RHomogeneousClockTreeLikelihood.h

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//
// File: RHomogeneousClockTreeLikelihood.h
// Created by: Benoît Nabholz
//             Julien Dutheil
// Created on: Fri Apr 06 14:11 2007
//

/*
Copyright or © or Copr. CNRS, (November 16, 2004)

This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.

This software is governed by the CeCILL  license under French law and
abiding by the rules of distribution of free software.  You can  use, 
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info". 

As a counterpart to the access to the source code and  rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty  and the software's author,  the holder of the
economic rights,  and the successive licensors  have only  limited
liability. 

In this respect, the user's attention is drawn to the risks associated
with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
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same conditions as regards security. 

The fact that you are presently reading this means that you have had
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*/

#ifndef _RHOMOGENEOUSCLOCKTREELIKELIHOOD_H_
#define _RHOMOGENEOUSCLOCKTREELIKELIHOOD_H_

#include "RHomogeneousTreeLikelihood.h"
#include "ClockTreeLikelihood.h"
#include "../TreeTemplate.h"

#include <Bpp/Numeric/ParameterList.h>

namespace bpp
{

class RHomogeneousClockTreeLikelihood:
  public RHomogeneousTreeLikelihood,
  public DiscreteRatesAcrossSitesClockTreeLikelihood
{
  public:
    RHomogeneousClockTreeLikelihood(
      const Tree& tree,
      SubstitutionModel* model,
      DiscreteDistribution* rDist,
      bool checkRooted = true,
      bool verbose = true)
      throw (Exception);
  
    RHomogeneousClockTreeLikelihood(
      const Tree& tree,
      const SiteContainer& data,
      SubstitutionModel* model,
      DiscreteDistribution* rDist,
      bool checkRooted = true,
      bool verbose = true)
      throw (Exception);

    RHomogeneousClockTreeLikelihood* clone() const { return new RHomogeneousClockTreeLikelihood(*this); }

    virtual ~RHomogeneousClockTreeLikelihood() {}

  private:

    void init_();

  public:

    void applyParameters() throw (Exception);
    void fireParameterChanged(const ParameterList& params);
    void initBranchLengthsParameters();
    ParameterList getDerivableParameters() const throw (Exception);
    ParameterList getNonDerivableParameters() const throw (Exception);
    double getFirstOrderDerivative(const std::string& variable) const throw (Exception);
    double getSecondOrderDerivative(const std::string& variable) const throw (Exception);
    double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const throw (Exception) { return 0; } // Not implemented for now.
  protected:

    void computeBranchLengthsFromHeights(Node* node, double height) throw (Exception);

};

} //end of namespace bpp.

#endif // _RHOMOGENEOUSCLOCKTREELIKELIHOOD_H_