/*
* LineageSpecificBranchModelParser.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.evomodel.branchmodel.lineagespecific;
import java.util.ArrayList;
import java.util.List;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.AbstractModel;
import dr.inference.model.Parameter;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
/**
* @author Filip Bielejec
* @version $Id$
*
*/
public class LineageSpecificBranchModelParser extends AbstractXMLObjectParser {
public static final String MODELS = "models";
public static final String CATEGORIES = "categories";
@Override
public String getParserName() {
return LineageSpecificBranchModel.LINEAGE_SPECIFIC_BRANCH_MODEL;
}
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
FrequencyModel rootFrequencyModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
List<SubstitutionModel> substitutionModels = new ArrayList<SubstitutionModel>();
XMLObject cxo = xo.getChild(MODELS);
for (int i = 0; i < cxo.getChildCount(); i++) {
SubstitutionModel substModel = (SubstitutionModel) cxo.getChild(i);
substitutionModels.add(substModel);
}//END: models loop
// TODO: check if categories numbering starts from zero
Parameter categories = (Parameter) xo.getElementFirstChild(CATEGORIES);
// CountableBranchCategoryProvider.CladeBranchCategoryModel provider = new CountableBranchCategoryProvider.CladeBranchCategoryModel(treeModel, categories);// false);
return new LineageSpecificBranchModel(treeModel, rootFrequencyModel, substitutionModels, //provider,
categories);
}
@Override
public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[]{
new ElementRule(TreeModel.class, false), //
new ElementRule(FrequencyModel.class, false), //
new ElementRule(MODELS,
new XMLSyntaxRule[] {
new ElementRule(AbstractModel.class, 1, Integer.MAX_VALUE),
}
), //
new ElementRule(CATEGORIES,
new XMLSyntaxRule[] {
new ElementRule(Parameter.class, 1, 1),
}
) //
};
}
@Override
public String getParserDescription() {
return "This element provides a branch model which has branches assigned to specific substitution models." +
"These assignments can then be changed in course of MCMC.";
}
@Override
public Class getReturnType() {
return LineageSpecificBranchModel.class;
}
}//END: class