Translator.java

/*************************************************************************
*                                                                        *
*  This file is part of the 20n/act project.                             *
*  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
*  Copyright (C) 2017 20n Labs, Inc.                                     *
*                                                                        *
*  Please direct all queries to act@20n.com.                             *
*                                                                        *
*  This program is free software: you can redistribute it and/or modify  *
*  it under the terms of the GNU General Public License as published by  *
*  the Free Software Foundation, either version 3 of the License, or     *
*  (at your option) any later version.                                   *
*                                                                        *
*  This program is distributed in the hope that it will be useful,       *
*  but WITHOUT ANY WARRANTY; without even the implied warranty of        *
*  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
*  GNU General Public License for more details.                          *
*                                                                        *
*  You should have received a copy of the GNU General Public License     *
*  along with this program.  If not, see <http://www.gnu.org/licenses/>. *
*                                                                        *
*************************************************************************/

package org.twentyn.proteintodna;

import java.util.HashMap;
import java.util.Map;

public class Translator {
    
    private  Map<String,String> GeneticCode;
    
    public Translator() {
        GeneticCode = new HashMap<>();
    
        GeneticCode.put("TCA", "S");
        GeneticCode.put("TCC", "S");
        GeneticCode.put("TCG", "S");
        GeneticCode.put("TCT", "S");
        GeneticCode.put("TTC", "F");
        GeneticCode.put("TTT", "F");
        GeneticCode.put("TTA", "L");
        GeneticCode.put("TTG", "L");
        GeneticCode.put("TAC", "Y");
        GeneticCode.put("TAT", "Y");
        GeneticCode.put("TAA", "*");
        GeneticCode.put("TAG", "*");
        GeneticCode.put("TGC", "C");
        GeneticCode.put("TGT", "C");
        GeneticCode.put("TGA", "*");
        GeneticCode.put("TGG", "W");
        GeneticCode.put("CTA", "L");
        GeneticCode.put("CTC", "L");
        GeneticCode.put("CTG", "L");
        GeneticCode.put("CTT", "L");
        GeneticCode.put("CCA", "P");
        GeneticCode.put("CCC", "P");
        GeneticCode.put("CCG", "P");
        GeneticCode.put("CCT", "P");
        GeneticCode.put("CAC", "H");
        GeneticCode.put("CAT", "H");
        GeneticCode.put("CAA", "Q");
        GeneticCode.put("CAG", "Q");
        GeneticCode.put("CGA", "R");
        GeneticCode.put("CGC", "R");
        GeneticCode.put("CGG", "R");
        GeneticCode.put("CGT", "R");
        GeneticCode.put("ATA", "I");
        GeneticCode.put("ATC", "I");
        GeneticCode.put("ATT", "I");
        GeneticCode.put("ATG", "M");
        GeneticCode.put("ACA", "T");
        GeneticCode.put("ACC", "T");
        GeneticCode.put("ACG", "T");
        GeneticCode.put("ACT", "T");
        GeneticCode.put("AAC", "N");
        GeneticCode.put("AAT", "N");
        GeneticCode.put("AAA", "K");
        GeneticCode.put("AAG", "K");
        GeneticCode.put("AGC", "S");
        GeneticCode.put("AGT", "S");
        GeneticCode.put("AGA", "R");
        GeneticCode.put("AGG", "R");
        GeneticCode.put("GTA", "V");
        GeneticCode.put("GTC", "V");
        GeneticCode.put("GTG", "V");
        GeneticCode.put("GTT", "V");
        GeneticCode.put("GCA", "A");
        GeneticCode.put("GCC", "A");
        GeneticCode.put("GCG", "A");
        GeneticCode.put("GCT", "A");
        GeneticCode.put("GAC", "D");
        GeneticCode.put("GAT", "D");
        GeneticCode.put("GAA", "E");
        GeneticCode.put("GAG", "E");
        GeneticCode.put("GGA", "G");
        GeneticCode.put("GGC", "G");
        GeneticCode.put("GGG", "G");
        GeneticCode.put("GGT", "G");
    }

    
    public String translate(String seq) {
        String dnaseq = seq.toUpperCase();
        StringBuilder out = new StringBuilder();
        for(int i=0; i<dnaseq.length(); i+=3) {
            String codon = dnaseq.substring(i, i+3);
            out.append(GeneticCode.get(codon));
        }
        return out.toString();
    }
    
}