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Packages that use LocatedSequenceAnnotation | |
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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 LocatedSequenceAnnotation in de.jstacs.data.sequences.annotation |
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Subclasses of LocatedSequenceAnnotation in de.jstacs.data.sequences.annotation | |
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class |
IntronAnnotation
Annotation class for an intron as defined by a donor and an acceptor splice site. |
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 . |
Constructors in de.jstacs.data.sequences.annotation with parameters of type LocatedSequenceAnnotation | |
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LocatedSequenceAnnotation(String type,
String identifier,
LocatedSequenceAnnotation[] 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(String type,
String identifier,
LocatedSequenceAnnotation[] 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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StrandedLocatedSequenceAnnotationWithLength(String type,
String identifier,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
LocatedSequenceAnnotation[] 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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