/*
 * ConstantLogisticModel.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.ConstLogistic;
import dr.evolution.coalescent.DemographicFunction;
import dr.evoxml.XMLUnits;
import dr.inference.model.Parameter;
import dr.xml.*;

/**
 * Logistic growth from a constant ancestral population size.
 *
 * @author Alexei Drummond
 * @author Andrew Rambaut
 * @version $Id: ConstantLogisticModel.java,v 1.7 2005/04/11 11:24:39 alexei Exp $
 */
public class ConstantLogisticModel extends DemographicModel {

    //
    // Public stuff
    //

    private static final String CONSTANT_LOGISTIC_MODEL = "constantLogistic";
    private static final String POPULATION_SIZE = "populationSize";
    private static final String ANCESTRAL_POPULATION_SIZE = "ancestralPopulationSize";

    private static final String GROWTH_RATE = "growthRate";
    private static final String SHAPE = "shape";
    private static final String ALPHA = "alpha";


    /**
     * Construct demographic model with default settings
     */
    private ConstantLogisticModel(Parameter N0Parameter, Parameter N1Parameter, Parameter growthRateParameter, Parameter shapeParameter, double alpha, Type units) {

        this(CONSTANT_LOGISTIC_MODEL, N0Parameter, N1Parameter, growthRateParameter, shapeParameter, alpha, units);
    }

    /**
     * Construct demographic model with default settings
     */
    private ConstantLogisticModel(String name, Parameter N0Parameter, Parameter N1Parameter, Parameter growthRateParameter, Parameter shapeParameter, double alpha, Type units) {

        super(name);

        constLogistic = new ConstLogistic(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, 0.0, 1));

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

        this.alpha = alpha;

        setUnits(units);
    }


    // general functions

    public DemographicFunction getDemographicFunction() {
        constLogistic.setN0(N0Parameter.getParameterValue(0));
        constLogistic.setN1(N1Parameter.getParameterValue(0));

        double r = growthRateParameter.getParameterValue(0);
        constLogistic.setGrowthRate(r);

        // AER 24/02/03
        // logisticGrowth.setShape(Math.exp(shapeParameter.getParameterValue(0)));

        // New parameterization of logistic shape to be the time at which the
        // population reached some proportion alpha:
        double C = ((1.0 - alpha) * Math.exp(-r * shapeParameter.getParameterValue(0))) / alpha;
        constLogistic.setShape(C);

        return constLogistic;
    }

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

        public String getParserName() {
            return CONSTANT_LOGISTIC_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(ANCESTRAL_POPULATION_SIZE);
            Parameter N1Param = (Parameter) cxo.getChild(Parameter.class);

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

            cxo = xo.getChild(SHAPE);
            Parameter cParam = (Parameter) cxo.getChild(Parameter.class);

            double alpha = xo.getDoubleAttribute(ALPHA);

            return new ConstantLogisticModel(N0Param, N1Param, rParam, cParam, alpha, units);
        }

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

        public String getParserDescription() {
            return "A demographic model of constant population size followed by logistic growth.";
        }

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

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

        private final XMLSyntaxRule[] rules = {
                XMLUnits.SYNTAX_RULES[0],
                new ElementRule(POPULATION_SIZE,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
                new ElementRule(ANCESTRAL_POPULATION_SIZE,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
                new ElementRule(GROWTH_RATE,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
                new ElementRule(SHAPE,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
                AttributeRule.newDoubleRule(ALPHA)
        };
    };
    //
    // protected stuff
    //

    private Parameter N0Parameter = null;
    private Parameter N1Parameter = null;
    private Parameter growthRateParameter = null;
    private Parameter shapeParameter = null;
    private double alpha = 0.5;
    private ConstLogistic constLogistic = null;
}
