de.jstacs.data.sequences.annotation
Class IntronAnnotation

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.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)
          Re-creates an IntronAnnotation from its XML-representation as returned by LocatedSequenceAnnotationWithLength.toXML().
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, 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, 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 - is thrown if donor or acceptor are not of the correct SinglePositionSequenceAnnotation.Type

IntronAnnotation

public IntronAnnotation(StringBuffer representation)
                 throws NonParsableException
Re-creates an IntronAnnotation from its XML-representation as returned by LocatedSequenceAnnotationWithLength.toXML().

Parameters:
representation - the XML-representation
Throws:
NonParsableException - is thrown if the XML-code could not be parsed