/*
 * ParsimonyStateStatistic.java
 *
 * Copyright (C) 2002-2006 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.tree;

import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.evolution.util.Taxa;
import dr.evolution.util.TaxonList;
import dr.inference.model.Statistic;
import dr.xml.*;

import java.util.Set;


/**
 * A statistic that reconstructs the parsimony state at a mrca
 *
 * @author Andrew Rambaut
 * @author Alexei Drummond
 * @version $Id: ParsimonyStateStatistic.java,v 1.11 2005/07/11 14:06:25 rambaut Exp $
 */
public class ParsimonyStateStatistic extends Statistic.Abstract implements TreeStatistic {

    public static final String PARSIMONY_STATE_STATISTIC = "parsimonyStateStatistic";
    public static final String STATE = "state";
    public static final String MRCA = "mrca";

    public ParsimonyStateStatistic(String name, Tree tree, TaxonList stateTaxa, TaxonList mrcaTaxa) throws Tree.MissingTaxonException {

        super(name);
        this.tree = tree;
        this.stateLeafSet = Tree.Utils.getLeavesForTaxa(tree, stateTaxa);
        if (mrcaTaxa != null) {
            this.mrcaLeafSet = Tree.Utils.getLeavesForTaxa(tree, mrcaTaxa);
        }
    }

    public void setTree(Tree tree) {
        this.tree = tree;
    }

    public Tree getTree() {
        return tree;
    }

    public int getDimension() {
        return 1;
    }

    /**
     * @return the parsimony tree length of the character.
     */
    public double getStatisticValue(int dim) {

        NodeRef node;

        if (mrcaLeafSet != null) {
            node = Tree.Utils.getCommonAncestorNode(tree, mrcaLeafSet);
        } else {
            node = tree.getRoot();
        }
        return Tree.Utils.getParsimonyState(tree, node, stateLeafSet);
    }

    public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {

        public String getParserName() {
            return PARSIMONY_STATE_STATISTIC;
        }

        public Object parseXMLObject(XMLObject xo) throws XMLParseException {

            String name = xo.getAttribute(NAME, xo.getId());

            Tree tree = (Tree) xo.getChild(Tree.class);
            XMLObject cxo = (XMLObject) xo.getChild(STATE);
            TaxonList stateTaxa = (TaxonList) cxo.getChild(TaxonList.class);

            cxo = (XMLObject) xo.getChild(MRCA);
            TaxonList mrcaTaxa = (TaxonList) cxo.getChild(TaxonList.class);

            try {
                return new ParsimonyStateStatistic(name, tree, stateTaxa, mrcaTaxa);
            } catch (Tree.MissingTaxonException mte) {
                throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
            }
        }

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

        public String getParserDescription() {
            return "A statistic that has as its value the parsimony state reconstruction of a " +
                    "binary state defined by a set of taxa at a given MRCA of a tree";
        }

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

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

        private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
                new StringAttributeRule(NAME, "A name for this statistic for the purposes of logging", true),
                new ElementRule(TreeModel.class),
                new ElementRule(STATE,
                        new XMLSyntaxRule[]{new ElementRule(Taxa.class)}),
                new ElementRule(MRCA,
                        new XMLSyntaxRule[]{new ElementRule(Taxa.class)})
        };
    };

    private Tree tree = null;
    private Set stateLeafSet = null;
    private Set<String> mrcaLeafSet = null;
}
