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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 reader;
import parser.ParseException;
import types.Sequence;
/**
* Provides static methods common to every reader.
* @author Daniel Gomez Blanco
* @version 1.0
*/
public class ReaderUtils
{
/**
* Replaces match characters with the character in the same position of the
* first sequence of the MSA.
* @param seq Current sequence.
* @param first First sequence of the MSA.
* @throws ParseException If a match character is trying to be replaced by a "?", "." or "-" character.
*/
public static void replaceMatch(Sequence seq, Sequence first) throws ParseException
{
if (seq.getData().contains("."))
//Lanzar excepcion si el caracter esta en la primera secuencia
if (seq == first)
throw new ParseException("Match character \".\" in first sequence of MSA.");
else
for(int j=0;j<seq.getData().length();j++)
if (seq.getData().charAt(j) == '.')
if (first.getData().charAt(j) == '?'
|| first.getData().charAt(j) == '-')
throw new ParseException("Match character \".\" cannot be replaced by \"?\" or \"-\".");
else
seq.replaceChar(j, first.getData().charAt(j));
}
}
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