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Sequence
s using a number of pre-defined annotation types, or additional
implementations of the SequenceAnnotation
class
See:
Description
Interface Summary | |
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SequenceAnnotationParser | This interface declares the methods which are used by
AbstractStringExtractor to annotate a String
which will be parsed to a Sequence . |
Class Summary | |
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CisRegulatoryModuleAnnotation | Annotation for a cis-regulatory module as defined by a set of
MotifAnnotation s of the motifs in the module. |
IntronAnnotation | Annotation class for an intron as defined by a donor and an acceptor splice site. |
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. for donor splice sites, exons or genes. |
MotifAnnotation | Class for a StrandedLocatedSequenceAnnotationWithLength that is a
motif. |
MotifAnnotationParser | Annotation parser for MotifAnnotation s. |
NullSequenceAnnotationParser | This SequenceAnnotationParser returns always null as SequenceAnnotation . |
ReferenceSequenceAnnotation | This class implements a SequenceAnnotation that contains a reference
sequence. |
ReferenceSequenceAnnotationParser | This class implements an SequenceAnnotationParser that parses a ReferenceSequenceAnnotation from the comment lines of a sequence. |
SequenceAnnotation | Class for a general annotation of a Sequence . |
SimpleSequenceAnnotationParser | This class implements a naive SequenceAnnotationParser which simply paste the comments into SequenceAnnotation . |
SinglePositionSequenceAnnotation | Class for some annotations that consist mainly of one position on a sequence. |
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 . |
Enum Summary | |
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SinglePositionSequenceAnnotation.Type | This enum defines possible types of a
SinglePositionSequenceAnnotation . |
StrandedLocatedSequenceAnnotationWithLength.Strand | This enum defines possible orientations on the strands. |
Provides the facilities to annotate Sequence
s using a number of pre-defined annotation types, or additional
implementations of the SequenceAnnotation
class.
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