/*
* HypermutantAlignmentParser.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.HypermutantAlignment;
import dr.evolution.datatype.*;
import dr.xml.*;
import java.util.logging.Logger;
/**
* This converts 'A's that are at specific APOBEC targeted contexts into an A/G ambiguity code for
* later recognition by the HypermutantErrorModel.
*
* @author Andrew Rambaut
*
* @version $Id$
*/
public class HypermutantAlignmentParser extends AbstractXMLObjectParser {
public final static String HYPERMUTANT_ALIGNMENT = "hypermutantAlignment";
public final static String CONTEXT_TYPE = "type";
public String getParserName() { return HYPERMUTANT_ALIGNMENT; }
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Alignment alignment = (Alignment)xo.getChild(Alignment.class);
if (alignment.getDataType().getType() != DataType.NUCLEOTIDES) {
throw new XMLParseException("HypermutantAlignment can only convert nucleotide alignments");
}
String typeName = xo.getStringAttribute(CONTEXT_TYPE);
HypermutantAlignment.APOBECType type = null;
try {
type = HypermutantAlignment.APOBECType.valueOf(typeName.toUpperCase());
} catch(IllegalArgumentException iae) {
throw new XMLParseException("Unrecognised hypermutation type: " + typeName);
}
HypermutantAlignment convert = new HypermutantAlignment(type, alignment);
int mutatedCount = convert.getMutatedContextCount();
int totalCount = mutatedCount + convert.getUnmutatedContextCount();
Logger.getLogger("dr.evoxml").info("Converted alignment, '" + xo.getId() + "' to a hypermutant alignment targeting " + type.toString() + " contexts.\r" +
"\tPotentially mutated contexts: " + mutatedCount + " out of a total of " + totalCount + " contexts");
return convert;
}
public String getParserDescription() {
return "Converts an alignment so that 'A's at specific APOBEC targeted contexts are set to an A/G ambiguity code.";
}
public Class getReturnType() { return Alignment.class; }
public XMLSyntaxRule[] getSyntaxRules() { return rules; }
private XMLSyntaxRule[] rules = new XMLSyntaxRule[] {
new ElementRule(Alignment.class),
new StringAttributeRule(CONTEXT_TYPE,
"The type of APOBEC molecule being modelled",
new String[] {HypermutantAlignment.APOBECType.ALL.toString(), HypermutantAlignment.APOBECType.BOTH.toString(), HypermutantAlignment.APOBECType.HA3G.toString(), HypermutantAlignment.APOBECType.HA3F.toString()},
false )
};
}