Class Cds

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Interval>, MarkerWithFrame, TxtSerializable

    public class Cds
    extends Marker
    implements MarkerWithFrame
    CDS: The coding region of a gene, also known as the coding sequence or CDS (from Coding DNA Sequence), is that portion of a gene's DNA or RNA, composed of exons, that codes for protein.
    Author:
    pcingola
    See Also:
    Serialized Form
    • Constructor Detail

      • Cds

        public Cds()
      • Cds

        public Cds​(Transcript parent,
                   int start,
                   int end,
                   boolean strandMinus,
                   java.lang.String id)
    • Method Detail

      • cloneShallow

        public Cds cloneShallow()
        Description copied from class: Marker
        Perform a shallow clone
        Overrides:
        cloneShallow in class Marker
      • frameCorrection

        public boolean frameCorrection​(int frameCorrection)
        Correct coordinates according to frame differences
        Parameters:
        frameCorrection -
      • setFrame

        public void setFrame​(int frame)
        Frame can be {-1, 0, 1, 2}, where '-1' means unknown
        Specified by:
        setFrame in interface MarkerWithFrame
        Parameters:
        frame -
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class Marker