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Packages that use SequenceAnnotation | |
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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 Sequence s using a number of pre-defined annotation types, or additional
implementations of the SequenceAnnotation class |
Uses of SequenceAnnotation in de.jstacs.data |
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Fields in de.jstacs.data declared as SequenceAnnotation | |
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protected SequenceAnnotation[] |
Sequence.annotation
The annotation of the sequence. |
Methods in de.jstacs.data that return SequenceAnnotation | |
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SequenceAnnotation[] |
Sequence.getAnnotation()
Returns the annotation of the sequence. |
Methods in de.jstacs.data with parameters of type SequenceAnnotation | |
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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 | |
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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 |
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Constructors in de.jstacs.data.sequences with parameters of type SequenceAnnotation | |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new sequence from a string representation using the delimiter delim . |
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ArbitrarySequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new sequence from a SymbolExctractor. |
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ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new sequence from a string representation using the delimiter delim . |
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ByteSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new sequence from a SymbolExctractor. |
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DiscreteSequence(AlphabetContainer container,
SequenceAnnotation[] annotation)
This constructor creates an instance with the AlphabetContainer and the annotation, but without the content. |
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IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new sequence from a string representation using the delimiter delim . |
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IntSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new sequence from a SymbolExctractor. |
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RecursiveSequence(AlphabetContainer alphabet,
SequenceAnnotation[] annotation,
Sequence seq)
This constructor creates a recursive sequence. |
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ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
String sequence,
String delim)
Creates a new sequence from a string representation using the delimiter delim . |
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ShortSequence(AlphabetContainer alphabetContainer,
SequenceAnnotation[] annotation,
SymbolExtractor extractor)
Creates a new sequence from a SymbolExctractor. |
Uses of SequenceAnnotation in de.jstacs.data.sequences.annotation |
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Subclasses of SequenceAnnotation in de.jstacs.data.sequences.annotation | |
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class |
CisRegulatoryModuleAnnotation
Annotation for a cis-regulatory module as defined by a set of MotifAnnotation s 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 | |
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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 | |
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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. |
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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. |
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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 . |
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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. |
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