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)
Re-creates a MotifAnnotation from its XML representation as returned by StrandedLocatedSequenceAnnotationWithLength.toXML().

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

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

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

Methods inherited from class de.jstacs.results.ResultSet

findColumn, getNumberOfResults, getResultAt, getResults

Methods inherited from class java.lang.Object

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

Constructor Detail

MotifAnnotation

public 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.

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

MotifAnnotation

public MotifAnnotation(StringBuffer representation)
                throws NonParsableException

Re-creates a MotifAnnotation from its XML representation as returned by StrandedLocatedSequenceAnnotationWithLength.toXML().

Parameters:

representation - the XML-representation

Throws:

NonParsableException - is thrown if the XML code could not be parsed