RNonHomogeneousTreeLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_RNONHOMOGENEOUSTREELIKELIHOOD_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_RNONHOMOGENEOUSTREELIKELIHOOD_H
 
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
#include <Bpp/Numeric/VectorTools.h>
 
#include "../Model/SubstitutionModelSet.h"
#include "AbstractNonHomogeneousTreeLikelihood.h"
#include "DRASRTreeLikelihoodData.h"
 
namespace bpp
{
class RNonHomogeneousTreeLikelihood :
  public AbstractNonHomogeneousTreeLikelihood
{
private:
  mutable std::shared_ptr<DRASRTreeLikelihoodData> likelihoodData_;
  double minusLogLik_;
 
public:
  RNonHomogeneousTreeLikelihood(
      const Tree& tree,
      std::shared_ptr<SubstitutionModelSet> modelSet,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool verbose = true,
      bool usePatterns = true,
      bool reparametrizeRoot = false);
 
  RNonHomogeneousTreeLikelihood(
      const Tree& tree,
      const AlignmentDataInterface& data,
      std::shared_ptr<SubstitutionModelSet> modelSet,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool verbose = true,
      bool usePatterns = true,
      bool reparametrizeRoot = false);
 
  RNonHomogeneousTreeLikelihood(const RNonHomogeneousTreeLikelihood& lik);
 
  RNonHomogeneousTreeLikelihood& operator=(const RNonHomogeneousTreeLikelihood& lik);
 
  virtual ~RNonHomogeneousTreeLikelihood();
 
  RNonHomogeneousTreeLikelihood* clone() const { return new RNonHomogeneousTreeLikelihood(*this); }
 
private:
  void init_(bool usePatterns);
 
public:
  void setData(const AlignmentDataInterface& sites);
  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 { return likelihoodData_->getRootArrayPosition(site); }
  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);
  double getValue() 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:
 
  DRASRTreeLikelihoodData& likelihoodData() { return *likelihoodData_; }
 
  const DRASRTreeLikelihoodData& likelihoodData() const { return *likelihoodData_; }
 
  virtual 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 RNonHomogeneousMixedTreeLikelihood;
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_RNONHOMOGENEOUSTREELIKELIHOOD_H