Uses of Package
de.jstacs.data.sequences.annotation

Packages that use de.jstacs.data.sequences.annotation

Package	Description
de.jstacs.data	Provides classes for the representation of data. The base classes to represent data are Alphabet and AlphabetContainer for representing alphabets, Sequence and its sub-classes to represent continuous and discrete sequences, and DataSet to represent data sets comprising a set of sequences.
de.jstacs.data.sequences	Provides classes for representing sequences. The implementations of sequences currently include DiscreteSequences prepared for alphabets of different sizes, and ArbitrarySequences that may contain continuous values as well. As sub-package provides the facilities to annotate 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

Class and Description
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

Class and Description
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

Class and Description
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.
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

Class and Description
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

Class and Description
MotifAnnotation Class for a StrandedLocatedSequenceAnnotationWithLength that is a motif.

Classes in de.jstacs.data.sequences.annotation used by de.jstacs.results

Class and Description
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

Class and Description
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

Class and Description
StrandedLocatedSequenceAnnotationWithLength.Strand This enum defines possible orientations on the strands.