/*************************************************************************
* *
* 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.List;
public class Mrna {
public RBSOption rbs;
public String peptide;
public int[] codons;
public String toSeq() throws Exception {
CodonIndexer indexer = CodonIndexer.initiate();
StringBuilder out = new StringBuilder();
for(int i=0; i<peptide.length(); i++) {
char aa = peptide.charAt(i);
List<String> codonList = indexer.aminoAcidToBestCodons.get(aa);
out.append(codonList.get(codons[i]));
}
out.append("TAA");
return rbs.rbs.toLowerCase() + out.toString().toUpperCase();
}
}