001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 * Created on DATE
021 *
022 */
023
024package org.biojava.nbio.core.sequence;
025
026
027/**
028 * Used to map the stop codon sequence on a gene
029 * @author Scooter Willis
030 */
031public class StopCodonSequence extends DNASequence {
032
033public DNASequence parentGeneSequence = null;
034
035
036        public StopCodonSequence(TranscriptSequence parentGeneSequence, int begin, int end){
037                this.parentGeneSequence = parentGeneSequence;
038                setBioBegin(begin);
039                setBioEnd(end);
040        }
041
042
043                @Override
044        public int getLength() {
045                return Math.abs(this.getBioEnd() - this.getBioBegin()) + 1;
046        }
047}