/*
 * GaussianProcessSkytrackLikelihood.java
 *
 * Copyright (c) 2002-2011 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.evomodel.coalescent;

import dr.evolution.tree.Tree;
import dr.inference.model.MatrixParameter;
import dr.inference.model.Parameter;

import java.util.List;

/**
 * @author US..
 */
public class GaussianProcessSkytrackLikelihood extends GMRFSkyrideLikelihood {

    public GaussianProcessSkytrackLikelihood(List<Tree> treeList, Parameter popParameter, Parameter groupParameter,
                                             Parameter precParameter, Parameter lambda, Parameter beta,
                                             MatrixParameter dMatrix, boolean timeAwareSmoothing,
                                             boolean rescaleByRootHeight, Parameter latentPoints) {
        super(treeList, popParameter, groupParameter, precParameter, lambda,beta, dMatrix, timeAwareSmoothing,
                rescaleByRootHeight);
        this.latentPoints = latentPoints;

        latentPoints.setDimension(1);
    }

    public double calculateLogLikelihood() {
        return 1.0; // TODO Return the correct log-density
    }

	public double getLogLikelihood() {
		if (!likelihoodKnown) {
			logLikelihood = calculateLogLikelihood();
			likelihoodKnown = true;
		}
		return logLikelihood;
	}

    private final Parameter latentPoints;
}

@@ -1993,17 +1993,17 @@
  return 
-1
+2
 .0; // T

How annoying can I get with these commits?