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    package org.biojava3.core.sequence;
024    
025    import java.util.logging.Logger;
026    
027    /**
028     * A gene contains a collection of Exon sequences
029     * @author Scooter Willis
030     */
031    public class ExonSequence extends DNASequence {
032    
033        private static final Logger log = Logger.getLogger(ExonSequence.class.getName());
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            this.setParentSequence(parentGeneSequence);
048            setBioBegin(bioBegin);
049            setBioEnd(bioEnd);
050    
051        }
052    }