NexusIoSequence.h

Go to the documentation of this file.

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

#ifndef BPP_SEQ_IO_NEXUSIOSEQUENCE_H
#define BPP_SEQ_IO_NEXUSIOSEQUENCE_H


#include "../Container/AlignedSequenceContainer.h"
#include "../Container/SequenceContainer.h"
#include "../Container/VectorSequenceContainer.h"
#include "../Sequence.h"
#include "AbstractIAlignment.h"

// From the STL:
#include <iostream>

namespace bpp
{
class NexusIOSequence :
  public AbstractIAlignment2,
  public virtual ISequence
{
protected:
  unsigned int charsByLine_;

  bool checkNames_;

public:
  NexusIOSequence(unsigned int charsByLine = 100, bool checkSequenceNames = true) :
    charsByLine_(charsByLine), checkNames_(checkSequenceNames) {}

  virtual ~NexusIOSequence() {}

public:
  void appendAlignmentFromStream(std::istream& input, SequenceContainerInterface& sc) const override;
  const std::string getFormatName() const override;

  const std::string getFormatDescription() const override;
  bool checkNames() const { return checkNames_; }

  void checkNames(bool yn) { checkNames_ = yn; }

private:
  // Reading tools:
  const std::vector<std::string> splitNameAndSequence_(const std::string& s) const;
};
} // end of namespace bpp.
#endif // BPP_SEQ_IO_NEXUSIOSEQUENCE_H