RHomogeneousTreeLikelihood.h

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//
// File: RHomogeneousTreeLikelihood.h
// Created by: Julien Dutheil
// Created on: Fri Oct 17 18:14:51 2003
//

/*
  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 _RHOMOGENEOUSTREELIKELIHOOD_H_
#define _RHOMOGENEOUSTREELIKELIHOOD_H_

#include "AbstractHomogeneousTreeLikelihood.h"
#include "../Model/SubstitutionModel.h"
#include "DRASRTreeLikelihoodData.h"

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

namespace bpp
{

  class RHomogeneousTreeLikelihood :
    public AbstractHomogeneousTreeLikelihood
  {
  private:

    mutable DRASRTreeLikelihoodData* likelihoodData_;

  protected:
    double minusLogLik_;

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

    RHomogeneousTreeLikelihood(const RHomogeneousTreeLikelihood& lik);
    
    RHomogeneousTreeLikelihood& operator=(const RHomogeneousTreeLikelihood& lik);

    virtual ~RHomogeneousTreeLikelihood();

    RHomogeneousTreeLikelihood* clone() const { return new RHomogeneousTreeLikelihood(*this); }
  
  private:

    void init_(bool usePatterns) throw (Exception);
  
  public:

    void setData(const SiteContainer& sites) throw (Exception);
    double getLikelihood() const;
    double getLogLikelihood() const;
    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;
    void setParameters(const ParameterList& parameters) throw (ParameterNotFoundException, ConstraintException);
    double getValue() const throw(Exception);
    
    size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }

    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:
  
    DRASRTreeLikelihoodData* getLikelihoodData() { return likelihoodData_; }
    const DRASRTreeLikelihoodData* getLikelihoodData() const { return likelihoodData_; }

    void computeTreeLikelihood();

    virtual double getDLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const;

    virtual double getDLikelihoodForASite(size_t site) const;

    virtual double getDLogLikelihoodForASite(size_t site) const;
    
    virtual double getDLogLikelihood() const;
    
    virtual void computeTreeDLikelihood(const std::string& variable);

    virtual double getD2LikelihoodForASiteForARateClass(size_t site, size_t rateClass) const;

    virtual double getD2LikelihoodForASite(size_t site) const;

    virtual double getD2LogLikelihoodForASite(size_t site) const;
    
    virtual double getD2LogLikelihood() const;
    
    virtual void computeTreeD2Likelihood(const std::string& variable);

  
  protected:
      
    virtual void computeSubtreeLikelihood(const Node* node); //Recursive method.      
    virtual void computeDownSubtreeDLikelihood(const Node*);
    
    virtual void computeDownSubtreeD2Likelihood(const Node*);
  
    void fireParameterChanged(const ParameterList& params);
  
    virtual void displayLikelihood(const Node* node);

    friend class RHomogeneousMixedTreeLikelihood;
  };


} //end of namespace bpp.

#endif  //_RHOMOGENEOUSTREELIKELIHOOD_H_