picard.sam.util

Interface PhysicalLocation

All Superinterfaces:

java.io.Serializable

All Known Implementing Classes:

Fragment, Pair, PhysicalLocationForMateCigar, PhysicalLocationInt, PhysicalLocationShort, ReadEnds, ReadEndsForMarkDuplicates, ReadEndsForMarkDuplicatesWithBarcodes, ReadEndsForMateCigar, TransientFieldPhysicalLocation

public interface PhysicalLocation
extends java.io.Serializable

Small interface that provides access to the physical location information about a cluster. All values should be defaulted to -1 if unavailable. ReadGroup and Tile should only allow non-zero positive integers, x and y coordinates may be negative.

Field Summary

Fields

Modifier and Type	Field and Description
static int	NO_VALUE

Method Summary

Modifier and Type	Method and Description
short	getLibraryId()
short	getReadGroup()
short	getTile()
int	getX()
int	getY()
default boolean	hasLocation() Default implementation of a method to check whether real location data has been set.
void	setLibraryId(short libraryId)
void	setReadGroup(short rg)
void	setTile(short tile)
void	setX(int x)
void	setY(int y)

Field Detail

NO_VALUE

static final int NO_VALUE

See Also:

Constant Field Values

Method Detail

getReadGroup

short getReadGroup()

setReadGroup

void setReadGroup(short rg)

getTile

short getTile()

setTile

void setTile(short tile)

getX

int getX()

setX

void setX(int x)

getY

int getY()

setY

void setY(int y)

getLibraryId

short getLibraryId()

setLibraryId

void setLibraryId(short libraryId)

hasLocation

default boolean hasLocation()

Default implementation of a method to check whether real location data has been set.