/*
 * ExternalInternalBranchSubstitutionModel.java
 *
 * Copyright (c) 2002-2012 Alexei Drummond, Andrew Rambaut and Marc Suchard
 *
 * 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.beagle.evomodel.sitemodel;

import beagle.Beagle;
import dr.app.beagle.evomodel.substmodel.EigenDecomposition;
import dr.app.beagle.evomodel.substmodel.FrequencyModel;
import dr.app.beagle.evomodel.substmodel.SubstitutionModel;
import dr.app.beagle.evomodel.treelikelihood.BufferIndexHelper;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.inference.model.AbstractModel;
import dr.inference.model.Model;
import dr.inference.model.Parameter;
import dr.inference.model.Variable;
import dr.util.Author;
import dr.util.Citable;
import dr.util.Citation;

import java.util.ArrayList;
import java.util.List;

/**
 * @author Marc A. Suchard
 * @version $Id$
 */
public class ExternalInternalBranchSubstitutionModel extends AbstractModel implements BranchSubstitutionModel, Citable {
    public ExternalInternalBranchSubstitutionModel(List<SubstitutionModel> substModelList, List<FrequencyModel> frequencyModelList) {
        super("ExternalInternalBranchSubstitutionModel");

        if (substModelList.size() != 2) {
            throw new IllegalArgumentException("ExternalInternalBranchSubstitutionModel requires two SubstitutionModels");
        }

        if (frequencyModelList.size() != 1) {
            throw new IllegalArgumentException("ExternalInternalBranchSubstitutionModel requires one FrequencyModel");
        }

        this.substModelList = substModelList;
        this.frequencyModelList = frequencyModelList;

        for (SubstitutionModel model : substModelList) {
            addModel(model);
        }
        for (FrequencyModel model : frequencyModelList) {
            addModel(model);
        }
    }
    
	@Override
	public void setEigenDecomposition(Beagle beagle, int eigenIndex,
			BufferIndexHelper bufferHelper, int dummy) {
        EigenDecomposition ed = getEigenDecomposition(eigenIndex, dummy);

        beagle.setEigenDecomposition(
//                offsetIndex,
        		eigenIndex,
                ed.getEigenVectors(),
                ed.getInverseEigenVectors(),
                ed.getEigenValues());
		
	}    

    public int getBranchIndex(final Tree tree, final NodeRef node, int bufferIndex) {
        return (tree.isExternal(node) ? 1 : 0);
    }

    public EigenDecomposition getEigenDecomposition(int branchIndex, int categoryIndex) {
        return substModelList.get(branchIndex).getEigenDecomposition();
    }

    public SubstitutionModel getSubstitutionModel(int branchIndex, int categoryIndex) {
        return substModelList.get(branchIndex);
    }

    public double[] getStateFrequencies(int categoryIndex) {
        return frequencyModelList.get(categoryIndex).getFrequencies();
    }

    public boolean canReturnComplexDiagonalization() {
        for (SubstitutionModel model : substModelList) {
            if (model.canReturnComplexDiagonalization()) {
                return true;
            }
        }
        return false;
    }

    public int getEigenCount() {
        return 2;
    }

    protected void handleModelChangedEvent(Model model, Object object, int index) {
        fireModelChanged();
    }

    protected void handleVariableChangedEvent(Variable variable, int index, Parameter.ChangeType type) {
    }

    protected void storeState() {
    }

    protected void restoreState() {
    }

    protected void acceptState() {
    }

    public void updateTransitionMatrices( Beagle beagle,
            int eigenIndex,
            BufferIndexHelper bufferHelper,
            final int[] probabilityIndices,
            final int[] firstDerivativeIndices,
            final int[] secondDervativeIndices,
            final double[] edgeLengths,
            int count) {
        beagle.updateTransitionMatrices(eigenIndex, probabilityIndices, firstDerivativeIndices,
                secondDervativeIndices, edgeLengths, count);
    }

    private final List<SubstitutionModel> substModelList;
    private final List<FrequencyModel> frequencyModelList;

    /**
     * @return a list of citations associated with this object
     */
    public List<Citation> getCitations() {
        List<Citation> citations = new ArrayList<Citation>();
        citations.add(
                new Citation(
                        new Author[]{
                                new Author("P", "Lemey"),
                                new Author("MA", "Suchard")
                        },
                        Citation.Status.IN_PREPARATION
                )
        );
        return citations;
    }

	@Override
	public int getExtraBufferCount() {
		// TODO Auto-generated method stub
		return 0;
	}

	@Override
	public void setFirstBuffer(int bufferCount) {
		// TODO Auto-generated method stub
		
	}
}
@@ -1383,16 +1383,51 @@
 e.Tree;%0A
+import dr.evomodel.tree.TreeModel;%0A
 import d
@@ -5588,24 +5588,43 @@
 BufferCount(
+TreeModel treeModel
 ) %7B%0A%09%09// TOD

pass the tree as argument