uk.ac.roslin.ensembl.model

Class Mapping

java.lang.Object

uk.ac.roslin.ensembl.model.Mapping

All Implemented Interfaces:

Serializable

Direct Known Subclasses:

VariationMapping

public class Mapping
extends Object
implements Serializable

Used to be abstract

Author:

paterson

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static uk.ac.roslin.ensembl.model.MappingOnSourceComparator	mappingOnSourceComparator
static uk.ac.roslin.ensembl.model.MappingOnTargetComparator	mappingOnTargetComparator
protected Mapping	reverseMapping
protected MappableObject	source
protected Coordinate	sourceCoordinates
protected CoordinateSystem	sourceCoordSystem
protected MappableObject	target
protected Coordinate	targetCoordinates
protected CoordinateSystem	targetCoordSystem

Constructor Summary

Constructors

Constructor and Description
Mapping()

Method Summary

Methods

Modifier and Type	Method and Description
static boolean	addReverseMapping(Mapping originalMapping)
boolean	equals(Object mapping)
Mapping	getReverseMapping()
MappableObject	getSource()
Coordinate	getSourceCoordinates()
String	getSourceHashID()
ObjectType	getSourceType()
MappableObject	getTarget()
Coordinate	getTargetCoordinates()
String	getTargetHashID()
ObjectType	getTargetType()
int	hashCode()
void	setReverseMapping(Mapping reverseMapping)
void	setSource(MappableObject source)
void	setSourceCoordinates(Coordinate coord)
void	setSourceCoordinates(Integer start, Integer end, Coordinate.Strand strand) Sets the source coordinate by creating a new Coordinate object form the given parameters.
void	setSourceCoordinates(Integer start, Integer end, Integer strand) Sets the source coordinate by creating a new Coordinate object form the given parameters.
void	setTarget(MappableObject target)
void	setTargetCoordinates(Coordinate coord)
void	setTargetCoordinates(Integer start, Integer end, Coordinate.Strand strand) Sets the target coordinate by creating a new Coordinate object form the given parameters.
void	setTargetCoordinates(Integer start, Integer end, Integer strand) Sets the target coordinate by creating a new Coordinate object form the given parameters.

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Detail

source

protected MappableObject source

target

protected MappableObject target

sourceCoordinates

protected Coordinate sourceCoordinates

targetCoordinates

protected Coordinate targetCoordinates

sourceCoordSystem

protected CoordinateSystem sourceCoordSystem

targetCoordSystem

protected CoordinateSystem targetCoordSystem

reverseMapping

protected Mapping reverseMapping

mappingOnSourceComparator

public static final uk.ac.roslin.ensembl.model.MappingOnSourceComparator mappingOnSourceComparator

mappingOnTargetComparator

public static final uk.ac.roslin.ensembl.model.MappingOnTargetComparator mappingOnTargetComparator

Constructor Detail

Mapping

public Mapping()

Method Detail

addReverseMapping

public static boolean addReverseMapping(Mapping originalMapping)

setSource

public void setSource(MappableObject source)

setTarget

public void setTarget(MappableObject target)

getSource

public MappableObject getSource()

getTarget

public MappableObject getTarget()

getTargetType

public ObjectType getTargetType()

getSourceType

public ObjectType getSourceType()

getTargetHashID

public String getTargetHashID()

getSourceHashID

public String getSourceHashID()

getSourceCoordinates

public Coordinate getSourceCoordinates()

getTargetCoordinates

public Coordinate getTargetCoordinates()

setSourceCoordinates

public void setSourceCoordinates(Coordinate coord)

setTargetCoordinates

public void setTargetCoordinates(Coordinate coord)

setSourceCoordinates

public void setSourceCoordinates(Integer start,
                        Integer end,
                        Coordinate.Strand strand)

Sets the source coordinate by creating a new Coordinate object form the given parameters. Note that ZERO and null locations are disallowed and will throw IllegalArgument RuntimeExceptions.

Parameters:

start -

end -

strand -

setSourceCoordinates

public void setSourceCoordinates(Integer start,
                        Integer end,
                        Integer strand)

Sets the source coordinate by creating a new Coordinate object form the given parameters. Note that ZERO and null locations are disallowed and will throw IllegalArgument RuntimeExceptions.

Parameters:

start -

end -

strand -

setTargetCoordinates

public void setTargetCoordinates(Integer start,
                        Integer end,
                        Coordinate.Strand strand)

Sets the target coordinate by creating a new Coordinate object form the given parameters. Note that ZERO and null locations are disallowed and will throw IllegalArgument RuntimeExceptions.

Parameters:

start -

end -

strand -

setTargetCoordinates

public void setTargetCoordinates(Integer start,
                        Integer end,
                        Integer strand)

Sets the target coordinate by creating a new Coordinate object form the given parameters. Note that ZERO and null locations are disallowed and will throw IllegalArgument RuntimeExceptions.

Parameters:

start -

end -

strand -

equals

public boolean equals(Object mapping)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getReverseMapping

public Mapping getReverseMapping()

setReverseMapping

public void setReverseMapping(Mapping reverseMapping)