de.jstacs.data.sequences.annotation
Class SinglePositionSequenceAnnotation

java.lang.Object
  de.jstacs.results.ResultSet
      de.jstacs.data.sequences.annotation.SequenceAnnotation
          de.jstacs.data.sequences.annotation.LocatedSequenceAnnotation
              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 - the additional annotation

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