Class GeneSequence

    • Constructor Detail

      • GeneSequence

        public GeneSequence​(ChromosomeSequence parentSequence,
                            int begin,
                            int end,
                            Strand strand)
        A class that keeps track of the details of a GeneSequence which is difficult to properly model. Two important concepts that is difficult to make everything flexible but still work. You can have GFF features that only describe Exons or Exons/Introns or CDS regions and one or more Transcriptions. You can have exon sequences but that does not imply transcription to the actual protein. The GeneSequence will keep track of Exons and Introns but to get a Protein sequence you need to start with a TranscriptSequence and then add CDS sequences. This is also a key class in the biojava-3-genome module for reading and writing GFF3 files
        parentDNASequence -
        begin -
        end - inclusive of end
        strand - force a gene to have strand and transcription sequence will inherit