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

Constructors

Constructor and Description
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) given as a Collection of Results 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) given as an array of Results 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) given as an array of Results additionalAnnotation and sub-annotations annotations.
LocatedSequenceAnnotation(StringBuffer representation) The standard constructor for the interface Storable.
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) given as an array of Results additionalAnnotation and sub-annotations annotations.

Method Summary

Modifier and Type	Method and Description
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 as StringBuffer of an instance of the implementing class.

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

getAnnotations, getIdentifier, getSubAnnotations, getType, hashCode

Methods inherited from class de.jstacs.results.ResultSet

findColumn, getNumberOfResults, getResultAt, getResultForName, getResults

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, 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) given as an array of Results 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

See Also:

SequenceAnnotation.SequenceAnnotation(String, String, Result[][])

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) given as a Collection of Results 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

See Also:

SequenceAnnotation.SequenceAnnotation(String, String, Collection)

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) given as an array of Results additionalAnnotation and sub-annotations 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

See Also:

SequenceAnnotation.SequenceAnnotation(String, String, SequenceAnnotation[], Result...)

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) given as an array of Results additionalAnnotation and sub-annotations 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

See Also:

SequenceAnnotation.SequenceAnnotation(String, String, SequenceAnnotation[], Result...)

LocatedSequenceAnnotation

public LocatedSequenceAnnotation(StringBuffer representation)
                          throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

SequenceAnnotation.SequenceAnnotation(StringBuffer), Storable

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 as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

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

getPosition

public int getPosition()

Returns the position of this LocatedSequenceAnnotation on the sequence.

Returns:

the position on the sequence

toString

public String toString()

Overrides:

toString in class SequenceAnnotation