DecompositionReward.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_DECOMPOSITIONREWARD_H
#define BPP_PHYL_MAPPING_DECOMPOSITIONREWARD_H
 
 
#include "DecompositionMethods.h"
#include "Reward.h"
 
namespace bpp
{
class DecompositionReward :
  public AbstractReward,
  public DecompositionMethods
{
private:
  mutable RowMatrix<double> rewards_;
  mutable double currentLength_;
 
public:
  DecompositionReward(
      std::shared_ptr<const SubstitutionModelInterface> model,
      std::shared_ptr<const AlphabetIndex1> alphIndex);
 
  DecompositionReward(
      const StateMapInterface& stateMap,
      std::shared_ptr<const AlphabetIndex1> alphIndex);
 
  DecompositionReward(const DecompositionReward& dr) :
    AbstractReward(dr),
    DecompositionMethods(dr),
    rewards_(dr.rewards_),
    currentLength_(dr.currentLength_)
  {}
 
  DecompositionReward& operator=(const DecompositionReward& dr)
  {
    AbstractReward::operator=(dr);
    DecompositionMethods::operator=(dr);
 
    rewards_        = dr.rewards_;
    currentLength_  = dr.currentLength_;
    return *this;
  }
 
  virtual ~DecompositionReward() {}
 
  DecompositionReward* clone() const override { return new DecompositionReward(*this); }
 
public:
  double getReward(size_t initialState, size_t finalState, double length) const override;
 
  Matrix<double>* getAllRewards(double length) const override;
 
  void storeAllRewards(double length, Eigen::MatrixXd& mat) const override;
 
  void setSubstitutionModel(std::shared_ptr<const SubstitutionModelInterface> model) override;
 
protected:
  void initRewards_();
 
  void computeRewards_(double length) const;
 
  void alphabetIndexHasChanged() override;
 
private:
  void fillBMatrice_();
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_DECOMPOSITIONREWARD_H