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 01-21-2010
021 */
022package org.biojava.nbio.core.sequence.compound;
023
024import org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet;
025
026/**
027 * @author Andy Yates
028 */
029public class DNACompoundSet extends AbstractNucleotideCompoundSet<NucleotideCompound> {
030
031        private static class InitaliseOnDemand {
032                public static final DNACompoundSet INSTANCE = new DNACompoundSet();
033        }
034
035        public static DNACompoundSet getDNACompoundSet() {
036                return InitaliseOnDemand.INSTANCE;
037        }
038
039        public DNACompoundSet() {
040                addNucleotideCompound("A", "T");
041                addNucleotideCompound("T", "A");
042                addNucleotideCompound("G", "C");
043                addNucleotideCompound("C", "G");
044                addNucleotideCompound("N", "N");
045                addNucleotideCompound("-", "-");
046        }
047
048        @Override
049public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) {
050                if(equivalents.length == 0) {
051                        return new NucleotideCompound(base, this, complement);
052                }
053                else {
054                        NucleotideCompound[] compounds = new NucleotideCompound[equivalents.length];
055                        for(int i=0; i<compounds.length; i++) {
056                                compounds[i] = getCompoundForString(equivalents[i]);
057                        }
058                        return new NucleotideCompound(base, this, complement, compounds);
059                }
060        }
061}