BppOAlphabetIndex2Format.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_IO_BPPOALPHABETINDEX2FORMAT_H
#define BPP_SEQ_IO_BPPOALPHABETINDEX2FORMAT_H
 
#include <Bpp/Io/IoFormat.h>
 
#include "../AlphabetIndex/AlphabetIndex2.h"
#include "../GeneticCode/GeneticCode.h"
 
// From the STL:
#include <string>
 
namespace bpp
{
class BppOAlphabetIndex2Format :
  public virtual IOFormat
{
private:
  std::shared_ptr<const Alphabet> alphabet_;
  std::shared_ptr<const GeneticCode> gencode_;
 
  std::string message_;
  bool verbose_;
 
public:
  BppOAlphabetIndex2Format(
      std::shared_ptr<const Alphabet>& alphabet,
      const std::string& message,
      bool verbose = true) :
    alphabet_(alphabet),
    gencode_(0),
    message_(message),
    verbose_(verbose)
  {}
 
  BppOAlphabetIndex2Format(
      std::shared_ptr<const CodonAlphabet>& alphabet,
      std::shared_ptr<const GeneticCode>& gencode,
      const std::string& message,
      bool verbose = true) :
    alphabet_(alphabet),
    gencode_(gencode),
    message_(message),
    verbose_(verbose)
  {}
 
  BppOAlphabetIndex2Format(const BppOAlphabetIndex2Format& format) :
    alphabet_(format.alphabet_),
    gencode_(format.gencode_),
    message_(format.message_),
    verbose_(format.verbose_) {}
 
  BppOAlphabetIndex2Format& operator=(const BppOAlphabetIndex2Format& format)
  {
    alphabet_ = format.alphabet_;
    gencode_ = format.gencode_;
    message_  = format.message_;
    verbose_  = format.verbose_;
    return *this;
  }
 
  virtual ~BppOAlphabetIndex2Format() {}
 
public:
  const std::string getFormatName() const { return "BppO"; }
 
  const std::string getFormatDescription() const { return "Bpp Options format."; }
 
  const std::string getDataType() const { return "AlphabetIndex2"; }
 
  std::unique_ptr<AlphabetIndex2> read(const std::string& description);
};
} // end of namespace bpp.
#endif // BPP_SEQ_IO_BPPOALPHABETINDEX2FORMAT_H