de.jstacs.data.sequences.annotation
Class ReferenceSequenceAnnotation

java.lang.Object
  de.jstacs.results.ResultSet
      de.jstacs.data.sequences.annotation.SequenceAnnotation
          de.jstacs.data.sequences.annotation.ReferenceSequenceAnnotation

All Implemented Interfaces:

Storable

public class ReferenceSequenceAnnotation
extends SequenceAnnotation

This class implements a SequenceAnnotation that contains a reference sequence. This sequence can be obtained using the method getReferenceSequence().

Author:

Jan Grau

Field Summary

static String

TYPE The type of a ReferenceSequenceAnnotation.

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

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

ReferenceSequenceAnnotation(String identifier, Sequence ref, Result... results)
Creates a new ReferenceSequenceAnnotation with identifier identifier, reference sequence ref, and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Result result.

Method Summary

Sequence	getReferenceSequence() Returns the reference sequence.
String	toString()
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

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

fromXML, 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

Field Detail

TYPE

public static final String TYPE

The type of a ReferenceSequenceAnnotation.

See Also:

SequenceAnnotation.getType(), Constant Field Values

Constructor Detail

ReferenceSequenceAnnotation

public ReferenceSequenceAnnotation(String identifier,
                                   Sequence ref,
                                   Result... results)

Creates a new ReferenceSequenceAnnotation with identifier identifier, reference sequence ref, and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Result result.

Parameters:

identifier - the identifier of the annotation

ref - the reference sequence

results - the additional annotation

See Also:

ResultSet.ResultSet(Result)

ReferenceSequenceAnnotation

public ReferenceSequenceAnnotation(StringBuffer representation)
                            throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

SequenceAnnotation.SequenceAnnotation(StringBuffer), Storable

Method Detail

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class SequenceAnnotation

Returns:

the XML representation

toString

public String toString()

Overrides:

toString in class SequenceAnnotation

getReferenceSequence

public Sequence getReferenceSequence()

Returns the reference sequence.

Returns:

the reference sequence