/*
* ConvertAlignmentParser.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST 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 Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.evoxml;
import dr.evolution.alignment.Alignment;
import dr.evolution.alignment.ConvertAlignment;
import dr.evolution.datatype.*;
import dr.evoxml.util.DataTypeUtils;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Alexei Drummond
* @author Andrew Rambaut
*
* @version $Id: ConvertAlignmentParser.java,v 1.3 2005/07/11 14:06:25 rambaut Exp $
*/
public class ConvertAlignmentParser extends AbstractXMLObjectParser {
public final static String CONVERT = "convert";
public String getParserName() { return CONVERT; }
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Alignment alignment = (Alignment)xo.getChild(Alignment.class);
// Old parser always returned UNIVERSAL type for codon conversion
DataType dataType = DataTypeUtils.getDataType(xo);
GeneticCode geneticCode = GeneticCode.UNIVERSAL;
if (dataType instanceof Codons) {
geneticCode = ((Codons)dataType).getGeneticCode();
}
ConvertAlignment convert = new ConvertAlignment(dataType, geneticCode, alignment);
Logger.getLogger("dr.evoxml").info("Converted alignment, '" + xo.getId() + "', from " +
alignment.getDataType().getDescription() + " to " + dataType.getDescription());
return convert;
}
public String getParserDescription() {
return "Converts an alignment to the given data type.";
}
public Class getReturnType() { return Alignment.class; }
public XMLSyntaxRule[] getSyntaxRules() { return rules; }
private XMLSyntaxRule[] rules = new XMLSyntaxRule[] {
new ElementRule(Alignment.class),
new StringAttributeRule(DataType.DATA_TYPE,
"The type of sequence data",
new String[] {Nucleotides.DESCRIPTION, AminoAcids.DESCRIPTION, Codons.DESCRIPTION, TwoStates.DESCRIPTION,
HiddenCodons.DESCRIPTION+"2",HiddenCodons.DESCRIPTION+"3"},
false )
};
}