FixedDriftModel.java

/*
 * FixedDriftModel.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.branchratemodel;

import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.evolution.util.TaxonList;
import dr.evomodel.tree.BackboneNodeFilter;
import dr.evomodel.tree.TreeModel;
import dr.evomodelxml.branchratemodel.FixedDriftModelParser;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;

/**
 * Created by mandevgill on 12/22/14.
 */
public class FixedDriftModel extends AbstractBranchRateModel {

    /*
    public FixedDriftModel(Parameter rateOne,
                           Parameter rateTwo,
                           Parameter remainingRates,
                           String rateOneID,
                           String rateTwoID) {

        super(FixedDriftModelParser.FIXED_DRIFT);


        //   addModel(treeModel);
        //  this.treeModel = treeModel;

        this.rateOne = rateOne;
        addVariable(rateOne);

        this.rateTwo = rateTwo;
        addVariable(rateTwo);

        this.remainingRates = remainingRates;
        addVariable(remainingRates);

        this.rateOneID = rateOneID;
        this.rateTwoID = rateTwoID;
    }
    */

    public FixedDriftModel(TreeModel treeModel, Parameter backboneDrift, Parameter otherDrift, TaxonList taxonList) {

        super(FixedDriftModelParser.FIXED_DRIFT);

        this.backboneDrift = backboneDrift;
        addVariable(backboneDrift);

        this.otherDrift = otherDrift;
        addVariable(otherDrift);


        this.backbone = new BackboneNodeFilter("backbone", treeModel, taxonList, true, true);

    }


    public void handleModelChangedEvent(Model model, Object object, int index) {
        fireModelChanged();
    }

    protected final void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
        fireModelChanged();
    }

    protected void storeState() {
    }

    protected void restoreState() {
        //  calculateBranchRates(treeModel);
        // recalculateScaleFactor();
        backbone.computeBackBoneMap();
    }

    protected void acceptState() {
    }

    public double getBranchRate(final Tree tree, final NodeRef node) {

        if (backbone.includeNode(tree, node)) {
            return backboneDrift.getParameterValue(0);
        } else {
            return otherDrift.getParameterValue(0);
        }
    }

    /*
    public double getBranchRate(final Tree tree, final NodeRef node) {

        if (tree.isExternal(node)) {
            if (tree.getTaxonId(node.getNumber()).matches(rateOneID)) {
                //  System.err.println("node one id " + tree.getTaxonId(node.getNumber()));
                return rateOne.getParameterValue(0);
            } else if (tree.getTaxonId(node.getNumber()).matches(rateTwoID)) {
                // System.err.println("node two id " + tree.getTaxonId(node.getNumber()));
                return rateTwo.getParameterValue(0);
            } else {
                return remainingRates.getParameterValue(0);
            }
        } else {
            return remainingRates.getParameterValue(0);
        }
    }
    */

    // the tree model
    private TreeModel treeModel;

    private Parameter backboneDrift;
    private Parameter otherDrift;
    private BackboneNodeFilter backbone;

    /*
    private Parameter remainingRates;
    private Parameter rateOne;
    private Parameter rateTwo;
    private String rateOneID;
    private String rateTwoID;
    */
}