SubstitutionCount.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MAPPING_SUBSTITUTIONCOUNT_H
#define BPP_PHYL_MAPPING_SUBSTITUTIONCOUNT_H
 
#include <Bpp/Numeric/Matrix/Matrix.h>
 
#include "../Model/SubstitutionModel.h"
#include "CategorySubstitutionRegister.h"
#include "SubstitutionRegister.h"
 
// From the STL:
#include <vector>
 
namespace bpp
{
class SubstitutionCountInterface :
  public virtual Clonable
{
public:
  SubstitutionCountInterface() {}
  virtual ~SubstitutionCountInterface() {}
  virtual SubstitutionCountInterface* clone() const = 0;
 
public:
  virtual bool hasSubstitutionRegister() const = 0;
 
  virtual std::shared_ptr<const SubstitutionRegisterInterface> getSubstitutionRegister() const = 0;
 
  virtual void setSubstitutionRegister(std::shared_ptr<const SubstitutionRegisterInterface> reg) = 0;
 
  virtual size_t getNumberOfSubstitutionTypes() const { return getSubstitutionRegister()->getNumberOfSubstitutionTypes(); }
 
  virtual std::shared_ptr<const Alphabet> getAlphabet() const { return getSubstitutionRegister()->getAlphabet(); }
 
  virtual size_t getNumberOfStates() const { return getSubstitutionRegister()->getAlphabet()->getSize(); }
 
 
  virtual double getNumberOfSubstitutions(size_t initialState, size_t finalState, double length, size_t type) const = 0;
 
  virtual std::unique_ptr< Matrix<double>> getAllNumbersOfSubstitutions(double length, size_t type) const = 0;
 
  virtual void storeAllNumbersOfSubstitutions(double length, size_t type, Eigen::MatrixXd& mat) const = 0;
 
  virtual std::vector<double> getNumberOfSubstitutionsPerType(size_t initialState, size_t finalState, double length) const = 0;
 
  virtual void setSubstitutionModel(std::shared_ptr<const SubstitutionModelInterface> model) = 0;
};
 
class AbstractSubstitutionCount :
  public virtual SubstitutionCountInterface
{
protected:
  std::shared_ptr<const SubstitutionRegisterInterface> register_;
 
public:
  AbstractSubstitutionCount(std::shared_ptr<const SubstitutionRegisterInterface> reg) :
    register_(reg)
  {}
 
  virtual ~AbstractSubstitutionCount() {}
 
public:
  bool hasSubstitutionRegister() const { return register_.get() != nullptr; }
 
  void setSubstitutionRegister(std::shared_ptr<const SubstitutionRegisterInterface> reg)
  {
    register_ = reg;
    substitutionRegisterHasChanged();
  }
 
  std::shared_ptr<const SubstitutionRegisterInterface> getSubstitutionRegister() const { return register_; }
 
protected:
  virtual void substitutionRegisterHasChanged() = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MAPPING_SUBSTITUTIONCOUNT_H