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 This enum defines possible types of a SinglePositionSequenceAnnotation.
StrandedLocatedSequenceAnnotationWithLength.Strand This enum defines 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.