DRHomogeneousTreeLikelihood.h

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

/*
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
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 _DRHOMOGENEOUSTREELIKELIHOOD_H_
#define _DRHOMOGENEOUSTREELIKELIHOOD_H_

#include "AbstractHomogeneousTreeLikelihood.h"
#include "DRTreeLikelihood.h"
#include "DRASDRTreeLikelihoodData.h"

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

namespace bpp
{

class DRHomogeneousTreeLikelihood:
  public AbstractHomogeneousTreeLikelihood,
  public DRTreeLikelihood
{
  private:
    mutable DRASDRTreeLikelihoodData* likelihoodData_;

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

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

    virtual ~DRHomogeneousTreeLikelihood();

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

  private:

    void init_() 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;
    size_t getSiteIndex(size_t site) const throw (IndexOutOfBoundsException) { return likelihoodData_->getRootArrayPosition(site); }
    void computeTreeLikelihood();

    
    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);
    
    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:

    DRASDRTreeLikelihoodData* getLikelihoodData() { return likelihoodData_; }
    const DRASDRTreeLikelihoodData* getLikelihoodData() const { return likelihoodData_; }
  
    virtual void computeLikelihoodAtNode(int nodeId, VVVdouble& likelihoodArray) const
    {
      computeLikelihoodAtNode_(tree_->getNode(nodeId), likelihoodArray);
    }
      
  protected:
    virtual void computeLikelihoodAtNode_(const Node* node, VVVdouble& likelihoodArray, const Node* sonNode = 0) const;
  
    virtual void computeSubtreeLikelihoodPostfix(const Node* node); //Recursive method.
    virtual void computeSubtreeLikelihoodPrefix(const Node* node); //Recursive method.

    virtual void computeRootLikelihood();

    virtual void computeTreeDLikelihoodAtNode(const Node* node);
    virtual void computeTreeDLikelihoods();
    
    virtual void computeTreeD2LikelihoodAtNode(const Node* node);
    virtual void computeTreeD2Likelihoods();

    virtual void fireParameterChanged(const ParameterList& params);

    virtual void resetLikelihoodArrays(const Node* node);
  
    virtual void displayLikelihood(const Node* node);

    static void computeLikelihoodFromArrays(
        const std::vector<const VVVdouble*>& iLik,
        const std::vector<const VVVdouble*>& tProb,
        VVVdouble& oLik, size_t nbNodes,
        size_t nbDistinctSites,
        size_t nbClasses,
        size_t nbStates,
        bool reset = true);

    static void computeLikelihoodFromArrays(
        const std::vector<const VVVdouble*>& iLik,
        const std::vector<const VVVdouble*>& tProb,
        const VVVdouble* iLikR,
        const VVVdouble* tProbR,
        VVVdouble& oLik,
        size_t nbNodes,
        size_t nbDistinctSites,
        size_t nbClasses,
        size_t nbStates,
        bool reset = true);

  friend class DRHomogeneousMixedTreeLikelihood;
};

} //end of namespace bpp.

#endif  //_DRHOMOGENEOUSTREELIKELIHOOD_H_