BppOAlignmentReaderFormat.h

Go to the documentation of this file.

// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1

#ifndef BPP_SEQ_IO_BPPOALIGNMENTREADERFORMAT_H
#define BPP_SEQ_IO_BPPOALIGNMENTREADERFORMAT_H


#include "IoSequenceFactory.h"

namespace bpp
{
class BppOAlignmentReaderFormat :
  public virtual IOFormat
{
private:
  std::map<std::string, std::string> unparsedArguments_;
  int warningLevel_;

public:
  BppOAlignmentReaderFormat(int warningLevel) :
    unparsedArguments_(), warningLevel_(warningLevel) {}
  virtual ~BppOAlignmentReaderFormat() {}

public:
  const std::string getFormatName() const { return "BppO"; }

  const std::string getFormatDescription() const { return "Bpp Options format."; }

  const std::string getDataType() const { return "Alignment reader"; }

  std::unique_ptr<IAlignment> read(const std::string& description);

  std::unique_ptr<IProbabilisticAlignment> readProbabilistic(const std::string& description);

  virtual const std::map<std::string, std::string>& getUnparsedArguments() const { return unparsedArguments_; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_IO_BPPOALIGNMENTREADERFORMAT_H