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## 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 `Sequence`s 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.

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