AbstractDFPSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_CODON_ABSTRACTDFPSUBSTITUTIONMODEL_H
#define BPP_PHYL_MODEL_CODON_ABSTRACTDFPSUBSTITUTIONMODEL_H
 
 
#include "../AbstractSubstitutionModel.h"
#include "CodonSubstitutionModel.h"
 
// From SeqLib:
#include <Bpp/Seq/Alphabet/CodonAlphabet.h>
 
namespace bpp
{
class AbstractDFPSubstitutionModel :
  public virtual CodonSubstitutionModelInterface,
  public AbstractSubstitutionModel
{
private:
  std::shared_ptr<const GeneticCode> gCode_;
 
  double tr_, trr_, tvv_, trv_, tsub_;
 
public:
  AbstractDFPSubstitutionModel(
      std::shared_ptr<const GeneticCode> gCode,
      const std::string& prefix = "AbstractDFP. ");
 
  AbstractDFPSubstitutionModel(const AbstractDFPSubstitutionModel& mod) :
    AbstractParameterAliasable(mod),
    AbstractSubstitutionModel(mod),
    gCode_(mod.gCode_),
    tr_(mod.tr_), trr_(mod.trr_), tvv_(mod.tvv_), trv_(mod.trv_), tsub_(mod.tsub_)
  {}
 
  AbstractDFPSubstitutionModel& operator=(const AbstractDFPSubstitutionModel& mod)
  {
    AbstractSubstitutionModel::operator=(mod);
    gCode_ = mod.gCode_;
    tr_ = mod.tr_;
    trr_ = mod.trr_;
    tvv_ =  mod.tvv_;
    trv_ = mod.trv_;
    tsub_ = mod.tsub_;
 
    return *this;
  }
 
  virtual ~AbstractDFPSubstitutionModel() {}
 
  AbstractDFPSubstitutionModel* clone() const override = 0;
 
public:
  std::shared_ptr<const GeneticCode> getGeneticCode() const override { return gCode_; }
 
  void fireParameterChanged(const ParameterList& parameters) override;
 
  using BranchModelInterface::getNumberOfStates;
 
  size_t getNumberOfStates() { return 64; }
 
  double getCodonsMulRate(size_t i, size_t j) const override;
 
protected:
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_CODON_ABSTRACTDFPSUBSTITUTIONMODEL_H