Interface PhysicalLocation

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.
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final int
     
  • Method Summary

    Modifier and Type
    Method
    Description
    short
     
    short
     
    short
     
    int
     
    int
     
    default boolean
    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 Details

  • Method Details

    • 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.