/*
* LocalClockModelParser.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.evomodelxml.branchratemodel;
import dr.evolution.tree.TreeUtils;
import dr.evolution.util.Taxa;
import dr.evolution.util.TaxonList;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.evomodel.branchratemodel.LocalClockModel;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
/**
*/
public class LocalClockModelParser extends AbstractXMLObjectParser {
public static final String LOCAL_CLOCK_MODEL = "localClockModel";
public static final String RATE = BranchRateModel.RATE;
public static final String RELATIVE = "relative";
public static final String CLADE = "clade";
public static final String INCLUDE_STEM = "includeStem";
public static final String STEM_PROPORTION = "stemProportion";
public static final String EXCLUDE_CLADE = "excludeClade";
public static final String EXTERNAL_BRANCHES = "externalBranches";
public static final String TRUNK = "trunk";
public static final String INDEX = "index";
public String getParserName() {
return LOCAL_CLOCK_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
Parameter globalRateParameter = (Parameter) xo.getElementFirstChild(RATE);
LocalClockModel localClockModel = new LocalClockModel(tree, globalRateParameter);
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)) {
boolean relative = xoc.getAttribute(RELATIVE, false);
Parameter rateParameter = (Parameter) xoc.getChild(Parameter.class);
TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
if (taxonList.getTaxonCount() == 1) {
throw new XMLParseException("A local clock for a clade must be defined by at least two taxa");
}
boolean excludeClade = false;
double stemProportion = 0.0;
if (xoc.hasAttribute(INCLUDE_STEM)) {
// if includeStem=true then assume it is the whole stem
stemProportion = xoc.getBooleanAttribute(INCLUDE_STEM) ? 1.0 : 0.0;
}
if (xoc.hasAttribute(STEM_PROPORTION)) {
stemProportion = xoc.getDoubleAttribute(STEM_PROPORTION);
if (stemProportion < 0.0 || stemProportion > 1.0) {
throw new XMLParseException("A stem proportion should be between 0, 1");
}
}
if (xoc.hasAttribute(EXCLUDE_CLADE)) {
excludeClade = xoc.getBooleanAttribute(EXCLUDE_CLADE);
}
try {
localClockModel.addCladeClock(taxonList, rateParameter, relative, stemProportion, excludeClade);
} catch (TreeUtils.MissingTaxonException mte) {
throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
}
} else if (xoc.getName().equals(EXTERNAL_BRANCHES)) {
boolean relative = xoc.getAttribute(RELATIVE, false);
Parameter rateParameter = (Parameter) xoc.getChild(Parameter.class);
TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
try {
localClockModel.addExternalBranchClock(taxonList, rateParameter, relative);
} catch (TreeUtils.MissingTaxonException mte) {
throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
}
} else if (xoc.getName().equals(TRUNK)) {
boolean relative = xoc.getAttribute(RELATIVE, false);
Parameter indexParameter = null;
if (xoc.hasChildNamed(INDEX)) {
indexParameter = (Parameter) xoc.getElementFirstChild(INDEX);
}
Parameter rateParameter = (Parameter) xoc.getChild(Parameter.class);
TaxonList taxonList = (TaxonList) xoc.getChild(TaxonList.class);
try {
localClockModel.addTrunkClock(taxonList, rateParameter, indexParameter, relative);
} catch (TreeUtils.MissingTaxonException mte) {
throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + " was not found in the tree.");
}
}
}
}
Logger.getLogger("dr.evomodel").info("\nUsing local clock branch rate model.");
return localClockModel;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return "This element returns a branch rate model that adds a delta to each terminal branch length.";
}
public Class getReturnType() {
return LocalClockModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(TreeModel.class),
new ElementRule(RATE, Parameter.class, "The molecular evolutionary rate parameter", false),
new ElementRule(EXTERNAL_BRANCHES,
new XMLSyntaxRule[]{
AttributeRule.newBooleanRule(RELATIVE, true),
new ElementRule(Taxa.class, "A local clock that will be applied only to " +
"the external branches for these taxa"),
new ElementRule(Parameter.class, "The rate parameter"),
}, 0, Integer.MAX_VALUE),
new ElementRule(CLADE,
new XMLSyntaxRule[]{
AttributeRule.newBooleanRule(RELATIVE, true),
AttributeRule.newBooleanRule(INCLUDE_STEM, true, "determines whether or not the stem branch above this clade is included in the siteModel (default false)."),
AttributeRule.newDoubleRule(STEM_PROPORTION, true, "proportion of stem to include in clade rate (default 0)."),
AttributeRule.newBooleanRule(EXCLUDE_CLADE, true, "determines whether to exclude actual branches of the clade from the siteModel (default false)."),
new ElementRule(Taxa.class, "A set of taxa which defines a clade to apply a different site model to"),
new ElementRule(Parameter.class, "The rate parameter")
}, 0, Integer.MAX_VALUE),
new ElementRule(TRUNK,
new XMLSyntaxRule[]{
AttributeRule.newBooleanRule(RELATIVE, true),
new ElementRule(Taxa.class, "A local clock that will be applied only to " +
"the 'trunk' branches defined by these taxa"),
new ElementRule(Parameter.class, "The rate parameter"),
new ElementRule(INDEX, Parameter.class, "The trunk taxon index", true),
}, 0, Integer.MAX_VALUE),
};
}