/*
* BranchSpecificBranchModelParser.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.branchmodel;
import dr.evolution.tree.TreeUtils;
import dr.evomodel.branchmodel.BranchSpecificBranchModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.evolution.util.Taxa;
import dr.evolution.util.TaxonList;
import dr.evomodel.tree.TreeModel;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Andrew Rambaut
*/
public class BranchSpecificBranchModelParser extends AbstractXMLObjectParser {
public static final String BRANCH_SPECIFIC_SUBSTITUTION_MODEL = "branchSpecificSubstitutionModel";
public static final String CLADE = "clade";
public static final String EXTERNAL_BRANCHES = "externalBranches";
public static final String BACKBONE = "backbone";
public static final String STEM_WEIGHT = "stemWeight";
public String getParserName() {
return BRANCH_SPECIFIC_SUBSTITUTION_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Logger.getLogger("dr.evomodel").info("\nUsing clade-specific branch model.");
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
BranchSpecificBranchModel branchModel = new BranchSpecificBranchModel(tree, substitutionModel);
for (int i = 0; i < xo.getChildCount(); i++) {
if (xo.getChild(i) instanceof XMLObject) {
XMLObject xoc = (XMLObject) xo.getChild(i);
if (xoc.getName().equals(CLADE)) {
double stemWeight = xoc.getAttribute(STEM_WEIGHT, 0.0);
substitutionModel = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
if (taxonList.getTaxonCount() == 1) {
throw new XMLParseException("A clade must be defined by at least two taxa");
}
try {
branchModel.addClade(taxonList, substitutionModel, stemWeight);
} catch (TreeUtils.MissingTaxonException mte) {
throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
}
} else if (xoc.getName().equals(EXTERNAL_BRANCHES)) {
substitutionModel = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
try {
branchModel.addExternalBranches(taxonList, substitutionModel);
} catch (TreeUtils.MissingTaxonException mte) {
throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
}
} else if (xoc.getName().equals(BACKBONE)) {
substitutionModel = (SubstitutionModel) xoc.getChild(SubstitutionModel.class);
TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
try {
branchModel.addBackbone(taxonList, substitutionModel);
} catch (TreeUtils.MissingTaxonException mte) {
throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
}
}
}
}
return branchModel;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return
"This element provides a branch model which allows different substitution models" +
"on different parts of the tree.";
}
public Class getReturnType() {
return BranchSpecificBranchModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(TreeModel.class, "The tree"),
new ElementRule(SubstitutionModel.class, "The substitution model for branches not explicitly included"),
new ElementRule(EXTERNAL_BRANCHES,
new XMLSyntaxRule[]{
new ElementRule(Taxa.class, "A substitution model will be applied to the external branches for these taxa"),
new ElementRule(SubstitutionModel.class, "The substitution model"),
}, 0, Integer.MAX_VALUE),
new ElementRule(CLADE,
new XMLSyntaxRule[]{
AttributeRule.newDoubleRule(STEM_WEIGHT, true, "What proportion of the stem branch to include [0 <= w <= 1] (default 0)."),
new ElementRule(Taxa.class, "A set of taxa which defines a clade to apply a different site model to"),
new ElementRule(SubstitutionModel.class, "The substitution model"),
}, 0, Integer.MAX_VALUE),
new ElementRule(BACKBONE,
new XMLSyntaxRule[]{
new ElementRule(Taxa.class, "A substitution model will be applied only to " +
"the 'backbone' branches defined by these taxa."),
new ElementRule(SubstitutionModel.class, "The substitution model"),
}, 0, Integer.MAX_VALUE),
};
}