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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.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.results | This package provides classes for results and sets of results.
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all `DifferentiableStatisticalModel`s, which can compute the gradient with respect to their parameters for a given input `Sequence`.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture | Provides `DifferentiableSequenceScore`s that are mixtures of other `DifferentiableSequenceScore`s.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.data
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`.
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.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`.
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`.
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.motifDiscovery
MotifAnnotation Class for a `StrandedLocatedSequenceAnnotationWithLength` that is a motif.

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

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

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