RNonHomogeneousMixedTreeLikelihood.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_LEGACY_LIKELIHOOD_RNONHOMOGENEOUSMIXEDTREELIKELIHOOD_H
#define BPP_PHYL_LEGACY_LIKELIHOOD_RNONHOMOGENEOUSMIXEDTREELIKELIHOOD_H
 
#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
#include <Bpp/Numeric/VectorTools.h>
 
#include "../Model/MixedSubstitutionModelSet.h"
#include "RNonHomogeneousTreeLikelihood.h"
 
namespace bpp
{
class RNonHomogeneousMixedTreeLikelihood :
  public RNonHomogeneousTreeLikelihood
{
private:
  std::map<int, std::vector< std::shared_ptr<RNonHomogeneousMixedTreeLikelihood>>> mvTreeLikelihoods_;
 
  MixedSubstitutionModelSet::HyperNode hyperNode_;
 
  int upperNode_;
 
  bool main_;
 
  RNonHomogeneousMixedTreeLikelihood(
      const Tree& tree,
      std::shared_ptr<MixedSubstitutionModelSet> modelSet,
      const MixedSubstitutionModelSet::HyperNode& hyperNode,
      int upperNode,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool verbose,
      bool usePatterns);
 
  RNonHomogeneousMixedTreeLikelihood(
      const Tree& tree,
      const AlignmentDataInterface& data,
      std::shared_ptr<MixedSubstitutionModelSet> modelSet,
      const MixedSubstitutionModelSet::HyperNode& hyperNode,
      int upperNode,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool verbose,
      bool usePatterns);
 
 
  void init(bool usePatterns);
 
public:
  RNonHomogeneousMixedTreeLikelihood(
      const Tree& tree,
      std::shared_ptr<MixedSubstitutionModelSet> modelSet,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool verbose = true,
      bool usePatterns = true);
 
  RNonHomogeneousMixedTreeLikelihood(
      const Tree& tree,
      const AlignmentDataInterface& data,
      std::shared_ptr<MixedSubstitutionModelSet> modelSet,
      std::shared_ptr<DiscreteDistributionInterface> rDist,
      bool verbose = true,
      bool usePatterns = true);
 
  RNonHomogeneousMixedTreeLikelihood(const RNonHomogeneousMixedTreeLikelihood& lik);
 
  RNonHomogeneousMixedTreeLikelihood& operator=(const RNonHomogeneousMixedTreeLikelihood& lik);
 
  virtual ~RNonHomogeneousMixedTreeLikelihood();
 
  RNonHomogeneousMixedTreeLikelihood* clone() const { return new RNonHomogeneousMixedTreeLikelihood(*this); }
 
public:
  void setData(const AlignmentDataInterface& sites);
 
public:
  // Specific methods:
  void initialize();
 
  void computeTreeDLikelihood(const std::string& variable);
 
  void computeTreeD2Likelihood(const std::string& variable);
 
  double getProbability() const;
 
  void setProbability(double x);
 
  const MixedSubstitutionModelSet::HyperNode& getHyperNode() { return hyperNode_;}
 
protected:
  virtual void computeSubtreeLikelihood(const Node* node); // Recursive method.
 
  virtual void computeDownSubtreeDLikelihood(const Node*);
 
  virtual void computeDownSubtreeD2Likelihood(const Node*);
 
  void fireParameterChanged(const ParameterList& params);
 
  void computeTransitionProbabilitiesForNode(const Node* node);
};
} // end of namespace bpp.
#endif // BPP_PHYL_LEGACY_LIKELIHOOD_RNONHOMOGENEOUSMIXEDTREELIKELIHOOD_H