Uses of Class
de.jstacs.data.sequences.annotation.SequenceAnnotation

Packages that use SequenceAnnotation

Package	Description
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.

Uses of SequenceAnnotation in de.jstacs.data.sequences

Fields in de.jstacs.data.sequences declared as SequenceAnnotation

Modifier and Type	Field and Description
protected SequenceAnnotation[]	Sequence.annotation The annotation of the Sequence.

Methods in de.jstacs.data.sequences that return SequenceAnnotation

Modifier and Type	Method and Description
SequenceAnnotation[]	Sequence.getAnnotation() Returns the annotation of the Sequence.
SequenceAnnotation[][]	MultiDimensionalSequence.getAnnotations() This method returns the SequenceAnnotation[] for each dimension of this multidimensional sequence.
SequenceAnnotation	Sequence.getSequenceAnnotationByType(String type, int idx) Returns the SequenceAnnotation no.
SequenceAnnotation	Sequence.getSequenceAnnotationByTypeAndIdentifier(String type, String identifier) Returns the SequenceAnnotation of this Sequence that has type type and identifier identifier.

Methods in de.jstacs.data.sequences with parameters of type SequenceAnnotation

Modifier and Type	Method and Description
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 delim and some annotation for the Sequence.
protected abstract MultiDimensionalSequence<T>	MultiDimensionalSequence.getInstance(SequenceAnnotation[] seqAn, Sequence... seqs)
protected MultiDimensionalDiscreteSequence	MultiDimensionalDiscreteSequence.getInstance(SequenceAnnotation[] seqAn, Sequence... seqs)
protected MultiDimensionalArbitrarySequence	MultiDimensionalArbitrarySequence.getInstance(SequenceAnnotation[] seqAn, Sequence... seqs)

Constructors in de.jstacs.data.sequences with parameters of type SequenceAnnotation

Constructor and Description
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) Creates a new ArbitraryFloatSequence from a String representation using the delimiter delim.
ArbitraryFloatSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) Creates a new ArbitraryFloatSequence from a SymbolExtractor.
ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) Creates a new ArbitrarySequence from a String representation using the delimiter delim.
ArbitrarySequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) Creates a new ArbitrarySequence from a SymbolExtractor.
ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) Creates a new ByteSequence from a String representation using the delimiter delim.
ByteSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) Creates a new ByteSequence from a SymbolExtractor.
IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) Creates a new IntSequence from a String representation using the delimiter delim.
IntSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) Creates a new IntSequence from a SymbolExtractor.
MappedDiscreteSequence(AlphabetContainer originalAlphabetContainer, SequenceAnnotation[] seqAn, DiscreteAlphabetMapping... transformation) This method allows to create an empty MappedDiscreteSequence.
MultiDimensionalArbitrarySequence(SequenceAnnotation[] seqAn, ArbitrarySequence... sequence) This constructor creates an MultiDimensionalDiscreteSequence from a set of individual Sequences.
MultiDimensionalDiscreteSequence(SequenceAnnotation[] seqAn, SimpleDiscreteSequence... sequence) This constructor creates an MultiDimensionalDiscreteSequence from a set of individual Sequences.
MultiDimensionalSequence(SequenceAnnotation[] seqAn, Sequence... sequence) This constructor creates an MultiDimensionalSequence from a set of individual Sequences.
Sequence.RecursiveSequence(AlphabetContainer alphabet, SequenceAnnotation[] annotation, Sequence<T> seq) Creates a new Sequence.RecursiveSequence on the Sequence seq with the AlphabetContainer alphabet and the annotation annotation.
Sequence(AlphabetContainer container, SequenceAnnotation[] annotation) Creates a new Sequence with the given AlphabetContainer and the given annotation, but without the content.
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, String sequence, String delim) Creates a new ShortSequence from a String representation using the delimiter delim.
ShortSequence(AlphabetContainer alphabetContainer, SequenceAnnotation[] annotation, SymbolExtractor extractor) Creates a new ShortSequence from a SymbolExtractor.
SimpleDiscreteSequence(AlphabetContainer container, SequenceAnnotation[] annotation) This constructor creates a new SimpleDiscreteSequence with the AlphabetContainer container and the annotation annotation but without the content.

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

Subclasses of SequenceAnnotation in de.jstacs.data.sequences.annotation

Modifier and Type	Class and Description
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.
class	MotifAnnotation Class for a StrandedLocatedSequenceAnnotationWithLength that is a motif.
class	ReferenceSequenceAnnotation This class implements a SequenceAnnotation that contains a reference sequence.
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.

Fields in de.jstacs.data.sequences.annotation with type parameters of type SequenceAnnotation

Modifier and Type	Field and Description
protected LinkedList<SequenceAnnotation>	SplitSequenceAnnotationParser.annot The internal list of current SequenceAnnotations.

Methods in de.jstacs.data.sequences.annotation that return SequenceAnnotation

Modifier and Type	Method and Description
SequenceAnnotation[]	SplitSequenceAnnotationParser.getCurrentAnnotation()
SequenceAnnotation[]	SimpleSequenceAnnotationParser.getCurrentAnnotation()
SequenceAnnotation[]	SequenceAnnotationParser.getCurrentAnnotation() This method returns the current SequenceAnnotation.
SequenceAnnotation[]	NullSequenceAnnotationParser.getCurrentAnnotation()
SequenceAnnotation[]	SequenceAnnotation.getSubAnnotations() Returns the sub-annotations of this SequenceAnnotation as given in the constructor.

Methods in de.jstacs.data.sequences.annotation with parameters of type SequenceAnnotation

Modifier and Type	Method and Description
String	SplitSequenceAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)
String	SimpleSequenceAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)
String	SequenceAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations) This method returns a String representation of the given SequenceAnnotations that can be used as comment line in a file.
String	ReferenceSequenceAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)
String	NullSequenceAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)
String	MotifAnnotationParser.parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations)

Constructors in de.jstacs.data.sequences.annotation with parameters of type SequenceAnnotation

Constructor and Description
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) given as an array of Results additionalAnnotation and sub-annotations 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) given as an array of Results additionalAnnotations and sub-annotations 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) given as an array of Results 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, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations annotations.

Uses of SequenceAnnotation in de.jstacs.io

Methods in de.jstacs.io that return SequenceAnnotation

Modifier and Type	Method and Description
SequenceAnnotation[]	SparseStringExtractor.getCurrentSequenceAnnotations()
SequenceAnnotation[]	LimitedStringExtractor.getCurrentSequenceAnnotations()
SequenceAnnotation[]	InfixStringExtractor.getCurrentSequenceAnnotations()
SequenceAnnotation[]	AbstractStringExtractor.getCurrentSequenceAnnotations() Returns the SequenceAnnotation or null if no SequenceAnnotation is available.