Reward.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_REWARD_H
#define BPP_PHYL_MAPPING_REWARD_H
 
#include <Bpp/Numeric/Matrix/Matrix.h>
#include <Bpp/Seq/AlphabetIndex/AlphabetIndex1.h>
 
#include "../Model/SubstitutionModel.h"
 
// From the STL:
#include <vector>
 
namespace bpp
{
class Reward :
  public virtual Clonable
{
public:
  Reward() {}
  virtual ~Reward() {}
  virtual Reward* clone() const = 0;
 
public:
  virtual bool hasAlphabetIndex() const = 0;
 
  virtual std::shared_ptr<const AlphabetIndex1> getAlphabetIndex() const = 0;
 
  virtual void setAlphabetIndex(std::shared_ptr<const AlphabetIndex1> alphind) = 0;
 
  virtual std::shared_ptr<const Alphabet> getAlphabet() const
  {
    return getAlphabetIndex()->getAlphabet();
  }
 
  virtual size_t getNumberOfStates() const { return getAlphabet()->getSize(); }
 
 
  virtual double getReward(size_t initialState, size_t finalState, double length) const = 0;
 
  virtual Matrix<double>* getAllRewards(double length) const = 0;
 
  virtual void storeAllRewards(double length, Eigen::MatrixXd& mat) const = 0;
 
  virtual void setSubstitutionModel(std::shared_ptr<const SubstitutionModelInterface> model) = 0;
};
 
 
class AbstractReward :
  public virtual Reward
{
protected:
  std::shared_ptr<const AlphabetIndex1> alphIndex_;
 
public:
  AbstractReward(std::shared_ptr<const AlphabetIndex1> alphIndex) :
    alphIndex_(alphIndex)
  {}
 
  AbstractReward(const AbstractReward& ar) :
    alphIndex_(ar.alphIndex_)
  {}
 
  AbstractReward& operator=(const AbstractReward& ar)
  {
    alphIndex_ = ar.alphIndex_;
    return *this;
  }
 
  virtual ~AbstractReward() {}
 
public:
  bool hasAlphabetIndex() const { return alphIndex_ != 0; }
 
  void setAlphabetIndex(std::shared_ptr<const AlphabetIndex1> alphIndex)
  {
    alphIndex_ = alphIndex;
    alphabetIndexHasChanged();
  }
 
  std::shared_ptr<const AlphabetIndex1> getAlphabetIndex() const { return alphIndex_; }
 
  const AlphabetIndex1& alphabetIndex() const { return *alphIndex_; }
 
protected:
  virtual void alphabetIndexHasChanged() = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_REWARD_H