/*
* MicrosatelliteSamplerTreeModelParser.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.tree;
import dr.evolution.alignment.Patterns;
import dr.evomodel.tree.MicrosatelliteSamplerTreeModel;
import dr.evomodel.tree.TreeModel;
import dr.inference.model.Parameter;
import dr.xml.*;
import java.util.HashMap;
/**
* @author Chieh-Hsi Wu
*
* Parser for MicrsatelliteSamplerTreeModel
*
*/
public class MicrosatelliteSamplerTreeModelParser extends AbstractXMLObjectParser {
public static final String TREE_MICROSATELLITE_SAMPLER_MODEL = "microsatelliteSamplerTreeModel";
public static final String TREE = "tree";
public static final String INTERNAL_VALUES = "internalValues";
public static final String EXTERNAL_VALUES = "externalValues";
public static final String USE_PROVIDED_INTERNAL_VALUES = "provideInternalNodeValues";
public String getParserName(){
return TREE_MICROSATELLITE_SAMPLER_MODEL;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TreeModel tree = (TreeModel)xo.getElementFirstChild(TREE);
Parameter internalVal = (Parameter)xo.getElementFirstChild(INTERNAL_VALUES);
Patterns microsatellitePattern = (Patterns)xo.getElementFirstChild(EXTERNAL_VALUES);
int[] externalValues = microsatellitePattern.getPattern(0);
HashMap<String, Integer> taxaMap = new HashMap<String, Integer>(externalValues.length);
boolean internalValuesProvided = false;
if(xo.hasAttribute(USE_PROVIDED_INTERNAL_VALUES)){
internalValuesProvided = xo.getBooleanAttribute(USE_PROVIDED_INTERNAL_VALUES);
}
for(int i = 0; i < externalValues.length; i++){
taxaMap.put(microsatellitePattern.getTaxonId(i),i);
}
String modelId = xo.getAttribute("id", "treeMicrosatelliteSamplerModel");
return new MicrosatelliteSamplerTreeModel(modelId, tree, internalVal, microsatellitePattern, externalValues, taxaMap, internalValuesProvided);
}
public XMLSyntaxRule[] getSyntaxRules() { return rules; }
private final XMLSyntaxRule[] rules = {
AttributeRule.newBooleanRule(USE_PROVIDED_INTERNAL_VALUES, true),
new ElementRule(TREE, TreeModel.class),
new ElementRule(INTERNAL_VALUES, Parameter.class),
new ElementRule(EXTERNAL_VALUES, Patterns.class)
};
public String getParserDescription(){
return "This parser returns a TreeMicrosatelliteSamplerModel Object";
}
public Class getReturnType(){
return MicrosatelliteSamplerTreeModel.class;
}
}