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; 024 025 026 027/** 028 * A gene contains a collection of Exon sequences 029 * @author Scooter Willis 030 */ 031public 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 } 052 053 @Override 054 public int getLength() { 055 return Math.abs(this.getBioEnd() - this.getBioBegin()) + 1; 056 } 057 058 059}