de.jstacs.data.sequences.annotation
Class MotifAnnotation

java.lang.Object
  extended by de.jstacs.results.ResultSet
      extended by de.jstacs.data.sequences.annotation.SequenceAnnotation
          extended by de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
              extended by de.jstacs.data.sequences.annotation.LocatedSequenceAnnotationWithLength
                  extended by de.jstacs.data.sequences.annotation.StrandedLocatedSequenceAnnotationWithLength
                      extended by 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