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

Interface Summary

Interface	Description
SequenceAnnotationParser	This interface declares the methods which are used by AbstractStringExtractor to annotate a String which will be parsed to a Sequence.

Class Summary

Class	Description
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.
MotifAnnotation	Class for a StrandedLocatedSequenceAnnotationWithLength that is a motif.
MotifAnnotationParser	Annotation parser for MotifAnnotations.
NullSequenceAnnotationParser	This SequenceAnnotationParser returns always null as SequenceAnnotation.
ReferenceSequenceAnnotation	This class implements a SequenceAnnotation that contains a reference sequence.
ReferenceSequenceAnnotationParser	This class implements an SequenceAnnotationParser that parses a ReferenceSequenceAnnotation from the comment lines of a sequence.
SequenceAnnotation	Class for a general annotation of a Sequence.
SimpleSequenceAnnotationParser	This class implements a naive SequenceAnnotationParser which simply paste the comments into SequenceAnnotation.
SinglePositionSequenceAnnotation	Class for some annotations that consist mainly of one position on a sequence.
SplitSequenceAnnotationParser	This class implements a simple SequenceAnnotationParser which simply splits the comments by specific delimiters.
StrandedLocatedSequenceAnnotationWithLength	Class for a SequenceAnnotation that has a position, a length and an orientation on the strand of a Sequence.

Enum Summary

Enum	Description
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.