Package picard.sam.util
Interface PhysicalLocation
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- All Superinterfaces:
Serializable
- All Known Implementing Classes:
PhysicalLocationForMateCigar
,PhysicalLocationInt
,PhysicalLocationShort
,ReadEnds
,ReadEndsForMarkDuplicates
,ReadEndsForMarkDuplicatesWithBarcodes
,ReadEndsForMateCigar
public interface PhysicalLocation extends 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.
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Field Summary
Fields Modifier and Type Field Description static int
NO_VALUE
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Method Summary
All Methods Instance Methods Abstract Methods Default Methods Modifier and Type Method 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)
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Field Detail
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NO_VALUE
static final int NO_VALUE
- See Also:
- Constant Field Values
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Method Detail
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getReadGroup
short getReadGroup()
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setReadGroup
void setReadGroup(short rg)
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getTile
short getTile()
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setTile
void setTile(short tile)
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getX
int getX()
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setX
void setX(int x)
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getY
int getY()
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setY
void setY(int y)
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getLibraryId
short getLibraryId()
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setLibraryId
void setLibraryId(short libraryId)
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hasLocation
default boolean hasLocation()
Default implementation of a method to check whether real location data has been set.
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