ALSBeagleTreeLikelihood.java

/*
 * ALSBeagleTreeLikelihood.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.evomodel.MSSD;

import dr.evomodel.branchmodel.BranchModel;
import dr.evomodel.siteratemodel.SiteRateModel;
import dr.evomodel.treelikelihood.BeagleTreeLikelihood;
import dr.evomodel.treelikelihood.LikelihoodPartialsProvider;
import dr.evomodel.treelikelihood.PartialsRescalingScheme;
import dr.evolution.alignment.PatternList;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.evomodel.tree.TreeModel;
import dr.evomodel.tipstatesmodel.TipStatesModel;
import dr.inference.model.Model;
import dr.inference.model.Parameter;

import java.util.Map;
import java.util.Set;

/**
 * Package: ALSTreeLikelihood
 * Description:
 * <p/>
 * <p/>
 * Created by
 * Alexander V. Alekseyenko (alexander.alekseyenko@gmail.com)
 * Date: Feb 13, 2008
 * Time: 10:13:07 AM
 */
public class ALSBeagleTreeLikelihood extends BeagleTreeLikelihood implements LikelihoodPartialsProvider {

    protected AbstractObservationProcess observationProcess;


    public ALSBeagleTreeLikelihood(AbstractObservationProcess observationProcess, PatternList patternList, TreeModel treeModel,
                                   BranchModel branchModel,
                                   SiteRateModel siteRateModel,
                                   BranchRateModel branchRateModel,
                                   TipStatesModel tipStatesModel,
                                   boolean useAmbiguities,
                                   PartialsRescalingScheme scalingScheme,
                                   boolean delayScaling,
                                   Map<Set<String>, Parameter> partialsRestrictions) {

        super(patternList, treeModel, branchModel, siteRateModel, branchRateModel, tipStatesModel, useAmbiguities, scalingScheme, delayScaling,
                partialsRestrictions);
//    }
//
//
//    public ALSBeagleTreeLikelihood(AbstractObservationProcess observationProcess, PatternList patternList, TreeModel treeModel,
//                SiteModel siteModel, BranchRateModel branchRateModel,
//        boolean useAmbiguities, boolean storePartials) {
//        super(patternList, treeModel, siteModel, branchRateModel, null, useAmbiguities, false, storePartials, false, false);

        this.observationProcess = observationProcess;
        addModel(observationProcess);

//        // TreeLikelihood does not initialize the partials for tips, we'll do it ourselves
//        int extNodeCount = treeModel.getExternalNodeCount();
//        for (int i = 0; i < extNodeCount; i++) {
//            String id = treeModel.getTaxonId(i);
//            int index = patternList.getTaxonIndex(id);
//            setPartials(likelihoodCore, patternList, categoryCount, index, i);
//        }

/*        //Examine the tree
        double totalTime=0.0;
        double realTime = 0.0;
        for(int i=0; i<treeModel.getNodeCount();++i){
            NodeRef node = treeModel.getNode(i);
            double branchRate = branchRateModel.getBranchRate(treeModel,node);
            double branchTime = treeModel.getBranchLength(node);
            totalTime+=branchRate*branchTime;
            realTime += branchTime;
            System.err.println("Node "+node.toString()+ " time: "+branchTime+ " rate "+branchRate+" together "+branchTime*branchRate);
        }
        System.err.println("TotalTime: "+totalTime);
        System.err.println("RealTime: "+realTime);*/
//        scaleFactorsHelper = new ScaleFactorsHelper(this, this,
//                treeModel, stateCount, patternCount, categoryCount);
    }

    protected double calculateLogLikelihood() {
        throw new UnsupportedOperationException("Not implemented for BEAGLE");
//        // Calculate the partial likelihoods
//        super.calculateLogLikelihood();
//        // get the frequency model
//        double[] freqs = substitutionModelDelegate.getRootStateFrequencies();
//        // let the observationProcess handle the rest
//        scaleFactorsHelper.resetScaleFactors();
//        return observationProcess.nodePatternLikelihood(freqs, this, scaleFactorsHelper);
    }

    protected void handleModelChangedEvent(Model model, Object object, int index) {
        if (model == observationProcess) {
            likelihoodKnown = false;
        } else {
            super.handleModelChangedEvent(model, object, index);
        }
    }

//    final private ScaleFactorsHelper scaleFactorsHelper;
}