Class FullBEDFeature.Exon

  • Enclosing class:
    FullBEDFeature

    public class FullBEDFeature.Exon
    extends Object
    A sub region of a feature. For example, a Gene exon
    • Constructor Detail

      • Exon

        public Exon​(int start,
                    int end)
        Constructs ...
        Parameters:
        start -
        end -
    • Method Detail

      • setMrnaBase

        public void setMrnaBase​(int base)
      • setUTR

        public void setUTR​(boolean utr)
        Flag indicating that the entire exon is the UTR.
        Parameters:
        utr -
      • setCodingStart

        public void setCodingStart​(int codingStart)
        Method description
        Parameters:
        codingStart -
      • setCodingEnd

        public void setCodingEnd​(int codingEnd)
        Method description
        Parameters:
        codingEnd -
      • setReadingFrame

        public void setReadingFrame​(int offset)
        Method description
        Parameters:
        offset -
      • setPhase

        public void setPhase​(int phase)
        Method description
        Parameters:
        phase -
      • getCdStart

        public int getCdStart()
        Method description
        Returns:
      • getCdEnd

        public int getCdEnd()
        Method description
        Returns:
      • getCodingLength

        public int getCodingLength()
        Method description
        Returns:
      • getValueString

        public String getValueString​(double position)
      • getNumber

        public int getNumber()
      • setNumber

        public void setNumber​(int number)