/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.core.sequence.compound;



/**
 *
 * @author Andy Yates
 */
public class AmbiguityDNACompoundSet extends DNACompoundSet {

  private static class InitaliseOnDemand {
    public static final AmbiguityDNACompoundSet INSTANCE = new AmbiguityDNACompoundSet();
  }

  public static AmbiguityDNACompoundSet getDNACompoundSet() {
    return InitaliseOnDemand.INSTANCE;
  }

  public AmbiguityDNACompoundSet() {
    super();

    addNucleotideCompound("M", "K",
        "A", "C");
    addNucleotideCompound("R", "Y",
        "A", "G");
    addNucleotideCompound("W", "W",
        "A", "T");
    addNucleotideCompound("S", "S",
        "C", "G");
    addNucleotideCompound("Y", "R",
        "C", "T");
    addNucleotideCompound("K", "M",
        "G", "T");
    addNucleotideCompound("V", "B",
        "A", "C", "G");
    addNucleotideCompound("H", "D",
        "A", "C", "T");
    addNucleotideCompound("D", "H",
        "A", "G", "T");
    addNucleotideCompound("B", "V",
        "C", "G", "T");
    addNucleotideCompound("N", "N", "A", "C", "G", "T");

    addNucleotideCompound("I", "I", "N", "A", "C", "G", "T");

    
    calculateIndirectAmbiguities();
  }
}
