GeneralSubstitutionModel.java

/*
 * GeneralSubstitutionModel.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.substmodel;

import dr.evolution.datatype.DataType;
import dr.inference.model.Parameter;
import dr.inference.model.DuplicatedParameter;

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

/**
 * <b>A general model of sequence substitution</b>. A general reversible class for any
 * data type.
 *
 * @author Andrew Rambaut
 * @author Alexei Drummond
 * @author Marc Suchard
 */
public class GeneralSubstitutionModel extends BaseSubstitutionModel {

    /**
     * the rate which the others are set relative to
     */
    protected int ratesRelativeTo;

    public GeneralSubstitutionModel(String name, DataType dataType, FrequencyModel freqModel,
                                    Parameter ratesParameter, int relativeTo) {
        this(name, dataType, freqModel, ratesParameter, relativeTo, null);

    }

    /**
     * constructor
     *
     * @param dataType the data type
     */
    public GeneralSubstitutionModel(String name, DataType dataType, FrequencyModel freqModel,
                                    Parameter ratesParameter, int relativeTo, EigenSystem eigenSystem) {

        super(name, dataType, freqModel, eigenSystem);

        this.ratesParameter = ratesParameter;
        if (ratesParameter != null) {
            addVariable(ratesParameter);
            if (!(ratesParameter instanceof DuplicatedParameter))
                ratesParameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0,
                        ratesParameter.getDimension()));

            setupDimensionNames(relativeTo);
        }
        setRatesRelativeTo(relativeTo);
    }

    protected void frequenciesChanged() {
        // Nothing to precalculate
    }

    protected void ratesChanged() {
        // Nothing to precalculate
    }

    protected void setupRelativeRates(double[] rates) {
        for (int i = 0; i < rates.length; i++) {
            if (i == ratesRelativeTo) {
                rates[i] = 1.0;
            } else if (ratesRelativeTo < 0 || i < ratesRelativeTo) {
                rates[i] = ratesParameter.getParameterValue(i);
            } else {
                rates[i] = ratesParameter.getParameterValue(i - 1);
            }
        }
    }

    protected void setupDimensionNames(int relativeTo) {
        List<String> rateNames = new ArrayList<String>();

        String ratePrefix = ratesParameter.getParameterName();

        int index = 0;

        for (int i = 0; i < dataType.getStateCount(); ++i) {
            for (int j = i + 1; j < dataType.getStateCount(); ++j) {
                if (index != relativeTo) {
                    rateNames.add(getDimensionString(i, j, ratePrefix));
                }
            }
            index++;
        }

        String[] tmp = new String[0];
        ratesParameter.setDimensionNames(rateNames.toArray(tmp));
    }

    protected String getDimensionString(int i, int j, String prefix) {
        String codes =  dataType.getCode(i) + "." + dataType.getCode(j);
        if (prefix == null) {
            return codes;
        } else {
            return prefix + "." + codes;
        }
    }

    /**
     * set which rate the others are relative to
     */
    public void setRatesRelativeTo(int ratesRelativeTo) {
        this.ratesRelativeTo = ratesRelativeTo;
    }

    // *****************************************************************
    // Interface Model
    // *****************************************************************


    protected void storeState() {
    } // nothing to do

    /**
     * Restore the additional stored state
     */
    protected void restoreState() {
        updateMatrix = true;
    }

    protected void acceptState() {
    } // nothing to do

    /**
     * Parses an element from an DOM document into a DemographicModel. Recognises
     * ConstantPopulation and ExponentialGrowth.
     */

    protected Parameter ratesParameter = null;
}