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 */
021
022package org.biojava.bio.molbio;
023
024import org.biojava.bio.BioError;
025import org.biojava.bio.seq.DNATools;
026import org.biojava.bio.symbol.IllegalSymbolException;
027
028/**
029 * Computes composition statistics about a DNA <code>SymbolList</code>.
030 * 
031 * @author Mark Schreiber
032 * @since 1.6
033 */
034public class DNAComposition extends Composition{
035
036    
037    public DNAComposition(){
038        super();
039        try {
040            setSymbolList(DNATools.createDNA("acgt"));
041        } catch (IllegalSymbolException ex) {
042            System.err.println("Severe Error. Cannot create DNA SymbolList with 'acgt");
043        }
044    }
045    
046    /**
047     * Get the relative compositon of 'A'.
048     * @return between 0.0 and 1.0
049     */
050    public double getA(){
051        try {
052            return getDistribution().getWeight(DNATools.a());
053        } catch (IllegalSymbolException ex) {
054            throw new BioError("Severe Error with DNA configuration.",ex);
055        }
056    }
057    
058    /**
059     * Get the relative compositon of 'C'.
060     * @return between 0.0 and 1.0
061     */
062    public double getC(){
063        try {
064            return getDistribution().getWeight(DNATools.c());
065        } catch (IllegalSymbolException ex) {
066            throw new BioError("Severe Error with DNA configuration.",ex);
067        }
068    }
069    
070    /**
071     * Get the relative compositon of 'G'.
072     * @return between 0.0 and 1.0
073     */
074    public double getG(){
075        try {
076            return getDistribution().getWeight(DNATools.g());
077        } catch (IllegalSymbolException ex) {
078            throw new BioError("Severe Error with DNA configuration.",ex);
079        }
080    }
081    
082    /**
083     * Get the relative compositon of 'T'.
084     * @return between 0.0 and 1.0
085     */
086    public double getT(){
087        try {
088            return getDistribution().getWeight(DNATools.t());
089        } catch (IllegalSymbolException ex) {
090            throw new BioError("Severe Error with DNA configuration.",ex);
091        }
092    }
093}