picard.sam.util

Class PhysicalLocationInt

java.lang.Object

picard.sam.util.PhysicalLocationInt

All Implemented Interfaces:

PhysicalLocation

Direct Known Subclasses:

PhysicalLocationShort

public class PhysicalLocationInt
extends java.lang.Object
implements PhysicalLocation

Small class that provides access to the physical location information about a cluster. All values should be defaulted to -1 if unavailable. Tile should only allow non-zero positive integers, x and y coordinates must be non-negative. This is different from PhysicalLocationShort in that the x and y positions are ints, not shorts thus, they do not overflow within a HiSeqX tile.

Field Summary

Fields

Modifier and Type	Field and Description
short	tile
int	x
int	y

Fields inherited from interface picard.sam.util.PhysicalLocation

NO_VALUE

Constructor Summary

Constructors

Constructor and Description
PhysicalLocationInt()

Method Summary

Modifier and Type	Method and Description
short	getLibraryId()
short	getReadGroup()
short	getTile()
int	getX()
int	getY()
void	setLibraryId(short libraryId)
void	setReadGroup(short readGroup)
void	setTile(short tile)
void	setX(int x)
void	setY(int y)

Methods inherited from class java.lang.Object

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

Methods inherited from interface picard.sam.util.PhysicalLocation

hasLocation

Field Detail

tile

public short tile

x

public int x

y

public int y

Constructor Detail

PhysicalLocationInt

public PhysicalLocationInt()

Method Detail

getReadGroup

public short getReadGroup()

Specified by:

getReadGroup in interface PhysicalLocation

setReadGroup

public void setReadGroup(short readGroup)

Specified by:

setReadGroup in interface PhysicalLocation

getTile

public short getTile()

Specified by:

getTile in interface PhysicalLocation

setTile

public void setTile(short tile)

Specified by:

setTile in interface PhysicalLocation

getX

public int getX()

Specified by:

getX in interface PhysicalLocation

setX

public void setX(int x)

Specified by:

setX in interface PhysicalLocation

getY

public int getY()

Specified by:

getY in interface PhysicalLocation

setY

public void setY(int y)

Specified by:

setY in interface PhysicalLocation

getLibraryId

public short getLibraryId()

Specified by:

getLibraryId in interface PhysicalLocation

setLibraryId

public void setLibraryId(short libraryId)

Specified by:

setLibraryId in interface PhysicalLocation