DRHomogeneousMixedTreeLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_DRHOMOGENEOUSMIXEDTREELIKELIHOOD_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_DRHOMOGENEOUSMIXEDTREELIKELIHOOD_H
 
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
#include <Bpp/Numeric/VectorTools.h>
 
#include "../../Model/MixedTransitionModel.h"
#include "../../Model/SubstitutionModel.h"
#include "DRHomogeneousTreeLikelihood.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,
      std::shared_ptr<TransitionModelInterface> model,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool checkRooted = true,
      bool verbose = true,
      bool rootArray = false);
 
  DRHomogeneousMixedTreeLikelihood(
      const Tree& tree,
      const AlignmentDataInterface& data,
      std::shared_ptr<TransitionModelInterface> model,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool checkRooted = true,
      bool verbose = true,
      bool rootArray = false);
 
  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 AlignmentDataInterface& sites);
  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;
  double getSecondOrderDerivative(const std::string& variable) const;
  double getSecondOrderDerivative(const std::string& variable1, const std::string& variable2) const { return 0; } // Not implemented for now.
public:
  // Specific methods:
  void initialize();
 
  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 // BPP_PHYL_LEGACY_LIKELIHOOD_DRHOMOGENEOUSMIXEDTREELIKELIHOOD_H