de.jstacs.data.sequences.annotation
Class SinglePositionSequenceAnnotation

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.SinglePositionSequenceAnnotation
All Implemented Interfaces:
Storable

public class SinglePositionSequenceAnnotation
extends LocatedSequenceAnnotation

Class for some annotations that consist mainly of one position on a sequence. This includes transcription start sites, translation start sites, splice donor sites, and splice acceptor sites.

Author:
Jan Grau

Nested Class Summary
static class SinglePositionSequenceAnnotation.Type
          The possible types of a SinglePositionSequenceAnnotation.
 
Field Summary
 
Fields inherited from class de.jstacs.results.ResultSet
results
 
Constructor Summary
SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type type, String identifier, int position)
          Creates a new SinglePositionSequenceAnnotation of type type, with identifier identifier and position position.
SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type type, String identifier, int position, Result... additionalAnnotation)
          Creates a new SinglePositionSequenceAnnotation of type type, with identifier identifier, position position, and additional annotations additionalAnnotation.
SinglePositionSequenceAnnotation(StringBuffer representation)
          Re-creates a SinglePositionSequenceAnnotation from its XML-representation as returned by LocatedSequenceAnnotation.toXML().
 
Method Summary
 
Methods inherited from class de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
fromXML, getPosition, toString, toXML
 
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

SinglePositionSequenceAnnotation

public SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type type,
                                        String identifier,
                                        int position)
Creates a new SinglePositionSequenceAnnotation of type type, with identifier identifier and position position.

Parameters:
position - the position of the SinglePositionSequenceAnnotation on the sequence
type - the type of the annotation
identifier - the identifier of the annotation

SinglePositionSequenceAnnotation

public SinglePositionSequenceAnnotation(SinglePositionSequenceAnnotation.Type type,
                                        String identifier,
                                        int position,
                                        Result... additionalAnnotation)
Creates a new SinglePositionSequenceAnnotation of type type, with identifier identifier, position position, and additional annotations additionalAnnotation.

Parameters:
position - the position of the SinglePositionSequenceAnnotation on the sequence
type - the type of the annotation
identifier - the identifier of the annotation
additionalAnnotation -

SinglePositionSequenceAnnotation

public SinglePositionSequenceAnnotation(StringBuffer representation)
                                 throws NonParsableException
Re-creates a SinglePositionSequenceAnnotation from its XML-representation as returned by LocatedSequenceAnnotation.toXML().

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