/*
 * MonophylyStatistic.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.Tree;
import dr.evolution.util.Taxa;
import dr.evolution.util.Taxon;
import dr.evolution.util.TaxonList;
import dr.inference.model.BooleanStatistic;
import dr.xml.*;

import java.util.Collections;
import java.util.Set;

/**
 * Performs monophyly test given a taxonList
 *
 * @author Roald Forsberg
 * @author Alexei Drummond
 * @author Andrew Rambaut
 * @version $Id: MonophylyStatistic.java,v 1.16 2005/07/11 14:06:25 rambaut Exp $
 */
public class MonophylyStatistic extends BooleanStatistic implements TreeStatistic {

    public static final String MONOPHYLY_STATISTIC = "monophylyStatistic";
    public static final String MRCA = "mrca";
    public static final String IGNORE = "ignore";

    public MonophylyStatistic(String name, Tree tree, TaxonList taxa, TaxonList ignore) throws Tree.MissingTaxonException {

        super(name);
        this.tree = tree;
        this.leafSet = Tree.Utils.getLeavesForTaxa(tree, taxa);
        if (ignore != null) {
            this.ignoreLeafSet = Tree.Utils.getLeavesForTaxa(tree, ignore);
        } else {
            this.ignoreLeafSet = Collections.emptySet();
        }

    }

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

    public Tree getTree() {
        return tree;
    }

    public int getDimension() {
        return 1;
    }

    /**
     * @return boolean result of test.
     */
    public boolean getBoolean(int dim) {
        return Tree.Utils.isMonophyletic(this.tree, this.leafSet, this.ignoreLeafSet);
    }

    public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {

        public String getParserName() {
            return MONOPHYLY_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(MRCA);
            TaxonList taxa = (TaxonList) cxo.getChild(TaxonList.class);
            if (taxa == null) {
                Taxa taxa1 = new Taxa();
                for (int i = 0; i < cxo.getChildCount(); i++) {
                    Object ccxo = cxo.getChild(i);
                    if (ccxo instanceof Taxon) {
                        taxa1.addTaxon((Taxon) ccxo);
                    }
                }
                taxa = taxa1;
            }

            TaxonList ignore = null;
            if (xo.hasChildNamed(IGNORE)) {
                cxo = (XMLObject) xo.getChild(IGNORE);
                ignore = (TaxonList) cxo.getChild(TaxonList.class);
                if (ignore == null) {
                    Taxa taxa1 = new Taxa();
                    for (int i = 0; i < cxo.getChildCount(); i++) {
                        Object ccxo = cxo.getChild(i);
                        if (ccxo instanceof Taxon) {
                            taxa1.addTaxon((Taxon) ccxo);
                        }
                    }
                    ignore = taxa1;
                }
            }

            try {
                return new MonophylyStatistic(name, tree, taxa, ignore);
            } 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 returns true if a given set of taxa are monophyletic for a given tree";
        }

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

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

        private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
                new StringAttributeRule(NAME, "A name for this statistic for the purpose of logging", true),
                new ElementRule(TreeModel.class),
                new ElementRule(MRCA, new XMLSyntaxRule[]{
                        new XORRule(
                                new ElementRule(Taxon.class, 1, Integer.MAX_VALUE),
                                new ElementRule(Taxa.class)
                        )
                }),
                new ElementRule(IGNORE, new XMLSyntaxRule[]{
                        new XORRule(
                                new ElementRule(Taxon.class, 1, Integer.MAX_VALUE),
                                new ElementRule(Taxa.class)
                        )
                }, "An optional list of taxa to ignore from the test of monophyly", true)
        };

    };

    private Tree tree = null;
    private Set<String> leafSet = null;
    private Set<String> ignoreLeafSet = null;

}

@@ -5067,16 +5067,87 @@
  true),%0A
+                // Any tree will do, no need to insist on a Tree Model%0A
         
@@ -5174,21 +5174,16 @@
 ule(Tree
-Model
 .class),

Allow any tree. Restriction of using only a tree model is silly