BppOTransitionModelFormat.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_IO_BPPOTRANSITIONMODELFORMAT_H
#define BPP_PHYL_IO_BPPOTRANSITIONMODELFORMAT_H
 
 
#include "../Model/MixedTransitionModel.h"
#include "BppOSubstitutionModelFormat.h"
 
namespace bpp
{
class BppOTransitionModelFormat :
  public BppOSubstitutionModelFormat
{
private:
  std::unique_ptr<MixedTransitionModelInterface> readMixed_(
      std::shared_ptr<const Alphabet> alphabet,
      const std::string& modelDescription,
      const std::map<size_t, std::shared_ptr<const AlignmentDataInterface>>& mData,
      size_t nData);
 
public:
  BppOTransitionModelFormat(unsigned char alphabetCode, bool allowCovarions, bool allowMixed, bool allowGaps, bool verbose, int warn) :
    BppOSubstitutionModelFormat(alphabetCode, allowCovarions, allowMixed, allowGaps, verbose, warn)
  {}
 
  BppOTransitionModelFormat(const BppOTransitionModelFormat& format) :
    BppOSubstitutionModelFormat(format)
  {}
 
  BppOTransitionModelFormat& operator=(const BppOTransitionModelFormat& format)
  {
    BppOSubstitutionModelFormat::operator=(format);
    return *this;
  }
 
  virtual ~BppOTransitionModelFormat() {}
 
public:
  std::unique_ptr<TransitionModelInterface> readTransitionModel(
      std::shared_ptr<const Alphabet> alphabet,
      const std::string& modelDescription,
      const std::map<size_t, std::shared_ptr<const AlignmentDataInterface>>& mData,
      size_t nData,
      bool parseArguments = true);
};
} // end of namespace bpp.
#endif // BPP_PHYL_IO_BPPOTRANSITIONMODELFORMAT_H