de.jstacs.data.sequences.annotation
Class StrandedLocatedSequenceAnnotationWithLength

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

All Implemented Interfaces:

Storable

Direct Known Subclasses:

MotifAnnotation

public class StrandedLocatedSequenceAnnotationWithLength
extends LocatedSequenceAnnotationWithLength

Class for a SequenceAnnotation that has a position, a length, and an orientation on the strand of a Sequence.

Author:

Jan Grau

Nested Class Summary

static class

StrandedLocatedSequenceAnnotationWithLength.Strand The possible orientations on the strands.

Field Summary

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

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

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

StrandedLocatedSequenceAnnotationWithLength(int position, int length, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) additionalAnnotations, and sub-annotations.

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

StrandedLocatedSequenceAnnotationWithLength(String type, String identifier, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations)
Creates a new StrandedLocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) additionalAnnotations, 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().
String	getStrandedness() Returns the orientation/strandedness of this annotation.
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.LocatedSequenceAnnotationWithLength

getEnd, getLength

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

getPosition

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

StrandedLocatedSequenceAnnotationWithLength

public StrandedLocatedSequenceAnnotationWithLength(int position,
                                                   int length,
                                                   StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
                                                   String type,
                                                   String identifier,
                                                   Result... results)

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

Parameters:

position - the position of the StrandedLocatedSequenceAnnotationWithLength on the sequence

length - the length of the StrandedLocatedSequenceAnnotationWithLength

strandedness - the orientation on the strand

type - the type of the annotation

identifier - the identifier of the annotation

results - the additional annotation

StrandedLocatedSequenceAnnotationWithLength

public StrandedLocatedSequenceAnnotationWithLength(int position,
                                                   int length,
                                                   StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
                                                   String type,
                                                   String identifier,
                                                   Collection<Result> results)

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

Parameters:

position - the position of the StrandedLocatedSequenceAnnotationWithLength on the sequence

length - the length of the StrandedLocatedSequenceAnnotationWithLength

strandedness - the orientation on the strand

type - the type of the annotation

identifier - the identifier of the annotation

results - the additional annotation

StrandedLocatedSequenceAnnotationWithLength

public StrandedLocatedSequenceAnnotationWithLength(int position,
                                                   int length,
                                                   StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
                                                   String type,
                                                   String identifier,
                                                   SequenceAnnotation[] annotations,
                                                   Result... additionalAnnotations)

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

Parameters:

position - the position of the StrandedLocatedSequenceAnnotationWithLength on the sequence

length - the length of the StrandedLocatedSequenceAnnotationWithLength

strandedness - the orientation on the strand

type - the type of the annotation

identifier - the identifier of the annotation

annotations - the sub-annotations

additionalAnnotations - the additional annotation

StrandedLocatedSequenceAnnotationWithLength

public StrandedLocatedSequenceAnnotationWithLength(String type,
                                                   String identifier,
                                                   StrandedLocatedSequenceAnnotationWithLength.Strand strandedness,
                                                   LocatedSequenceAnnotation[] annotations,
                                                   Result... additionalAnnotations)

Creates a new StrandedLocatedSequenceAnnotationWithLength of type type, with identifier identifier, and additional annotation (that does not fit the SequenceAnnotation definitions) additionalAnnotations, and sub-annotations. The position of the new LocatedSequenceAnnotationWithLength is the minimal position of all positions of annotations and the length is determined such that it is the maximum of these positions and (if applicable) the corresponding values of LocatedSequenceAnnotationWithLength.getEnd().

Parameters:

strandedness - the orientation on the strand

type - the type of the annotation

identifier - the identifier of the annotation

annotations - the sub-annotations

additionalAnnotations - the additional annotation

StrandedLocatedSequenceAnnotationWithLength

public StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation)
                                            throws NonParsableException

Re-creates a StrandedLocatedSequenceAnnotationWithLength 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

getStrandedness

public String getStrandedness()

Returns the orientation/strandedness of this annotation.

Returns:

the strandedness

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 LocatedSequenceAnnotationWithLength

Parameters:

representation - the XML-representation

Throws:

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

toString

public String toString()

Overrides:

toString in class LocatedSequenceAnnotationWithLength

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 LocatedSequenceAnnotationWithLength

Returns:

the XML-representation