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java.lang.Objectde.jstacs.results.ResultSet
de.jstacs.data.sequences.annotation.SequenceAnnotation
de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength
de.jstacs.data.sequences.annotation.MotifAnnotation
public class MotifAnnotation
Class for a StrandedLocatedSequenceAnnotationWithLength
that is a motif. The usefulness of this class amounts to having a defined type for all motifs.
Nested Class Summary |
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Nested classes/interfaces inherited from class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength |
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StrandedLocatedSequenceAnnotationWithLength.Strand |
Field Summary |
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Fields inherited from class de.jstacs.results.ResultSet |
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results |
Constructor Summary | |
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MotifAnnotation(StringBuffer representation)
Re-creates a MotifAnnotation from its XML-representation as returned by StrandedLocatedSequenceAnnotationWithLength.toXML() . |
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MotifAnnotation(String identifier,
int position,
int length,
StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
Result... additionalAnnotation)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type type , with identifier identifier , and additional annotation
(that does not fit the SequenceAnnotation definitions)
additionalAnnotation . |
Method Summary |
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Methods inherited from class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength |
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fromXML, getStrandedness, toString, toXML |
Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength |
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getEnd, getLength |
Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation |
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getPosition |
Methods inherited from class de.jstacs.data.sequences.annotation.SequenceAnnotation |
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getAnnotations, getIdentifier, getSubAnnotations, getType |
Methods inherited from class de.jstacs.results.ResultSet |
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findColumn, getNumberOfResults, getResultAt, getResults |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public MotifAnnotation(String identifier, int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, Result... additionalAnnotation)
StrandedLocatedSequenceAnnotationWithLength
of type type
, with identifier identifier
, and additional annotation
(that does not fit the SequenceAnnotation
definitions)
additionalAnnotation
.
position
- the position of the StrandedLocatedSequenceAnnotationWithLength
on the sequencelength
- the length of the StrandedLocatedSequenceAnnotationWithLength
strandedness
- the orientation on the strandidentifier
- the identifier of the annotationadditionalAnnotation
- the additional annotationpublic MotifAnnotation(StringBuffer representation) throws NonParsableException
MotifAnnotation
from its XML-representation as returned by StrandedLocatedSequenceAnnotationWithLength.toXML()
.
representation
- the XML-representation
NonParsableException
- is thrown if the XML-code could not be parsed
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