/*
 * SampleStateModel.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.sitemodel;

import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.evomodel.substmodel.YangCodonModel;
import dr.inference.model.*;
import dr.xml.*;

import java.util.Vector;


/**
 * DiscreteSampleModel - A SiteModel that has a discrete distribution of substitutionmodels over sites
 * designed for sampling of rate categories.
 *
 * @author Roald Forsberg
 */

public class SampleStateModel extends AbstractModel implements SiteModel {

    public static final String SAMPLE_STATE_MODEL = "sampleStateModel";
    public static final String MUTATION_RATE = "mutationRate";
    public static final String PROPORTIONS = "proportions";
    public static final double OMEGA_MAX_VALUE = 100.0;
    public static final double OMEGA_MIN_VALUE = 0.0;


    /**
     * Constructor
     */
    public SampleStateModel(Parameter muParameter,
                            Parameter proportionParameter,
                            Vector substitutionModels) {

        super(SAMPLE_STATE_MODEL);


        this.substitutionModels = substitutionModels;

        for (int i = 0; i < substitutionModels.size(); i++) {
            addModel((SubstitutionModel) substitutionModels.elementAt(i));
        }

        this.categoryCount = substitutionModels.size();

//		stateCount = ((SubstitutionModel)substitutionModels.elementAt(0)).getDataType().getStateCount();

        addVariable(muParameter);
        muParameter.addBounds(new Parameter.DefaultBounds(1000.0, 0.0, 1));

        this.proportionParameter = proportionParameter;
        addVariable(proportionParameter);
        proportionParameter.addBounds(new Parameter.DefaultBounds(1.0, 0.0, proportionParameter.getDimension()));

        proportionParameter.setParameterValue(0, (0.5));
        for (int i = 1; i < categoryCount; i++) {
            proportionParameter.setParameterValue(i, (0.5 / (categoryCount - 1)));
        }

        if (categoryCount > 1) {
            for (int i = 0; i < categoryCount; i++) {
                Parameter p = (Parameter) ((YangCodonModel) substitutionModels.elementAt(i)).getVariable(0);
                Parameter lower = null;
                Parameter upper = null;

                if (i == 0) {
                    upper = (Parameter) ((YangCodonModel) substitutionModels.elementAt(i + 1)).getVariable(0);
                    p.addBounds(new omegaBounds(lower, upper));
                } else {
                    if (i == (categoryCount - 1)) {
                        lower = (Parameter) ((YangCodonModel) substitutionModels.elementAt(i - 1)).getVariable(0);
                        p.addBounds(new omegaBounds(lower, upper));
                    } else {
                        upper = (Parameter) ((YangCodonModel) substitutionModels.elementAt(i + 1)).getVariable(0);
                        lower = (Parameter) ((YangCodonModel) substitutionModels.elementAt(i - 1)).getVariable(0);
                        p.addBounds(new omegaBounds(lower, upper));
                    }
                }
            }
        }
    }

    // *****************************************************************
    // Interface SiteModel
    // *****************************************************************

    public SubstitutionModel getSubstitutionModel() {
        return null;
    }

    public boolean integrateAcrossCategories() {
        return true;
    }

    public int getCategoryCount() {
        return categoryCount;
    }

    public int getCategoryOfSite(int site) {
        throw new IllegalArgumentException("Integrating across categories");
    }

    public double[] getCategoryRates() {
        throw new RuntimeException("getCategoryRates not available in this siteModel");
    }

    public double getRateForCategory(int category) {
        throw new RuntimeException("getRateForCategory not available in this siteModel");
    }

    public double getSubstitutionsForCategory(int category, double time) {
        throw new RuntimeException("getSubstitutionsForCategory not available in this siteModel");
    }

    public void getTransitionProbabilities(double substitutions, double[] matrix) {
        throw new RuntimeException("getTransitionProbabilities not available in this siteModel");
    }

    /**
     * Get the frequencyModel for this SiteModel.
     *
     * @return the frequencyModel.
     */
    public FrequencyModel getFrequencyModel() {
        return ((SubstitutionModel) substitutionModels.elementAt(0)).getFrequencyModel();
    }

    /**
     * Get the expected proportion of sites in this category.
     *
     * @param category the category number
     * @return the proportion.
     */
    public double getProportionForCategory(int category) {
        return proportionParameter.getParameterValue(category);
    }

    /**
     * Get an array of the expected proportion of sites in this category.
     *
     * @return an array of the proportion.
     */
    public double[] getCategoryProportions() {
        double[] probs = new double[categoryCount];

        for (int i = 0; i < categoryCount; i++) {
            probs[i] = proportionParameter.getParameterValue(i);
        }

        return probs;
    }

    // *****************************************************************
    // Interface ModelComponent
    // *****************************************************************

    protected void handleModelChangedEvent(Model model, Object object, int index) {
        // Substitution model has changed so fire model changed event
        listenerHelper.fireModelChanged(this, object, index);
    }


    protected final void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
        /*if(categoryCount > 1){
              for(int i = 0; i < categoryCount; i++){
                  if(parameter == classSizes[i] && i == 0) // proportions have changed
                      resetProportions(i+1);// adjust the proportion of class above
                  if(parameter == classSizes[i] && i != 0) // proportions have changed
                      resetProportions(i-1);// adjust the proportion of class below
              }
          } else{}*/
    }

    protected void storeState() {
    }

    protected void restoreState() {
    }

    protected void acceptState() {
    } // no additional state needs accepting

    public String toString() {
        StringBuffer s = new StringBuffer();

        return s.toString();
    }

    /*private void resetProportions(int classToAlter){
         double[] probs = getCategoryProportions();
         double sum = 0.0;
         double current = classSizes[classToAlter].getParameterValue(0);
         for(int i = 0; i < categoryCount; i++){
             sum += probs[i];
         }
         sum = 1 - sum;
         classSizes[classToAlter].setParameterValue(0,(current+sum));
     }*/

    public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {

        public String getParserName() {
            return SAMPLE_STATE_MODEL;
        }

        public Object parseXMLObject(XMLObject xo) throws XMLParseException {

            XMLObject cxo = xo.getChild(MUTATION_RATE);
            Parameter muParam = (Parameter) cxo.getChild(Parameter.class);

            cxo = xo.getChild(PROPORTIONS);
            Parameter proportionParameter = (Parameter) cxo.getChild(Parameter.class);

            Vector<Object> subModels = new Vector<Object>();

            for (int i = 0; i < xo.getChildCount(); i++) {
                if (xo.getChild(i) instanceof SubstitutionModel) {
                    subModels.addElement(xo.getChild(i));
                }
            }

            return new SampleStateModel(muParam, proportionParameter, subModels);
        }

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

        public String getParserDescription() {
            return "A SiteModel that has a discrete distribution of substitution models over sites, " +
                    "designed for sampling of internal states.";
        }

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

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

        private final XMLSyntaxRule[] rules = {
                new ElementRule(MUTATION_RATE,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
                new ElementRule(PROPORTIONS,
                        new XMLSyntaxRule[]{new ElementRule(Parameter.class)}),
                new ElementRule(SubstitutionModel.class, 1, Integer.MAX_VALUE)
        };
    };

    private class omegaBounds implements Bounds<Double>  {

        private final Parameter lowerOmega, upperOmega;

        public omegaBounds(Parameter lowerOmega, Parameter upperOmega) {

            this.lowerOmega = lowerOmega;
            this.upperOmega = upperOmega;
        }

        public omegaBounds(Parameter nearestOmega, boolean isUpper) {

            if (isUpper) {
                lowerOmega = nearestOmega;
                upperOmega = null;
            } else {
                lowerOmega = null;
                upperOmega = nearestOmega;
            }
        }

        /**
         * @return the upper limit of this hypervolume in the given dimension.
         */
        public Double getUpperLimit(int dimension) {

            if (dimension != 0)
                throw new RuntimeException("omega parameters have wrong dimension " + dimension);

            if (upperOmega == null)
                return OMEGA_MAX_VALUE;
            else
                return upperOmega.getParameterValue(dimension);

        }

        /**
         * @return the lower limit of this hypervolume in the given dimension.
         */
        public Double getLowerLimit(int dimension) {

            if (dimension != 0)
                throw new RuntimeException("omega parameters have wrong dimension " + dimension);

            if (lowerOmega == null)
                return OMEGA_MIN_VALUE;

            else
                return lowerOmega.getParameterValue(dimension);
        }

        /**
         * @return the dimensionality of this hypervolume.
         */
        public int getBoundsDimension() {
            return 1;
        }

    }

    class classSizeBounds implements Bounds {

        private final Parameter catProportionUnder;
        private final Parameter catProportionAbove;
        private final Parameter catProportion;

        public classSizeBounds(Parameter catProportion, Parameter catProportionUnder, Parameter catProportionAbove) {

            this.catProportionUnder = catProportionUnder;
            this.catProportionAbove = catProportionAbove;
            this.catProportion = catProportion;
        }

        /**
         * @return the upper limit of this hypervolume in the given dimension.
         */
        public Double getUpperLimit(int dimension) {

            if (dimension != 0)
                throw new RuntimeException("class size parameters have wrong dimension " + dimension);
            if (catProportionUnder == null)
                return catProportion.getParameterValue(dimension) + catProportionAbove.getParameterValue(dimension);
            else
                return catProportion.getParameterValue(dimension) + catProportionUnder.getParameterValue(dimension);
        }

        /**
         * @return the lower limit of this hypervolume in the given dimension.
         */
        public Double getLowerLimit(int dimension) {

            if (dimension != 0)
                throw new RuntimeException("class size parameters have wrong dimension " + dimension);

            return 0.0;
        }

        /**
         * @return the dimensionality of this hypervolume.
         */
        public int getBoundsDimension() {
            return 1;
        }

    }

    private final Vector substitutionModels;

    /**
     * class size parameters
     */
    private final Parameter proportionParameter;

    private final int categoryCount;

//	private int stateCount;
}
