Class SCF

  • All Implemented Interfaces:
    Chromatogram

    public class SCF
    extends AbstractChromatogram
    A Chromatogram as loaded from an SCF v2 or v3 file. Also loads and exposes the SCF format's "private data" and "comments" sections. The quality values from the SCF are stored as additional sequences on the base call alignment. The labels are the PROB_* constants in this class. The values are IntegerAlphabet.IntegerSymbol objects in the range 0 to 255.
    Author:
    Rhett Sutphin (UI CBCB)
    • Field Detail

      • BYTE_MAX_VALUE

        public static final int BYTE_MAX_VALUE
        Represents the maximum unsigned value of a byte for wrapping purposes
        See Also:
        Constant Field Values
      • SHORT_MAX_VALUE

        public static final int SHORT_MAX_VALUE
        Represents the maximum unsigned value of a short for wrapping purposes
        See Also:
        Constant Field Values
      • PROB_NUC_A

        public static final java.lang.Object PROB_NUC_A
        Base call alignment sequence label for the probability that call should be A.
      • PROB_NUC_C

        public static final java.lang.Object PROB_NUC_C
        Base call alignment sequence label for the probability that call should be C.
      • PROB_NUC_G

        public static final java.lang.Object PROB_NUC_G
        Base call alignment sequence label for the probability that call should be G.
      • PROB_NUC_T

        public static final java.lang.Object PROB_NUC_T
        Base call alignment sequence label for the probability that call should be T.
      • PROB_SUBSTITUTION

        public static final java.lang.Object PROB_SUBSTITUTION
        Base call alignment sequence label for the substitution probability. In versions of the SCF spec before 3.10, this is called spareQual[0].
      • PROB_OVERCALL

        public static final java.lang.Object PROB_OVERCALL
        Base call alignment sequence label for the overcall probability. In versions of the SCF spec before 3.10, this is called spareQual[1].
      • PROB_UNDERCALL

        public static final java.lang.Object PROB_UNDERCALL
        Base call alignment sequence label for the undercall probability. In versions of the SCF spec before 3.10, this is called spareQual[2].
    • Constructor Detail

      • SCF

        protected SCF()
        Creates a new, completely empty SCF.