Class CDSSequence

  • All Implemented Interfaces:
    java.lang.Iterable<NucleotideCompound>, Accessioned, Sequence<NucleotideCompound>

    public class CDSSequence
    extends DNASequence
    Represents a exon or coding sequence in a gene. It has a parent TranscriptSequence where a TranscriptSequence is the child of a GeneSequence Not important for protein construction but the phase is used if outputting the gene to a gff3 file. {@link http://www.sequenceontology.org/gff3.shtml}
    Author:
    Scooter Willis
    • Constructor Detail

      • CDSSequence

        public CDSSequence​(TranscriptSequence parentSequence,
                           int bioBegin,
                           int bioEnd,
                           int phase)
        Parameters:
        parentSequence -
        bioBegin -
        bioEnd -
        phase -
    • Method Detail

      • getPhase

        public java.lang.Integer getPhase()
        Returns:
        get the phase
      • getStrand

        public Strand getStrand()
        Returns:
        get the strand
      • getCodingSequence

        public java.lang.String getCodingSequence()
        A CDS sequence if negative stranded needs to be reverse complement to represent the actual coding sequence. When getting a ProteinSequence from a TranscriptSequence this method is callled for each CDSSequence {@link http://www.sequenceontology.org/gff3.shtml} {@link http://biowiki.org/~yam/bioe131/GFF.ppt}
        Returns:
        coding sequence