DRHomogeneousMixedTreeLikelihood.h

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//
// File: DRHomogeneousMixedTreeLikelihood.h
// Created by: Laurent Gueguen
//

/*
   Copyright or © or Copr. Bio++ Development Team, (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
   requirements in conditions enabling the security of their systems and/or
   data to be ensured and,  more generally, to use and operate it in the
   same conditions as regards security.

   The fact that you are presently reading this means that you have had
   knowledge of the CeCILL license and that you accept its terms.
 */

#ifndef _DRHOMOGENEOUSMIXEDTREELIKELIHOOD_H_
#define _DRHOMOGENEOUSMIXEDTREELIKELIHOOD_H_

#include "DRHomogeneousTreeLikelihood.h"
#include "../Model/SubstitutionModel.h"
#include "../Model/MixedSubstitutionModel.h"

#include <Bpp/Numeric/VectorTools.h>
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>

namespace bpp
{

class DRHomogeneousMixedTreeLikelihood :
  public DRHomogeneousTreeLikelihood
{
private:
  std::vector<DRHomogeneousTreeLikelihood*> treeLikelihoodsContainer_;
  std::vector<double> probas_;

  // true if the root Array should be computed (for ancestral
  // reconstruction)
  
  bool rootArray_;
  
public:
  DRHomogeneousMixedTreeLikelihood(
    const Tree& tree,
    SubstitutionModel* model,
    DiscreteDistribution* rDist,
    bool checkRooted = true,
    bool verbose = true,
    bool rootArray = false)
  throw (Exception);

  DRHomogeneousMixedTreeLikelihood(
    const Tree& tree,
    const SiteContainer& data,
    SubstitutionModel* model,
    DiscreteDistribution* rDist,
    bool checkRooted = true,
    bool verbose = true,
    bool rootArray = false)
  throw (Exception);

  DRHomogeneousMixedTreeLikelihood(const DRHomogeneousMixedTreeLikelihood& lik);

  DRHomogeneousMixedTreeLikelihood& operator=(const DRHomogeneousMixedTreeLikelihood& lik);

  virtual ~DRHomogeneousMixedTreeLikelihood();

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

public:
  double getLikelihood() const;
  double getLogLikelihood() const;
  
  void setData(const SiteContainer& sites) throw (Exception);
  double getLikelihoodForASite (size_t site) const;
  double getLogLikelihoodForASite(size_t site) const;
  double getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const;
  double getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const;
  double getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const;
  double getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const;
  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.
public:
  // Specific methods:
  void initialize() throw (Exception);

  void fireParameterChanged(const ParameterList& params);

  void computeTreeLikelihood();

  virtual void computeTreeDLikelihoods();

protected:
  virtual void computeLikelihoodAtNode_(const Node* node, VVVdouble& likelihoodArray, const Node* sonNode = 0) const;

  virtual void computeSubtreeLikelihoodPostfix(const Node* node);

  virtual void computeSubtreeLikelihoodPrefix(const Node* node);

  virtual void computeRootLikelihood();

  virtual void computeTreeD2LikelihoodAtNode(const Node*);
  virtual void computeTreeD2Likelihoods();

  void resetLikelihoodArrays(const Node* node);

  virtual void displayLikelihood(const Node* node);
};
} // end of namespace bpp.

#endif  // _DRHOMOGENEOUSMIXEDTREELIKELIHOOD_H_