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     */
022    package org.biojava3.core.sequence.compound;
023    
024    import org.biojava3.core.sequence.template.AbstractNucleotideCompoundSet;
025    
026    /**
027     * @author Andy Yates
028     */
029    public 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      public NucleotideCompound newNucleotideCompound(String base, String complement, String... equivalents) {
049        if(equivalents.length == 0) {
050          return new NucleotideCompound(base, this, complement);
051        }
052        else {
053          NucleotideCompound[] compounds = new NucleotideCompound[equivalents.length];
054          for(int i=0; i<compounds.length; i++) {
055            compounds[i] = getCompoundForString(equivalents[i]);
056          }
057          return new NucleotideCompound(base, this, complement, compounds);
058        }
059      }
060    }