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.sequenceScores.statisticalModels.differentiable	Provides all DifferentiableStatisticalModels, which can compute the gradient with respect to their parameters for a given input Sequence.
de.jstacs.sequenceScores.statisticalModels.differentiable.mixture	Provides DifferentiableSequenceScores that are mixtures of other DifferentiableSequenceScores.

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.