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 Sequences 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 Storables 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.scoringFunctions	Provides ScoringFunctions that can be used in a ScoreClassifier.
de.jstacs.scoringFunctions.mix	Provides ScoringFunctions that are mixtures of other ScoringFunctions.

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.

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.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.