Class Substitution

  • All Implemented Interfaces:
    ReadFeature, Serializable

    public class Substitution
    extends Object
    implements Serializable, ReadFeature
    A substitution event captured in read coordinates. It is characterized by position in read, read base and reference base. The class is also responsible for converting combinations of read base and reference base into a byte value (code). Both reference and read bases must be ACGTN only.
    See Also:
    Serialized Form
    • Constructor Detail

      • Substitution

        public Substitution()
      • Substitution

        public Substitution​(int position,
                            byte base,
                            byte referenceBase)
    • Method Detail

      • getCode

        public byte getCode()
      • setCode

        public void setCode​(byte code)
      • getOperator

        public byte getOperator()
        Description copied from interface: ReadFeature
        Read features are distinguished by operator, similar to cigar operator.
        Specified by:
        getOperator in interface ReadFeature
        Returns:
        type of the read feature
      • getPosition

        public int getPosition()
        Specified by:
        getPosition in interface ReadFeature
        Returns:
        zero-based position in the read
      • setPosition

        public void setPosition​(int position)
        Specified by:
        setPosition in interface ReadFeature
      • getBase

        public byte getBase()
      • setBase

        public void setBase​(byte base)
      • getReferenceBase

        public byte getReferenceBase()
      • setReferenceBase

        public void setReferenceBase​(byte referenceBase)