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}