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 Sequences using a number of pre-defined annotation types, or additional implementations of the SequenceAnnotation class 
 

Uses of SequenceAnnotation in de.jstacs.data
 

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

Methods in de.jstacs.data that return SequenceAnnotation
 SequenceAnnotation[] Sequence.getAnnotation()
          Returns the annotation of the sequence.
 

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.
static Sequence Sequence.create(AlphabetContainer con, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a sequence from a string based on the given AlphabetContainer using the given delimiter.
 

Constructors in de.jstacs.data with parameters of type SequenceAnnotation
Sequence(AlphabetContainer container, SequenceAnnotation[] annotation)
          This constructor creates an instance with the AlphabetContainer and the 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 sequence from a string representation using the delimiter delim.
ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
          Creates a new sequence from a SymbolExctractor.
ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a new sequence from a string representation using the delimiter delim.
ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
          Creates a new sequence from a SymbolExctractor.
DiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation)
          This constructor creates an instance with the AlphabetContainer and the annotation, but without the content.
IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a new sequence from a string representation using the delimiter delim.
IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
          Creates a new sequence from a SymbolExctractor.
RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence seq)
          This constructor creates a recursive sequence.
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim)
          Creates a new sequence from a string representation using the delimiter delim.
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor)
          Creates a new sequence from a SymbolExctractor.
 

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 MotifAnnotations 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 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.
 

Methods in de.jstacs.data.sequences.annotation that return SequenceAnnotation
 SequenceAnnotation[] SequenceAnnotation.getSubAnnotations()
          Returns the sub-annotations of this SequenceAnnotation as given in the constructor.
 

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) result, and sub 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) result, and sub-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) 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, and additional annotation (that does not fit the SequenceAnnotation definitions) additionalAnnotations, and sub-annotations.