AbstractKroneckerWordSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_ABSTRACTKRONECKERWORDSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_ABSTRACTKRONECKERWORDSUBSTITUTIONMODEL_H
 
#include <set>
 
#include "AbstractWordSubstitutionModel.h"
 
// From bpp-core:
#include <Bpp/Numeric/Prob/Simplex.h>
 
namespace bpp
{
class AbstractKroneckerWordSubstitutionModel :
  public AbstractWordSubstitutionModel
{
private:
  std::vector<std::set< size_t>> sChangingPos_;
 
  std::vector< RowMatrix<double>> vGenerators_;
 
protected:
  void initGenerators_();
 
  bool checkChangingPositions_();
 
private:
  void fillBasicGenerator_();
 
public:
  AbstractKroneckerWordSubstitutionModel(
      ModelList& modelList,
      const std::string& prefix);
 
  AbstractKroneckerWordSubstitutionModel(
      ModelList& modelList,
      const std::vector<std::set< size_t>>& vPos,
      const std::string& prefix);
 
  AbstractKroneckerWordSubstitutionModel(
      std::unique_ptr<SubstitutionModelInterface> pmodel,
      unsigned int num,
      const std::string& prefix);
 
  AbstractKroneckerWordSubstitutionModel(
      std::unique_ptr<SubstitutionModelInterface> pmodel,
      unsigned int num,
      const std::vector<std::set< size_t>>& vPos,
      const std::string& prefix);
 
 
  virtual ~AbstractKroneckerWordSubstitutionModel() {}
 
  AbstractKroneckerWordSubstitutionModel(const AbstractKroneckerWordSubstitutionModel&);
 
  AbstractKroneckerWordSubstitutionModel& operator=(const AbstractKroneckerWordSubstitutionModel&);
 
protected:
  AbstractKroneckerWordSubstitutionModel(
      std::shared_ptr<const Alphabet> alph,
      std::shared_ptr<const StateMapInterface> stateMap,
      const std::string& prefix);
 
  void setChangingPositions(const std::vector<std::set<size_t>>& vPos);
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_ABSTRACTKRONECKERWORDSUBSTITUTIONMODEL_H