de.jstacs.data.sequences.annotation
Class IntronAnnotation

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.IntronAnnotation

All Implemented Interfaces:

Storable

public class IntronAnnotation
extends LocatedSequenceAnnotationWithLength

Annotation class for an intron as defined by a donor and an acceptor splice site.

Author:

Jan Grau

Field Summary

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

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

IntronAnnotation(String identifier, SinglePositionSequenceAnnotation donor, SinglePositionSequenceAnnotation acceptor, Result... additionalAnnotation)
Creates a new IntronAnnotation from a donor SinglePositionSequenceAnnotation and an acceptor SinglePositionSequenceAnnotation and a set of additional annotations.

Method Summary

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

fromXML, getEnd, getLength, overlaps, toString, toXML

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, getResultForName, getResults

Methods inherited from class java.lang.Object

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

Constructor Detail

IntronAnnotation

public IntronAnnotation(String identifier,
                        SinglePositionSequenceAnnotation donor,
                        SinglePositionSequenceAnnotation acceptor,
                        Result... additionalAnnotation)
                 throws Exception

Creates a new IntronAnnotation from a donor SinglePositionSequenceAnnotation and an acceptor SinglePositionSequenceAnnotation and a set of additional annotations.

Parameters:

identifier - the identifier of this annotation

donor - the donor annotation

acceptor - the acceptor annotation

additionalAnnotation - the additional annotations

Throws:

Exception - if donor or acceptor are not of the correct SinglePositionSequenceAnnotation.Type

See Also:

SinglePositionSequenceAnnotation, SinglePositionSequenceAnnotation.Type

IntronAnnotation

public IntronAnnotation(StringBuffer representation)
                 throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

LocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(StringBuffer), Storable