/*
 * ExpConstExpDemographicModel.java
 *
 * Copyright (C) 2002-2009 Alexei Drummond and Andrew Rambaut
 *
 * 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.coalescent;

import dr.evolution.coalescent.DemographicFunction;
import dr.evolution.coalescent.ExpConstExpDemographic;
import dr.evoxml.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;

/**
 * This class models a two growth-phase demographic with a plateau in the middle
 *
 * @author Alexei Drummond
 * @author Andrew Rambaut
 * @version $Id: ExpConstExpDemographicModel.java,v 1.2 2006/08/18 07:44:25 alexei Exp $
 */
public class ExpConstExpDemographicModel extends DemographicModel {

    //
    // Public stuff
    //

    public static String POPULATION_SIZE = "populationSize";
    public static String RELATIVE_PLATEAU_SIZE = "relativePlateauSize";
    public static String RELATIVE_TIME_OF_MODERN_GROWTH = "relTimeModGrowth";
    public static String TIME_PLATEAU = "plateauStartTime";
    public static String ANCIENT_GROWTH_RATE = "ancientGrowthRate";

    public static String EXP_CONST_EXP_MODEL = "expConstExp";


    /**
     * Construct demographic model with default settings
     */
    public ExpConstExpDemographicModel(
            Parameter N0Parameter,
            Parameter N1Parameter,
            Parameter growthRateParameter,
            Parameter timeParameter,
            Parameter relTimeParameter,
            Type units) {

        this(EXP_CONST_EXP_MODEL, N0Parameter, N1Parameter, growthRateParameter, timeParameter, relTimeParameter, units);
    }

    /**
     * Construct demographic model with default settings
     */
    public ExpConstExpDemographicModel(String name, Parameter N0Parameter, Parameter N1Parameter, Parameter growthRateParameter, Parameter timeParameter, Parameter relTimeParameter, Type units) {

        super(name);

        expConstExp = new ExpConstExpDemographic(units);

        this.N0Parameter = N0Parameter;
        addVariable(N0Parameter);
        N0Parameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));

        this.N1Parameter = N1Parameter;
        addVariable(N1Parameter);
        N1Parameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));

        this.growthRateParameter = growthRateParameter;
        addVariable(growthRateParameter);
        growthRateParameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, Double.MIN_VALUE, 1));

        this.timeParameter = timeParameter;
        addVariable(timeParameter);
        timeParameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, Double.MIN_VALUE, 1));

        this.relTimeParameter = relTimeParameter;
        addVariable(relTimeParameter);
        relTimeParameter.addBounds(new Parameter.DefaultBounds(1.0, Double.MIN_VALUE, 1));

        setUnits(units);
    }


    // general functions

    public DemographicFunction getDemographicFunction() {

        expConstExp.setN0(N0Parameter.getParameterValue(0));

        double relTime = relTimeParameter.getParameterValue(0);
        double time2 = timeParameter.getParameterValue(0);

        //System.out.println("relTime=" + relTime);
        //System.out.println("time2=" + (time2));


        double timeInModernGrowthPhase = time2 * relTime;

        double r = -Math.log(N1Parameter.getParameterValue(0)) / timeInModernGrowthPhase;

        //System.out.println("N0=" + N0Parameter.getParameterValue(0));
        //System.out.println("r=" + r);
        //System.out.println("r2=" + growthRateParameter.getParameterValue(0));
        //System.out.println("time1=" + timeInModernGrowthPhase);
        //System.out.println("plateauTime=" + (time2-timeInModernGrowthPhase));

        expConstExp.setGrowthRate(r);
        expConstExp.setGrowthRate2(growthRateParameter.getParameterValue(0));

        expConstExp.setTime1(timeInModernGrowthPhase);
        expConstExp.setPlateauTime(time2 - timeInModernGrowthPhase);

        return expConstExp;
    }

    /**
     * Parses an element from an DOM document into a ExponentialGrowth.
     */
    public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {

        public String getParserName() {
            return EXP_CONST_EXP_MODEL;
        }

        public Object parseXMLObject(XMLObject xo) throws XMLParseException {

            Type units = XMLUnits.Utils.getUnitsAttr(xo);

            XMLObject cxo = xo.getChild(POPULATION_SIZE);
            Parameter N0Param = (Parameter) cxo.getChild(Parameter.class);

            cxo = xo.getChild(RELATIVE_PLATEAU_SIZE);
            Parameter N1Param = (Parameter) cxo.getChild(Parameter.class);

            cxo = xo.getChild(RELATIVE_TIME_OF_MODERN_GROWTH);
            Parameter rtParam = (Parameter) cxo.getChild(Parameter.class);

            cxo = xo.getChild(TIME_PLATEAU);
            Parameter tParam = (Parameter) cxo.getChild(Parameter.class);

            cxo = xo.getChild(ANCIENT_GROWTH_RATE);
            Parameter rParam = (Parameter) cxo.getChild(Parameter.class);

            return new ExpConstExpDemographicModel(N0Param, N1Param, rParam, tParam, rtParam, units);
        }

        //************************************************************************
        // AbstractXMLObjectParser implementation
        //************************************************************************

        public String getParserDescription() {
            return "A demographic model of exponential growth.";
        }

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

        public XMLSyntaxRule[] getSyntaxRules() {
            return rules;
        }

        private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
                new ElementRule(POPULATION_SIZE,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
                new ElementRule(RELATIVE_PLATEAU_SIZE,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
                        "The size of plateau relative to modern population size."),
                new ElementRule(RELATIVE_TIME_OF_MODERN_GROWTH,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
                        "The time spanned by modern growth phase relative to time back to start of plateau phase."),
                new ElementRule(TIME_PLATEAU,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
                        "The time of the start of plateauPhase."),
                new ElementRule(ANCIENT_GROWTH_RATE,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)},
                        "The growth rate of early growth phase"),
                XMLUnits.SYNTAX_RULES[0]
        };
    };
    //
    // protected stuff
    //

    Parameter N0Parameter = null;
    Parameter N1Parameter = null;
    Parameter growthRateParameter = null;
    Parameter timeParameter = null;
    Parameter relTimeParameter = null;
    ExpConstExpDemographic expConstExp = null;
}
