Class ClusterData


  • public class ClusterData
    extends Object
    Store the information from Illumina files for a single cluster with one or more reads.
    • Constructor Detail

      • ClusterData

        public ClusterData​(ReadData... reads)
        Used for testing, reads is set directly with no copying to the input array
      • ClusterData

        public ClusterData​(ReadType[] readTypes)
        Creates a ClusterData with one read for each type provided
    • Method Detail

      • getTile

        public int getTile()
      • setTile

        public void setTile​(int tile)
      • tileIsSet

        public boolean tileIsSet()
      • getRead

        public ReadData getRead​(int index)
      • getNumReads

        public int getNumReads()
      • setOrCheckTile

        public void setOrCheckTile​(int tile)
        Either set this value if not already set, or if already set, throw an exception if new value != current value.
      • getLane

        public int getLane()
      • setLane

        public void setLane​(int lane)
      • laneIsSet

        public boolean laneIsSet()
      • setOrCheckLane

        public void setOrCheckLane​(int lane)
        Either set this value if not already set, or if already set, throw an exception if new value != current value.
      • getX

        public int getX()
      • setX

        public void setX​(int x)
      • xIsSet

        public boolean xIsSet()
      • setOrCheckX

        public void setOrCheckX​(int x)
        Either set this value if not already set, or if already set, throw an exception if new value != current value.
      • getY

        public int getY()
      • setY

        public void setY​(int y)
      • yIsSet

        public boolean yIsSet()
      • setOrCheckY

        public void setOrCheckY​(int y)
        Either set this value if not already set, or if already set, throw an exception if new value != current value.
      • setPf

        public void setPf​(boolean pf)
      • setOrCheckPf

        public void setOrCheckPf​(boolean pf)
        Either set this value if not already set, or if already set, throw an exception if new value != current value.
      • getMatchedBarcode

        public String getMatchedBarcode()
        Returns:
        The barcode matched (not the actual sequence from the read, which may not perfectly match the barcode).
      • setMatchedBarcode

        public void setMatchedBarcode​(String matchedBarcode)