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/*
* This file is part of ALTER.
*
* ALTER 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.
*
* ALTER 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 Lesser General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with ALTER. If not, see <http://www.gnu.org/licenses/>.
*/
package writer;
import java.util.logging.Level;
import types.MSA;
import types.Protein;
import types.Type;
import types.Typeable;
/**
* Extiende la clase PirWriter para adaptar la salida a dnaSP.
* @author Daniel Gomez Blanco
* @version 1.0
*/
public class PirDnaSPWriter extends PirWriter
{
/**
* Constructor de la clase. Llama al constructor de la superclase.
* @param os Sistema operativo de salida.
* @param lowerCase Salida en letras minusculas.
* @param match Salida codificada con caracteres match.
* @param logger Nombre del logger a instanciar.
*/
public PirDnaSPWriter(String os, boolean lowerCase, boolean match, String logger)
{
super(os,lowerCase,match,logger);
}
/**
* Escribe un MSA en formato PIR adaptado a dnaSP. Para ello
* comprueba que el MSA no sea de proteinas. Luego llama al metodo de la superclase.
* @param msa MSA de entrada.
* @return Cadena con la el MSA en formato PIR.
*/
@Override
public String write(MSA msa)
{
Type type = null;
if (msa instanceof Typeable)
type = ((Typeable) msa).getType();
if (type == null)
{
type = WriterUtils.inferType(msa);
}
if (type instanceof Protein)
{
logger.log(Level.WARNING,"MSA is an amino acids MSA. " +
"It will not be processed by dnaSP (only DNA is processed).");
}
return super.write(msa);
}
}
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