/*
* DiscreteTraitBranchRateModelParser.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.alignment.PatternList;
import dr.evolution.datatype.DataType;
import dr.evolution.tree.TreeTrait;
import dr.evolution.tree.TreeTraitProvider;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.evomodel.branchratemodel.ContinuousTraitBranchRateModel;
import dr.evomodel.branchratemodel.DiscreteTraitBranchRateModel;
import dr.evomodel.continuous.SampledMultivariateTraitLikelihood;
import dr.evomodel.tree.TreeModel;
import dr.evoxml.util.DataTypeUtils;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.logging.Logger;
public class DiscreteTraitBranchRateModelParser extends AbstractXMLObjectParser {
public static final String RATE = "rate";
public static final String RATES = "rates";
public static final String RELATIVE_RATES = "relativeRates";
public static final String INDICATORS = "indicators";
public static final String TRAIT_INDEX = "traitIndex";
public static final String TRAIT_NAME = "traitName";
public String getParserName() {
return DiscreteTraitBranchRateModel.DISCRETE_TRAIT_BRANCH_RATE_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
PatternList patternList = (PatternList) xo.getChild(PatternList.class);
TreeTraitProvider traitProvider = (TreeTraitProvider) xo.getChild(TreeTraitProvider.class);
DataType dataType = DataTypeUtils.getDataType(xo);
Parameter rateParameter = null;
Parameter relativeRatesParameter = null;
Parameter indicatorsParameter = null;
if (xo.getChild(RATE) != null) {
rateParameter = (Parameter) xo.getElementFirstChild(RATE);
}
if (xo.getChild(RATES) != null) {
rateParameter = (Parameter) xo.getElementFirstChild(RATES);
}
if (xo.getChild(RELATIVE_RATES) != null) {
relativeRatesParameter = (Parameter) xo.getElementFirstChild(RELATIVE_RATES);
}
if (xo.getChild(INDICATORS) != null) {
indicatorsParameter = (Parameter) xo.getElementFirstChild(INDICATORS);
}
int traitIndex = xo.getAttribute(TRAIT_INDEX, 1) - 1;
String traitName = "states";
Logger.getLogger("dr.evomodel").info("Using discrete trait branch rate model.\n" +
"\tIf you use this model, please cite:\n" +
"\t\tDrummond and Suchard (in preparation)");
if (traitProvider == null) {
// Use the version that reconstructs the trait using parsimony:
return new DiscreteTraitBranchRateModel(treeModel, patternList, traitIndex, rateParameter);
} else {
if (traitName != null) {
TreeTrait trait = traitProvider.getTreeTrait(traitName);
if (trait == null) {
throw new XMLParseException("A trait called, " + traitName + ", was not available from the TreeTraitProvider supplied to " + getParserName() + ", with ID " + xo.getId());
}
if (relativeRatesParameter != null) {
return new DiscreteTraitBranchRateModel(traitProvider, dataType, treeModel, trait, traitIndex, rateParameter, relativeRatesParameter, indicatorsParameter);
} else {
return new DiscreteTraitBranchRateModel(traitProvider, dataType, treeModel, trait, traitIndex, rateParameter);
}
} else {
TreeTrait[] traits = new TreeTrait[dataType.getStateCount()];
for (int i = 0; i < dataType.getStateCount(); i++) {
traits[i] = traitProvider.getTreeTrait(dataType.getCode(i));
if (traits[i] == null) {
throw new XMLParseException("A trait called, " + dataType.getCode(i) + ", was not available from the TreeTraitProvider supplied to " + getParserName() + ", with ID " + xo.getId());
}
}
return new DiscreteTraitBranchRateModel(traitProvider, traits, treeModel, rateParameter);
}
}
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public String getParserDescription() {
return
"This Branch Rate Model takes a discrete trait reconstruction (provided by a TreeTraitProvider) and " +
"gives the rate for each branch of the tree based on the child trait of " +
"that branch. The rates for each trait value are specified in a multidimensional parameter.";
}
public Class getReturnType() {
return DiscreteTraitBranchRateModel.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(TreeModel.class, "The tree model"),
new XORRule(
new AndRule(
new ElementRule(TreeTraitProvider.class, "The trait provider"),
new XORRule(
new StringAttributeRule(DataType.DATA_TYPE, "The type of general data",
DataType.getRegisteredDataTypeNames(), false),
new ElementRule(DataType.class))
),
new ElementRule(PatternList.class)),
new XORRule(
new AndRule(
new ElementRule(RATE, Parameter.class, "The over-all rate"),
new ElementRule(RELATIVE_RATES, Parameter.class, "The state-specific relative rates")
),
new ElementRule(RATES, Parameter.class, "The state-specific rates")),
AttributeRule.newIntegerRule(TRAIT_INDEX, true),
AttributeRule.newStringRule(TRAIT_NAME, true)
};
}