IndependentCoalescentSampler.java

/*
 * IndependentCoalescentSampler.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.continuous;

import java.util.ArrayList;
import java.util.List;

import dr.evolution.tree.SimpleTree;
import dr.evolution.tree.Tree;
import dr.evolution.util.Taxa;
import dr.evolution.util.TaxonList;
import dr.evomodel.coalescent.CoalescentLikelihood;
import dr.evomodel.coalescent.CoalescentSimulator;
import dr.evomodel.coalescent.DemographicModel;
import dr.evomodel.tree.TreeModel;
import dr.inference.operators.MCMCOperator;
import dr.inference.operators.SimpleMCMCOperator;
import dr.xml.AttributeRule;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;

/**
 * An independent coalescent sampler, based on the coalescent simulator parser code.
 *
 * @author Guy Baele
 * 
 */
public class IndependentCoalescentSampler extends SimpleMCMCOperator {

	public static final String OPERATOR_NAME = "independentCoalescentSampler";
    
    private TreeModel treeModel;
    private DemographicModel demoModel;
    private CoalescentLikelihood coalescent;
    private XMLObject xo;
	
	public IndependentCoalescentSampler(XMLObject xo, TreeModel treeModel, DemographicModel demoModel, CoalescentLikelihood coalescent, double weight) {
		
		this.xo = xo;
		this.treeModel = treeModel;
		this.demoModel = demoModel;
		this.coalescent = coalescent;
		setWeight(weight);
		
	}
	
	public String getPerformanceSuggestion() {
		return "";
	}

	public String getOperatorName() {
		return "independentCoalescent(" + treeModel.getModelName() + ")";
	}

    /**
	 * change the parameter and return the hastings ratio.
     */
	public double doOperation() {
		
		CoalescentSimulator simulator = new CoalescentSimulator();
        
        List<TaxonList> taxonLists = new ArrayList<TaxonList>();

        double rootHeight = -1.0;
        double oldLikelihood = 0.0;
        double newLikelihood = 0.0;

        // should have one child that is node
        for (int i = 0; i < xo.getChildCount(); i++) {
            final Object child = xo.getChild(i);
            
            //careful: Trees are TaxonLists ... (AER); see OldCoalescentSimulatorParser
            if (child instanceof Tree) {
                //do nothing
            } else if (child instanceof TaxonList) {
                //taxonLists.add((TaxonList) child);
                taxonLists.add((Taxa) child);
                //taxa added
                break;
            } 
        }

        try {
        	
        	Tree[] trees = new Tree[taxonLists.size()];
            // simulate each taxonList separately
            for (int i = 0; i < taxonLists.size(); i++) {
                trees[i] = simulator.simulateTree(taxonLists.get(i), demoModel);
            }

            oldLikelihood = coalescent.getLogLikelihood();
            
            SimpleTree simTree = simulator.simulateTree(trees, demoModel, rootHeight, trees.length != 1);
            
            //this would be the normal way to do it
            treeModel.beginTreeEdit();
            //now it's allowed to adjust the tree structure
            treeModel.adoptTreeStructure(simTree);
            //endTreeEdit() would then fire the events
            treeModel.endTreeEdit();
            
            newLikelihood = coalescent.getLogLikelihood();
            
        } catch (IllegalArgumentException iae) {
            try {
				throw new XMLParseException(iae.getMessage());
			} catch (XMLParseException e) {
				// TODO Auto-generated catch block
				e.printStackTrace();
			}
        }
		
		return oldLikelihood - newLikelihood;
	}
	
	public static dr.xml.XMLObjectParser PARSER = new dr.xml.AbstractXMLObjectParser() {
		
		public String getParserName() {
            return OPERATOR_NAME;
        }

		public Object parseXMLObject(XMLObject xo) throws XMLParseException {
			
			TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
			double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
	        DemographicModel demoModel = (DemographicModel) xo.getChild(DemographicModel.class);
	        CoalescentLikelihood coalescent = (CoalescentLikelihood) xo.getChild(CoalescentLikelihood.class);
	        
			return new IndependentCoalescentSampler(xo, treeModel, demoModel, coalescent, weight);
			
		}
		
		//************************************************************************
        // AbstractXMLObjectParser implementation
        //************************************************************************

		public XMLSyntaxRule[] getSyntaxRules() {
			return rules;
		}
		
		private final XMLSyntaxRule[] rules = {
				AttributeRule.newDoubleRule(MCMCOperator.WEIGHT),
				new ElementRule(Taxa.class),
                new ElementRule(TreeModel.class),
                new ElementRule(DemographicModel.class),
                new ElementRule(CoalescentLikelihood.class)
        };

		public String getParserDescription() {
			return "This element returns an independence coalescent sampler from a demographic model.";
		}

		public Class getReturnType() {
			return MCMCOperator.class;
		}
		
	};

}