de.jstacs.data.sequences.annotation

Class LocatedSequenceAnnotationWithLength

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

All Implemented Interfaces:

Storable

Direct Known Subclasses:

IntronAnnotation, StrandedLocatedSequenceAnnotationWithLength

public class LocatedSequenceAnnotationWithLength
extends LocatedSequenceAnnotation

Class for a SequenceAnnotation that has a position on the sequence and a length, e.g. for donor splice sites, exons or genes.

Author:

Jan Grau

Field Summary

Fields inherited from class de.jstacs.results.ResultSet

results

Constructor Summary

Constructors

Constructor and Description
LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, Collection<Result> results) Creates a new LocatedSequenceAnnotationWithLength of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as a Collection of Results result.
LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, Result... results) Creates a new LocatedSequenceAnnotationWithLength of type type with identifier identifier and additional annotation (that does not fit the SequenceAnnotation definitions) given as an array of Results result.
LocatedSequenceAnnotationWithLength(int position, int length, String type, String identifier, SequenceAnnotation[] annotations, Result... additionalAnnotations) Creates a new LocatedSequenceAnnotationWithLength 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.
LocatedSequenceAnnotationWithLength(StringBuffer representation) The standard constructor for the interface Storable.
LocatedSequenceAnnotationWithLength(String type, String identifier, LocatedSequenceAnnotation[] annotations, Result... additionalAnnotations) Creates a new LocatedSequenceAnnotationWithLength 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

Methods

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	getEnd() Returns the end of this LocatedSequenceAnnotationWithLength, i.e.
int	getLength() Returns the length of this LocatedSequenceAnnotationWithLength as given in the constructor.
boolean	overlaps(LocatedSequenceAnnotationWithLength second) Returns true if this LocatedSequenceAnnotationWithLength overlaps with the location of second.
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.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

LocatedSequenceAnnotationWithLength

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

Creates a new LocatedSequenceAnnotationWithLength 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 LocatedSequenceAnnotationWithLength on the sequence

length - the length of the LocatedSequenceAnnotationWithLength

type - the type of the annotation

identifier - the identifier of the annotation

results - the additional annotation

See Also:

LocatedSequenceAnnotation.LocatedSequenceAnnotation(int, String, String, Result...)

LocatedSequenceAnnotationWithLength

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

Creates a new LocatedSequenceAnnotationWithLength 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 LocatedSequenceAnnotationWithLength on the sequence

length - the length of the LocatedSequenceAnnotationWithLength

type - the type of the annotation

identifier - the identifier of the annotation

results - the additional annotation

See Also:

LocatedSequenceAnnotation.LocatedSequenceAnnotation(int, String, String, Collection)

LocatedSequenceAnnotationWithLength

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

Creates a new LocatedSequenceAnnotationWithLength 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 LocatedSequenceAnnotationWithLength on the sequence

length - the length of the LocatedSequenceAnnotationWithLength

type - the type of the annotation

identifier - the identifier of the annotation

annotations - the sub-annotations

additionalAnnotations - the additional annotation

See Also:

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

LocatedSequenceAnnotationWithLength

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

Creates a new LocatedSequenceAnnotationWithLength 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 getEnd().

Parameters:

type - the type of the annotation

identifier - the identifier of the annotation

annotations - the sub-annotations

additionalAnnotations - the additional annotation

See Also:

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

LocatedSequenceAnnotationWithLength

public LocatedSequenceAnnotationWithLength(StringBuffer representation)
                                    throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

LocatedSequenceAnnotation.LocatedSequenceAnnotation(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 LocatedSequenceAnnotation

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 LocatedSequenceAnnotation

Returns:

the XML representation

getLength

public int getLength()

Returns the length of this LocatedSequenceAnnotationWithLength as given in the constructor.

Returns:

the length of this LocatedSequenceAnnotationWithLength

getEnd

public int getEnd()

Returns the end of this LocatedSequenceAnnotationWithLength, i.e. LocatedSequenceAnnotation.getPosition() + getLength().

Returns:

the end of this LocatedSequenceAnnotationWithLength

See Also:

LocatedSequenceAnnotation.getPosition(), getLength()

toString

public String toString()

Overrides:

toString in class LocatedSequenceAnnotation

overlaps

public boolean overlaps(LocatedSequenceAnnotationWithLength second)

Returns true if this LocatedSequenceAnnotationWithLength overlaps with the location of second.

Parameters:

second - the other LocatedSequenceAnnotationWithLength

Returns:

if both annotations overlap