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## Uses of Interface
de.jstacs.data.sequences.annotation.SequenceAnnotationParser

Packages that use SequenceAnnotationParser
de.jstacs.data | Provides classes for the representation of data.
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.results | This package provides classes for results and sets of results.

Uses of SequenceAnnotationParser in de.jstacs.data

Methods in de.jstacs.data with parameters of type SequenceAnnotationParser
`void` | `Sample.save(OutputStream stream, char commentChar, SequenceAnnotationParser p)` This method allows to write all `Sequence`s including their `SequenceAnnotation`s into a `OutputStream`.

Constructors in de.jstacs.data with parameters of type SequenceAnnotationParser
`DNASample(String fName, char ignore, SequenceAnnotationParser parser)` Creates a new sample of DNA sequence from a file with file name `fName` using the given `parser`.

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

Classes in de.jstacs.data.sequences.annotation that implement SequenceAnnotationParser
`class` | `MotifAnnotationParser` Annotation parser for `MotifAnnotation`s.
`class` | `NullSequenceAnnotationParser` This `SequenceAnnotationParser` returns always `null` as `SequenceAnnotation`.
`class` | `ReferenceSequenceAnnotationParser` This class implements an `SequenceAnnotationParser` that parses a `ReferenceSequenceAnnotation` from the comment lines of a sequence.
`class` | `SimpleSequenceAnnotationParser` This class implements a naive `SequenceAnnotationParser` which simply paste the comments into `SequenceAnnotation`.
`class` | `SplitSequenceAnnotationParser` This class implements a simple `SequenceAnnotationParser` which simply splits the comments by specific delimiters.

Uses of SequenceAnnotationParser in de.jstacs.io

Fields in de.jstacs.io declared as SequenceAnnotationParser
`protected SequenceAnnotationParser` | `SparseStringExtractor.annotationParser` A parser for the sequence annotation.

Constructors in de.jstacs.io with parameters of type SequenceAnnotationParser
`SparseStringExtractor(File f, char ignore, String annotation, SequenceAnnotationParser parser)` A constructor that reads the lines from a file, ignores those starting with the comment character `ignore` and sets the annotation of the source to `annotation`.
`SparseStringExtractor(String fName, char ignore, SequenceAnnotationParser parser)` A constructor that reads the lines from a file and ignores those starting with the comment character `ignore`.
`SparseStringExtractor(String fName, char ignore, String annotation, SequenceAnnotationParser parser)` A constructor that reads the lines from a file, ignores those starting with the comment character `ignore` and sets the annotation of the source to `annotation`.
`SparseStringExtractor(String fName, SequenceAnnotationParser parser)` A constructor that reads the lines from a file.
`SparseStringExtractor(String fName, String annotation, SequenceAnnotationParser parser)` A constructor that reads the lines from a file and sets the annotation of the source to `annotation`.

Uses of SequenceAnnotationParser in de.jstacs.results

Methods in de.jstacs.results that return SequenceAnnotationParser
`SequenceAnnotationParser` | `SampleResult.getParser()` Returns the `SequenceAnnotationParser` that can be used to write this `SampleResult` including annotations on the contained `Sequence`s to a file.

Methods in de.jstacs.results with parameters of type SequenceAnnotationParser
`void` | `SampleResult.setParser(SequenceAnnotationParser parser)` Sets the `SequenceAnnotationParser` that can be used to write this `SampleResult` including annotations on the contained `Sequence`s to a file

Constructors in de.jstacs.results with parameters of type SequenceAnnotationParser
`SampleResult(String name, String comment, Sample data, SequenceAnnotationParser parser)` Creates a new `SampleResult` from a `Sample` with the annotation `name` and `comment`.

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