Coala.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_MODEL_PROTEIN_COALA_H
#define BPP_PHYL_MODEL_PROTEIN_COALA_H
 
 
#include "../AbstractSubstitutionModel.h"
#include "CoalaCore.h"
#include "ProteinSubstitutionModel.h"
 
// From bpp-seq:
#include <Bpp/Seq/Alphabet/ProteicAlphabet.h>
 
namespace bpp
{
class Coala :
  public AbstractReversibleProteinSubstitutionModel,
  public CoalaCore
{
protected:
  bool init_;
  unsigned int nbrOfAxes_;
  std::string exch_;
  std::string file_;
  bool param_;
 
public:
  Coala(std::shared_ptr<const ProteicAlphabet> alpha,
      const ProteinSubstitutionModelInterface& model,
      unsigned int nbAxes = 0,
      bool param = true);
 
  virtual ~Coala() {}
 
  Coala* clone() const override { return new Coala(*this); }
 
public:
  std::string getName() const override { return "Coala"; }
  std::string getExch() const { return exch_; }
  void setFreqFromData(const SequenceDataInterface& data, double pseudoCount = 0) override;
  std::string getEmpiricalMatrixFile() const { return file_; }
 
protected:
  void readFromFile(std::string& file);
  void computeEquilibriumFrequencies();
  void updateMatrices_() override;
};
} // end of namespace bpp.
#endif // BPP_PHYL_MODEL_PROTEIN_COALA_H