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

Nested Classes

Modifier and Type	Class and Description
static class	StrandedLocatedSequenceAnnotationWithLength.Strand This enum defines possible orientations on the strands.

Field Summary

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

Constructors

Constructor and Description
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) given as a Collection of Results results.
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) given as an array of Results results.
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, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations annotations.
StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation) The standard constructor for the interface Storable.
StrandedLocatedSequenceAnnotationWithLength(String type, String identifier, StrandedLocatedSequenceAnnotationWithLength.Strand strandedness, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations) Creates a new StrandedLocatedSequenceAnnotationWithLength of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations 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().
StrandedLocatedSequenceAnnotationWithLength.Strand	getStrandedness() Returns the strandedness, i.e the orientation of this annotation.
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.LocatedSequenceAnnotationWithLength

getEnd, getLength, overlaps

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, 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

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) given as an array of Results results.

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

See Also:

LocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(int, int, String, String, Result...)

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) given as a Collection of Results results.

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

See Also:

LocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(int, int, String, String, Collection)

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, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations 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

See Also:

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

StrandedLocatedSequenceAnnotationWithLength

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

Creates a new StrandedLocatedSequenceAnnotationWithLength of type type with identifier identifier, additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results additionalAnnotations and sub-annotations annotations. The position of the new LocatedSequenceAnnotationWithLength is the minimal position of all positions of annotations and the length is determined so 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

See Also:

LocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(String, String, LocatedSequenceAnnotation[], Result...), LocatedSequenceAnnotationWithLength.getEnd()

StrandedLocatedSequenceAnnotationWithLength

public StrandedLocatedSequenceAnnotationWithLength(StringBuffer representation)
                                            throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

LocatedSequenceAnnotationWithLength.LocatedSequenceAnnotationWithLength(StringBuffer), Storable

Method Detail

getStrandedness

public StrandedLocatedSequenceAnnotationWithLength.Strand getStrandedness()

Returns the strandedness, i.e the orientation of this annotation.

Returns:

the strandedness, i.e. the orientation

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 as StringBuffer

Throws:

NonParsableException - 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 as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class LocatedSequenceAnnotationWithLength

Returns:

the XML representation