/*
* EmpiricalAminoAcidModelParser.java
*
* Copyright (c) 2002-2016 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.evomodelxml.substmodel;
import dr.evomodel.substmodel.EmpiricalRateMatrix;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.aminoacid.*;
import dr.xml.*;
/**
* BEAGLE parser for empirical amino acid models
*/
public class EmpiricalAminoAcidModelParser extends AbstractXMLObjectParser {
public static final String EMPIRICAL_AMINO_ACID_MODEL = "aminoAcidModel";
public static final String FREQUENCIES = "frequencies";
public static final String TYPE = "type";
public String getParserName() {
return EMPIRICAL_AMINO_ACID_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
FrequencyModel freqModel = null;
if (xo.hasAttribute(FREQUENCIES)) {
XMLObject cxo = xo.getChild(FREQUENCIES);
freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
}
EmpiricalRateMatrix rateMatrix = null;
String type = xo.getStringAttribute(TYPE);
if (type.equals(AminoAcidModelType.BLOSUM_62.getXMLName())) {
rateMatrix = Blosum62.INSTANCE;
} else if (type.equals(AminoAcidModelType.DAYHOFF.getXMLName())) {
rateMatrix = Dayhoff.INSTANCE;
} else if (type.equals(AminoAcidModelType.JTT.getXMLName())) {
rateMatrix = JTT.INSTANCE;
} else if (type.equals(AminoAcidModelType.MT_REV_24.getXMLName())) {
rateMatrix = MTREV.INSTANCE;
} else if (type.equals(AminoAcidModelType.CP_REV_45.getXMLName())) {
rateMatrix = CPREV.INSTANCE;
} else if (type.equals(AminoAcidModelType.WAG.getXMLName())) {
rateMatrix = WAG.INSTANCE;
} else if (type.equals(AminoAcidModelType.LG.getXMLName())) {
rateMatrix = LG.INSTANCE;
} else if (type.equals(AminoAcidModelType.FLU.getXMLName())) {
rateMatrix = FLU.INSTANCE;
} else {
throw new XMLParseException("Unrecognized empirical amino acid model: " + type);
}
return new EmpiricalAminoAcidModel(rateMatrix, freqModel);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new StringAttributeRule(TYPE, "The type of empirical amino-acid rate matrix", AminoAcidModelType.xmlNames(), false),
new ElementRule(FREQUENCIES, FrequencyModel.class, "If the frequencies are omitted than the empirical frequencies associated with the selected model are used.", true)
};
public String getParserDescription() {
return "An empirical amino acid substitution model.";
}
public Class getReturnType() {
return EmpiricalAminoAcidModel.class;
}
}