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 This enum defines 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)
The standard constructor for the interface Storable.

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, getResultForName, 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

See Also:

LocatedSequenceAnnotation.LocatedSequenceAnnotation(int, String, String, Result...)

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

See Also:

LocatedSequenceAnnotation.LocatedSequenceAnnotation(int, String, String, Result...)

SinglePositionSequenceAnnotation

public SinglePositionSequenceAnnotation(StringBuffer representation)
                                 throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

LocatedSequenceAnnotation.LocatedSequenceAnnotation(StringBuffer), Storable