/*
 * 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.app.beauti.options;


import dr.app.beauti.types.PriorType;
import dr.evolution.util.Taxa;

import java.util.List;


/**
 * @author Alexei Drummond
 * @author Andrew Rambaut
 * @author Walter Xie
 * @version $Id$
 */
public class TreeModelOptions extends ModelOptions {

    // Instance variables
    private final BeautiOptions options;


    public TreeModelOptions(BeautiOptions options) {
        this.options = options;

        initGlobalTreeModelParaAndOpers();
    }

    private void initGlobalTreeModelParaAndOpers() {

    }

    /**
     * return a list of parameters that are required
     *
     * @param params the parameter list
     */
    public void selectParameters(List<Parameter> params) {

    }

    /**
     * return a list of operators that are required
     *
     * @param ops the operator list
     */
    public void selectOperators(List<Operator> ops) {

    }

    /////////////////////////////////////////////////////////////
//    public double getRandomStartingTreeInitialRootHeight(PartitionTreeModel model) {
//    	Parameter rootHeight = model.getParameter("treeModel.rootHeight");
//    	
//    	if (rootHeight.priorType != PriorType.NONE_TREE_PRIOR) {
//    		return rootHeight.initial;
//    	} else {    		
//    		return calculateMeanDistance(model.getAllPartitionData());
//    	}   	
//		
//    }

    public double getExpectedAvgBranchLength(double rootHeight) {
        double sum = 0;
        int taxonCount = options.taxonList.getTaxonCount();

        for (int i = 2; i <= taxonCount; i++) {
            sum += (double) 1 / i;
        }

        return rootHeight * sum / (double) (2 * taxonCount - 2);
    }

    public int isNodeCalibrated(PartitionTreeModel treeModel) {
        if (options.treeModelOptions.isNodeCalibrated(treeModel.getParameter("treeModel.rootHeight"))) {
            return 0; // root node
        } else if (options.getKeysFromValue(options.taxonSetsTreeModel, treeModel).size() > 0) {
            return 1; // internal node (tmrca)
        } else {
            return -1;
        }
    }

    public boolean isNodeCalibrated(Parameter para) {
        return (para.taxaId != null && hasProperPriorOn(para)) // param.taxa != null is TMRCA
                || (para.getBaseName().endsWith("treeModel.rootHeight") && hasProperPriorOn(para));
    }

    private boolean hasProperPriorOn(Parameter para) {
        return para.priorType == PriorType.EXPONENTIAL_PRIOR
//                || para.priorType == PriorType.TRUNC_NORMAL_PRIOR
                || (para.priorType == PriorType.UNIFORM_PRIOR && para.truncationLower > 0 && para.truncationUpper < Double.POSITIVE_INFINITY)
                || para.priorType == PriorType.LAPLACE_PRIOR
                || para.priorType == PriorType.NORMAL_PRIOR
                || para.priorType == PriorType.LOGNORMAL_PRIOR
                || para.priorType == PriorType.GAMMA_PRIOR
                || para.priorType == PriorType.INVERSE_GAMMA_PRIOR
                || para.priorType == PriorType.BETA_PRIOR
                || para.priorType == PriorType.CMTC_RATE_REFERENCE_PRIOR
                || para.priorType == PriorType.LOGNORMAL_HPM_PRIOR
                || para.priorType == PriorType.POISSON_PRIOR;
    }

}

@@ -3527,26 +3527,23 @@
 && para.
-truncation
+uniform
 Lower %3E 
@@ -3556,18 +3556,15 @@
 ara.
-truncation
+uniform
 Uppe

fix a bug to use uniform lower and upper.