de.jstacs.data.sequences.annotation
Class LocatedSequenceAnnotation

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

All Implemented Interfaces:

Storable

Direct Known Subclasses:

LocatedSequenceAnnotationWithLength, SinglePositionSequenceAnnotation

public class LocatedSequenceAnnotation
extends SequenceAnnotation

Class for a SequenceAnnotation that has a position on the sequence, e.g for transcription start sites or intron-exon junctions.

Author:

Jan Grau

Field Summary

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

LocatedSequenceAnnotation(int position, String type, String identifier, Collection<Result> results)
Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.

LocatedSequenceAnnotation(int position, String type, String identifier, Result... results)
Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.

LocatedSequenceAnnotation(int position, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotation)
Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) result, and sub annotations.

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

LocatedSequenceAnnotation(String type, String identifier, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotation)
Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) result, and sub annotations.

Method Summary

protected void	fromXML(StringBuffer representation) Parses the contents of a ResultSet from its XML-representation as returned by ResultSet.toXML().
int	getPosition() Returns the position of this LocatedSequenceAnnotation on the sequence.
String	toString()
StringBuffer	toXML() This method returns an XML-representation of an instance of the implementing class.

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

LocatedSequenceAnnotation

public LocatedSequenceAnnotation(int position,
                                 String type,
                                 String identifier,
                                 Result... results)

Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.

Parameters:

position - the position of the LocatedSequenceAnnotation on the sequence

type - the type of the annotation

identifier - the identifier of the annotation

results - the additional annotation

LocatedSequenceAnnotation

public LocatedSequenceAnnotation(int position,
                                 String type,
                                 String identifier,
                                 Collection<Result> results)

Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) result.

Parameters:

position - the position of the LocatedSequenceAnnotation on the sequence

type - the type of the annotation

identifier - the identifier of the annotation

results - the additional annotation

LocatedSequenceAnnotation

public LocatedSequenceAnnotation(int position,
                                 String type,
                                 String identifier,
                                 SequenceAnnotation[] annotations,
                                 Result... additionalAnnotation)

Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) result, and sub annotations.

Parameters:

position - the position of the LocatedSequenceAnnotation on the sequence

type - the type of the annotation

identifier - the identifier of the annotation

annotations - the sub-annotations

additionalAnnotation - the additional annotation

LocatedSequenceAnnotation

public LocatedSequenceAnnotation(String type,
                                 String identifier,
                                 LocatedSequenceAnnotation[] annotations,
                                 Result... additionalAnnotation)

Creates a new LocatedSequenceAnnotation of type type, with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) result, and sub annotations. The position of this LocatedSequenceAnnotation is the minimum of the positions of annotations.,

Parameters:

type - the type of the annotation

identifier - the identifier of the annotation

annotations - the sub-annotations

additionalAnnotation - the additional annotation

LocatedSequenceAnnotation

public LocatedSequenceAnnotation(StringBuffer representation)
                          throws NonParsableException

Re-creates a LocatedSequenceAnnotation from its XML-representation as returned by toXML().

Parameters:

representation - the XML-representation

Throws:

NonParsableException - is thrown if the XML-code could not be parsed

Method Detail

fromXML

protected void fromXML(StringBuffer representation)
                throws NonParsableException

Description copied from class: ResultSet

Parses the contents of a ResultSet from its XML-representation as returned by ResultSet.toXML().

Overrides:

fromXML in class SequenceAnnotation

Parameters:

representation - the XML-representation

Throws:

NonParsableException - is thrown if the XML-code could not be parsed

toXML

public StringBuffer toXML()

Description copied from interface: Storable

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

Specified by:

toXML in interface Storable

Overrides:

toXML in class SequenceAnnotation

Returns:

the XML-representation

getPosition

public int getPosition()

Returns the position of this LocatedSequenceAnnotation on the sequence.

Returns:

the position

toString

public String toString()

Overrides:

toString in class SequenceAnnotation