementations of the SequenceAnnotation class.