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## Uses of Class
de.jstacs.data.sequences.annotation.SequenceAnnotation

Packages that use SequenceAnnotation
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

Uses of SequenceAnnotation in de.jstacs.data

Fields in de.jstacs.data declared as SequenceAnnotation
`protected SequenceAnnotation[]` | `Sequence.annotation` The annotation of the sequence.

Methods in de.jstacs.data that return SequenceAnnotation
`SequenceAnnotation[]` | `Sequence.getAnnotation()` Returns the annotation of the sequence.

Methods in de.jstacs.data with parameters of type SequenceAnnotation
`Sequence` | `Sequence.annotate(boolean add, SequenceAnnotation... annotation)` This method allows to append annotation to a sequence.
`static Sequence` | `Sequence.create(AlphabetContainer con, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a sequence from a string based on the given AlphabetContainer using the given delimiter.

Constructors in de.jstacs.data with parameters of type SequenceAnnotation
`Sequence(AlphabetContainer container, SequenceAnnotation[] annotation)` This constructor creates an instance with the AlphabetContainer and the annotation, but without the content.

Uses of SequenceAnnotation in de.jstacs.data.sequences

Constructors in de.jstacs.data.sequences with parameters of type SequenceAnnotation
`ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new sequence from a string representation using the delimiter `delim`.
`ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new sequence from a SymbolExctractor.
`ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new sequence from a string representation using the delimiter `delim`.
`ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new sequence from a SymbolExctractor.
`DiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation)` This constructor creates an instance with the AlphabetContainer and the annotation, but without the content.
`IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new sequence from a string representation using the delimiter `delim`.
`IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new sequence from a SymbolExctractor.
`RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)` This constructor creates a recursive sequence.
`ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new sequence from a string representation using the delimiter `delim`.
`ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new sequence from a SymbolExctractor.

Uses of SequenceAnnotation in de.jstacs.data.sequences.annotation

Subclasses of SequenceAnnotation in de.jstacs.data.sequences.annotation
`class` | `CisRegulatoryModuleAnnotation` Annotation for a cis-regulatory module as defined by a set of `MotifAnnotation`s of the motifs in the module.
`class` | `IntronAnnotation` Annotation class for an intron as defined by a donor and an acceptor splice site.
`class` | `LocatedSequenceAnnotation` Class for a `SequenceAnnotation` that has a position on the sequence, e.g for transcription start sites or intron-exon junctions.
`class` | `LocatedSequenceAnnotationWithLength` Class for a `SequenceAnnotation` that has a position on the sequence and a length, e.g. for donor splice sites, exons, or genes.
`class` | `MotifAnnotation` Class for a `StrandedLocatedSequenceAnnotationWithLength` that is a motif.
`class` | `SinglePositionSequenceAnnotation` Class for some annotations that consist mainly of one position on a sequence.
`class` | `StrandedLocatedSequenceAnnotationWithLength` Class for a `SequenceAnnotation` that has a position, a length, and an orientation on the strand of a `Sequence`.

Methods in de.jstacs.data.sequences.annotation that return SequenceAnnotation
`SequenceAnnotation[]` | `SequenceAnnotation.getSubAnnotations()` Returns the sub-annotations of this `SequenceAnnotation` as given in the constructor.

Constructors in de.jstacs.data.sequences.annotation with parameters of type SequenceAnnotation
`LocatedSequenceAnnotation(int position, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotation)` Creates a new `LocatedSequenceAnnotation` of type `type`, with identifier `identifier`, additional annotation (that does not fit the `SequenceAnnotation` definitions) `result`, and sub annotations.
`LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations)` Creates a new `LocatedSequenceAnnotationWithLength` of type `type`, with identifier `identifier`, additional annotation (that does not fit the `SequenceAnnotation` definitions) `result`, and sub-annotations.
`SequenceAnnotation(String type, String identifier, SequenceAnnotation[] subAnnotations, Result... additionalAnnotation)` Creates a new `SequenceAnnotation` of type `type`, with identifier `identifier`, and additional annotation (that does not fit the `SequenceAnnotation` definitions) `additionalAnnotation`.
`StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations)` Creates a new `StrandedLocatedSequenceAnnotationWithLength` of type `type`, with identifier `identifier`, and additional annotation (that does not fit the `SequenceAnnotation` definitions) `additionalAnnotations`, and sub-annotations.

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