RHomogeneousMixedTreeLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_RHOMOGENEOUSMIXEDTREELIKELIHOOD_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_RHOMOGENEOUSMIXEDTREELIKELIHOOD_H
 
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
#include <Bpp/Numeric/VectorTools.h>
 
#include "../../Model/MixedTransitionModel.h"
#include "../../Model/SubstitutionModel.h"
#include "RHomogeneousTreeLikelihood.h"
 
namespace bpp
{
class RHomogeneousMixedTreeLikelihood :
  public RHomogeneousTreeLikelihood
{
private:
  std::vector< std::shared_ptr<RHomogeneousTreeLikelihood>> treeLikelihoodsContainer_;
  std::vector<double> probas_;
 
public:
  RHomogeneousMixedTreeLikelihood(
      const Tree& tree,
      std::shared_ptr<TransitionModelInterface> model,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool checkRooted = true,
      bool verbose = true,
      bool usePatterns = true);
 
  RHomogeneousMixedTreeLikelihood(
      const Tree& tree,
      const AlignmentDataInterface& data,
      std::shared_ptr<TransitionModelInterface> model,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool checkRooted = true,
      bool verbose = true,
      bool usePatterns = true);
 
  RHomogeneousMixedTreeLikelihood(const RHomogeneousMixedTreeLikelihood& lik);
 
  RHomogeneousMixedTreeLikelihood& operator=(const RHomogeneousMixedTreeLikelihood& lik);
 
  virtual ~RHomogeneousMixedTreeLikelihood();
 
  RHomogeneousMixedTreeLikelihood* clone() const { return new RHomogeneousMixedTreeLikelihood(*this); }
 
public:
  void setData(const AlignmentDataInterface& sites);
 
  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;
public:
  // Specific methods:
  void initialize();
 
  void fireParameterChanged(const ParameterList& params);
 
  void computeTreeLikelihood();
 
  virtual double getDLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const;
 
  virtual void computeTreeDLikelihood(const std::string& variable);
 
  virtual double getD2LikelihoodForASiteForARateClass(size_t site, size_t rateClass) 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 computeAllTransitionProbabilities();
  void computeTransitionProbabilitiesForNode(const Node* node);
 
  virtual void displayLikelihood(const Node* node);
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_RHOMOGENEOUSMIXEDTREELIKELIHOOD_H