IoSubstitutionModel.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_IO_IOSUBSTITUTIONMODEL_H
#define BPP_PHYL_IO_IOSUBSTITUTIONMODEL_H
 
 
#include "../Model/SubstitutionModel.h"
 
// From bpp-core:
#include <Bpp/Exceptions.h>
#include <Bpp/Io/IoFormat.h>
#include <Bpp/Io/OutputStream.h>
 
// From bpp-seq:
#include <Bpp/Seq/Container/AlignmentData.h>
 
namespace bpp
{
class TransitionModelInterface;
class SubstitutionModelInterface;
 
class IoSubstitutionModel :
  public virtual IOFormat
{
public:
  IoSubstitutionModel() {}
  virtual ~IoSubstitutionModel() {}
 
public:
  virtual const std::string getDataType() const { return "Substitution Model"; }
};
 
class ISubstitutionModel :
  public virtual IoSubstitutionModel
{
public:
  ISubstitutionModel() {}
  virtual ~ISubstitutionModel() {}
 
public:
  virtual std::unique_ptr<SubstitutionModelInterface> readSubstitutionModel(
      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) = 0;
 
  virtual const std::map<std::string, std::string>& getUnparsedArguments() const = 0;
};
 
class OSubstitutionModel :
  public virtual IoSubstitutionModel
{
public:
  OSubstitutionModel() {}
  virtual ~OSubstitutionModel() {}
 
public:
  virtual void write(
      const BranchModelInterface& model,
      OutputStream& out,
      std::map<std::string, std::string>& globalAliases,
      std::vector<std::string>& writtenNames) const = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_IO_IOSUBSTITUTIONMODEL_H