de.jstacs.data.sequences.annotation
Class MotifAnnotation

java.lang.Object
  de.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

All Implemented Interfaces:

Storable

public class MotifAnnotation
extends StrandedLocatedSequenceAnnotationWithLength

Class for a StrandedLocatedSequenceAnnotationWithLength that is a motif. The usefulness of this class amounts to having a defined type for all motifs.

Author:

Jan Grau

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength

StrandedLocatedSequenceAnnotationWithLength.Strand

Field Summary

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

MotifAnnotation(StringBuffer representation)
The standard constructor for the interface Storable.

MotifAnnotation(String identifier, int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, Result... additionalAnnotation)
Creates a new MotifAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotation.

Method Summary

Methods inherited from class de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength

fromXML, getStrandedness, toString, toXML

Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength

getEnd, getLength, overlaps

Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation

getPosition

Methods inherited from class de.jstacs.data.sequences.annotation.SequenceAnnotation

getAnnotations, getIdentifier, getSubAnnotations, getType, hashCode

Methods inherited from class de.jstacs.results.ResultSet

findColumn, getNumberOfResults, getResultAt, getResultForName, getResults

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

MotifAnnotation

public MotifAnnotation(String identifier,
                       int position,
                       int length,
                       StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
                       Result... additionalAnnotation)

Creates a new MotifAnnotation of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotation. The orientation of the motif on the strand is also considered by the value strandedness of the enum StrandedLocatedSequenceAnnotationWithLength.Strand.

Parameters:

position - the position of the StrandedLocatedSequenceAnnotationWithLength on the sequence

length - the length of the StrandedLocatedSequenceAnnotationWithLength

strandedness - the orientation on the strand

identifier - the identifier of the annotation

additionalAnnotation - the additional annotation

See Also:

StrandedLocatedSequenceAnnotationWithLength.Strand, StrandedLocatedSequenceAnnotationWithLength.StrandedLocatedSequenceAnnotationWithLength(int, int, StrandedLocatedSequenceAnnotationWithLength.Strand, String, String, Result[])

MotifAnnotation

public MotifAnnotation(StringBuffer representation)
                throws NonParsableException

The standard constructor for the interface Storable. Creates a new MotifAnnotation out of its XML representation.

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the MotifAnnotation could not be reconstructed out of the XML representation (the StringBuffer representation could not be parsed)

See Also:

StrandedLocatedSequenceAnnotationWithLength.StrandedLocatedSequenceAnnotationWithLength(StringBuffer), Storable