BppOSubstitutionModelFormat.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_IO_BPPOSUBSTITUTIONMODELFORMAT_H
#define BPP_PHYL_IO_BPPOSUBSTITUTIONMODELFORMAT_H
 
 
#include "IoSubstitutionModelFactory.h"
#include "../Model/MixedTransitionModel.h"
 
// From bpp-seq
#include <Bpp/Seq/Container/AlignmentData.h>
#include <Bpp/Seq/GeneticCode/GeneticCode.h>
 
namespace bpp
{
class BppOSubstitutionModelFormat :
  public ISubstitutionModel,
  public OSubstitutionModel
{
public:
  static unsigned char DNA;
  static unsigned char RNA;
  static unsigned char NUCLEOTIDE;
  static unsigned char PROTEIN;
  static unsigned char CODON;
  static unsigned char WORD;
  static unsigned char BINARY;
  static unsigned char INTEGER;
  static unsigned char ALL;
 
protected:
  unsigned char alphabetCode_;
  bool allowCovarions_;
  bool allowMixed_;
  bool allowGaps_;
  bool verbose_;
  std::map<std::string, std::string> unparsedArguments_;
  std::shared_ptr<const GeneticCode> geneticCode_;
  int warningLevel_;
 
public:
  BppOSubstitutionModelFormat(unsigned char alphabetCode, bool allowCovarions, bool allowMixed, bool allowGaps, bool verbose, int warn) :
    alphabetCode_(alphabetCode),
    allowCovarions_(allowCovarions),
    allowMixed_(allowMixed),
    allowGaps_(allowGaps),
    verbose_(verbose),
    unparsedArguments_(),
    geneticCode_(0),
    warningLevel_(warn)
  {}
 
  BppOSubstitutionModelFormat(const BppOSubstitutionModelFormat& format) :
    alphabetCode_(format.alphabetCode_),
    allowCovarions_(format.allowCovarions_),
    allowMixed_(format.allowMixed_),
    allowGaps_(format.allowGaps_),
    verbose_(format.verbose_),
    unparsedArguments_(format.unparsedArguments_),
    geneticCode_(format.geneticCode_),
    warningLevel_(format.warningLevel_)
  {}
 
  BppOSubstitutionModelFormat& operator=(const BppOSubstitutionModelFormat& format)
  {
    alphabetCode_      = format.alphabetCode_;
    allowCovarions_    = format.allowCovarions_;
    allowMixed_        = format.allowMixed_;
    allowGaps_         = format.allowGaps_;
    verbose_           = format.verbose_;
    unparsedArguments_ = format.unparsedArguments_;
    geneticCode_       = format.geneticCode_;
    warningLevel_      = format.warningLevel_;
    return *this;
  }
 
  virtual ~BppOSubstitutionModelFormat() {}
 
public:
  const std::string getFormatName() const override { return "BppO"; }
 
  const std::string getFormatDescription() const override { return "Bpp Options format."; }
 
  void setGeneticCode(std::shared_ptr<const GeneticCode> gCode)
  {
    geneticCode_ = gCode;
  }
 
  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) override;
 
  const std::map<std::string, std::string>& getUnparsedArguments() const override
  {
    return unparsedArguments_;
  }
 
  void write(const BranchModelInterface& model,
      OutputStream& out,
      std::map<std::string, std::string>& globalAliases,
      std::vector<std::string>& writtenNames) const override;
 
  void setVerbose(bool verbose) { verbose_ = verbose;}
 
private:
  std::unique_ptr<SubstitutionModelInterface> readWord_(
      std::shared_ptr<const Alphabet> alphabet,
      const std::string& modelDescription,
      const std::map<size_t, std::shared_ptr<const AlignmentDataInterface>>& mData,
      size_t nData);
 
  void writeMixed_(const MixedTransitionModelInterface& model,
      OutputStream& out,
      std::map<std::string, std::string>& globalAliases,
      std::vector<std::string>& writtenNames) const;
 
protected:
  void updateParameters_(
      BranchModelInterface& model,
      std::map<std::string, std::string>& args);
 
  void initialize_(
      BranchModelInterface& model,
      std::shared_ptr<const AlignmentDataInterface> data);
};
} // end of namespace bpp.
#endif // BPP_PHYL_IO_BPPOSUBSTITUTIONMODELFORMAT_H