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## Package de.jstacs.data.sequences.annotation

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

See:
Description

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

Class Summary
CisRegulatoryModuleAnnotation | Annotation for a cis-regulatory module as defined by a set of `MotifAnnotation`s 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.
MotifAnnotationParser | Annotation parser for `MotifAnnotation`s.
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
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 `Sequence`s using a number of pre-defined annotation types, or additional implementations of the `SequenceAnnotation` class.

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