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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.io | Provides classes for reading data from and writing to a file and storing a number of datatypes, including all primitives, arrays of primitives, and `Storable`s to an XML-representation
de.jstacs.models.mixture.motif |
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.scoringFunctions | Provides `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.
de.jstacs.scoringFunctions.mix.motifSearch |

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.data
SequenceAnnotation Class for a general annotation of a `Sequence`.
SequenceAnnotationParser This interface declares the methods which are used by `AbstractStringExtractor` to annotate a `String` which will be parsed to 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.
NullSequenceAnnotationParser This `SequenceAnnotationParser` returns always `null` as `SequenceAnnotation`.
SequenceAnnotation Class for a general annotation of a `Sequence`.
SequenceAnnotationParser This interface declares the methods which are used by `AbstractStringExtractor` to annotate a `String` which will be parsed to a `Sequence`.
SinglePositionSequenceAnnotation Class for some annotations that consist mainly of one position on a sequence.
SinglePositionSequenceAnnotation.Type This `enum` defines 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 This enum defines possible orientations on the strands.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.io
SequenceAnnotation Class for a general annotation of a `Sequence`.
SequenceAnnotationParser This interface declares the methods which are used by `AbstractStringExtractor` to annotate a `String` which will be parsed to a `Sequence`.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.models.mixture.motif
StrandedLocatedSequenceAnnotationWithLength.Strand This enum defines possible orientations on the strands.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.motifDiscovery
MotifAnnotation Class for a `StrandedLocatedSequenceAnnotationWithLength` that is a motif.
StrandedLocatedSequenceAnnotationWithLength.Strand This enum defines possible orientations on the strands.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.scoringFunctions
StrandedLocatedSequenceAnnotationWithLength.Strand This enum defines possible orientations on the strands.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.scoringFunctions.mix
StrandedLocatedSequenceAnnotationWithLength.Strand This enum defines possible orientations on the strands.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.scoringFunctions.mix.motifSearch
StrandedLocatedSequenceAnnotationWithLength.Strand This enum defines possible orientations on the strands.

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