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 */
021package org.biojava.nbio.core.sequence.compound;
022
023
024/**
025 *
026 * @author Andy Yates
027 */
028public class AmbiguityRNACompoundSet extends RNACompoundSet {
029
030        private static class InitaliseOnDemand {
031        public static final AmbiguityRNACompoundSet INSTANCE = new AmbiguityRNACompoundSet();
032        }
033
034        public static AmbiguityRNACompoundSet getRNACompoundSet() {
035        return InitaliseOnDemand.INSTANCE;
036        }
037
038        public AmbiguityRNACompoundSet() {
039
040        addNucleotideCompound("A", "U");
041        addNucleotideCompound("U", "A");
042        addNucleotideCompound("G", "C");
043        addNucleotideCompound("C", "G");
044
045        addNucleotideCompound("M", "K",
046                "A", "C");
047        addNucleotideCompound("R", "Y",
048                "A", "G");
049        addNucleotideCompound("W", "W",
050                "A", "U");
051        addNucleotideCompound("S", "S",
052                "C", "G");
053        addNucleotideCompound("Y", "R",
054                "C", "U");
055        addNucleotideCompound("K", "M",
056                "G", "U");
057        addNucleotideCompound("V", "B",
058                "A", "C", "G");
059        addNucleotideCompound("H", "D",
060                "A", "C", "U");
061        addNucleotideCompound("D", "H",
062                "A", "G", "U");
063        addNucleotideCompound("B", "V",
064                "C", "G", "U");
065        addNucleotideCompound("N", "N",
066                "A", "C", "G", "U", "M", "R", "W", "S", "Y", "K", "V", "H", "D", "B");
067
068        calculateIndirectAmbiguities();
069        }
070
071}