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 05-06-2018
021 */
022
023package org.biojava.nbio.core.sequence.compound;
024
025import org.biojava.nbio.core.sequence.template.AbstractNucleotideCompoundSet;
026
027/**
028 * @author Maximilian Greil
029 */
030public class ABITracerCompoundSet extends AbstractNucleotideCompoundSet<NucleotideCompound> {
031
032        private static class InitaliseOnDemand {
033                public static final ABITracerCompoundSet INSTANCE = new ABITracerCompoundSet();
034        }
035
036        public static ABITracerCompoundSet getABITracerCompoundSet() {
037                return InitaliseOnDemand.INSTANCE;
038        }
039
040        public ABITracerCompoundSet() {
041                addNucleotideCompound("A", "T");
042                addNucleotideCompound("T", "A");
043                addNucleotideCompound("G", "C");
044                addNucleotideCompound("C", "G");
045                addNucleotideCompound("N", "N");
046                addNucleotideCompound("K", "K");
047                addNucleotideCompound("Y", "Y");
048                addNucleotideCompound("R", "R");
049                addNucleotideCompound("-", "-");
050        }
051
052        @Override
053        public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) {
054                if(equivalents.length == 0) {
055                        return new NucleotideCompound(base, this, complement);
056                }
057                else {
058                        NucleotideCompound[] compounds = new NucleotideCompound[equivalents.length];
059                        for(int i=0; i<compounds.length; i++) {
060                                compounds[i] = getCompoundForString(equivalents[i]);
061                        }
062                        return new NucleotideCompound(base, this, complement, compounds);
063                }
064        }
065}