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 */
023package org.biojava.nbio.core.sequence;
024
025import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
026import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
027
028/**
029 * A gene contains a collection of Exon sequences
030 * @author Scooter Willis
031 */
032public class ExonSequence extends DNASequence {
033
034
035        /**
036         * Need a parent gene sequence and the bioBegin and bioEnd. An Exon sequence doesn't actually imply what the
037         * protein coding sequence will be. This is a little difficult to model and have it make sense.
038         * A gene has a collection of Exon and Intron sequences where the Exon sequences will join up. A gene
039         * sequences has a collection of different possible isoform proteins based on the transcription rules.
040         * A TranscriptionSequence will contain CDSSequence where the CDSSequence will be contained in the ExonSequence.
041         * Thus a ExonSequence is the union of overlapping CDSSequences.
042         * @param parentGeneSequence
043         * @param bioBegin
044         * @param bioEnd
045         */
046        public ExonSequence(GeneSequence parentGeneSequence, int bioBegin, int bioEnd) {
047                setCompoundSet(DNACompoundSet.getDNACompoundSet());
048                try {
049                        initSequenceStorage(parentGeneSequence.getSequenceAsString());
050                } catch (CompoundNotFoundException e) {
051                        throw new IllegalArgumentException(e);
052                }
053                this.setParentSequence(parentGeneSequence);
054                setBioBegin(bioBegin);
055                setBioEnd(bioEnd);
056
057        }
058
059        @Override
060        public int getLength() {
061                return Math.abs(this.getBioEnd() - this.getBioBegin()) + 1;
062        }
063
064
065}