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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
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

Uses of SequenceAnnotation in de.jstacs.data

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

Methods in de.jstacs.data that return SequenceAnnotation
`SequenceAnnotation[]` | `Sequence.getAnnotation()` Returns the annotation of the `Sequence.RecursiveSequence`.
`SequenceAnnotation` | `Sequence.getSequenceAnnotationByType(String type, int idx)` Returns the `SequenceAnnotation` no.
`SequenceAnnotation` | `Sequence.getSequenceAnnotationByTypeAndIdentifier(String type, String identifier)` Returns the `SequenceAnnotation` of this `Sequence.RecursiveSequence` that has type `type` and identifier `identifier`.

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.RecursiveSequence`.
`static Sequence` | `Sequence.create(AlphabetContainer con, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a `Sequence.RecursiveSequence` from a `String` based on the given `AlphabetContainer` using the given delimiter `delim` and some `annotation` for the `Sequence.RecursiveSequence`.

Constructors in de.jstacs.data with parameters of type SequenceAnnotation
`Sequence.RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence<T> seq)` Creates a new `Sequence.RecursiveSequence` on the `Sequence` `seq` with the `AlphabetContainer` `alphabet` and the annotation `annotation`.
`Sequence(AlphabetContainer container, SequenceAnnotation[] annotation)` Creates a new `Sequence.RecursiveSequence` with the given `AlphabetContainer` and the given 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 `ArbitrarySequence` from a `String` representation using the delimiter `delim`.
`ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new `ArbitrarySequence` from a `SymbolExtractor`.
`ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new `ByteSequence` from a `String` representation using the delimiter `delim`.
`ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new `ByteSequence` from a `SymbolExtractor`.
`DiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation)` This constructor creates a new `DiscreteSequence` with the `AlphabetContainer` `container` and the annotation `annotation` but without the content.
`IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new `IntSequence` from a `String` representation using the delimiter `delim`.
`IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new `IntSequence` from a `SymbolExtractor`.
`MappedDiscreteSequence(AlphabetContainer originalAlphabetContainer, SequenceAnnotation[] seqAn, DiscreteAlphabetMapping... transformation)` This method allows to create an empty `MappedDiscreteSequence`.
`MultiDimensionalDiscreteSequence(SequenceAnnotation[] seqAnnotations, SimpleDiscreteSequence... sequence)` This constructor creates an `MultiDimensionalDiscreteSequence` from a set of individual `SimpleDiscreteSequence`s.
`ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)` Creates a new `ShortSequence` from a `String` representation using the delimiter `delim`.
`ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)` Creates a new `ShortSequence` from a `SymbolExtractor`.
`SimpleDiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation)` This constructor creates a new `SimpleDiscreteSequence` with the `AlphabetContainer` `container` and the annotation `annotation` but without the content.

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` | `ReferenceSequenceAnnotation` This class implements a `SequenceAnnotation` that contains a reference sequence.
`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`.

Fields in de.jstacs.data.sequences.annotation with type parameters of type SequenceAnnotation
`protected LinkedList<SequenceAnnotation>` | `SplitSequenceAnnotationParser.annot` The internal list of current `SequenceAnnotation`s.

Methods in de.jstacs.data.sequences.annotation that return SequenceAnnotation
`SequenceAnnotation[]` | `SplitSequenceAnnotationParser.getCurrentAnnotation()`
`SequenceAnnotation[]` | `SimpleSequenceAnnotationParser.getCurrentAnnotation()`
`SequenceAnnotation[]` | `SequenceAnnotationParser.getCurrentAnnotation()` This method returns the current `SequenceAnnotation`.
`SequenceAnnotation[]` | `NullSequenceAnnotationParser.getCurrentAnnotation()`
`SequenceAnnotation[]` | `SequenceAnnotation.getSubAnnotations()` Returns the sub-annotations of this `SequenceAnnotation` as given in the constructor.

Methods in de.jstacs.data.sequences.annotation with parameters of type SequenceAnnotation
`String` | `SplitSequenceAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)`
`String` | `SimpleSequenceAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)`
`String` | `SequenceAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)` This method returns a `String` representation of the given `SequenceAnnotation`s that can be used as comment line in a file.
`String` | `NullSequenceAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)`

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) given as an array of `Result`s `additionalAnnotation` and sub-annotations `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) given as an array of `Result`s `additionalAnnotations` and sub-annotations `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) given as an array of `Result`s `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`, additional annotation (that does not fit the `SequenceAnnotation` definitions) given as an array of `Result`s `additionalAnnotations` and sub-annotations `annotations`.

Uses of SequenceAnnotation in de.jstacs.io

Methods in de.jstacs.io that return SequenceAnnotation
`SequenceAnnotation[]` | `SparseStringExtractor.getCurrentSequenceAnnotations()`
`SequenceAnnotation[]` | `LimitedStringExtractor.getCurrentSequenceAnnotations()`
`SequenceAnnotation[]` | `InfixStringExtractor.getCurrentSequenceAnnotations()`
`SequenceAnnotation[]` | `AbstractStringExtractor.getCurrentSequenceAnnotations()` Returns the `SequenceAnnotation` or `null` if no `SequenceAnnotation` is available.

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