Stockholm.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_IO_STOCKHOLM_H
#define BPP_SEQ_IO_STOCKHOLM_H
 
 
#include "../Container/AlignedSequenceContainer.h"
#include "../Container/SequenceContainer.h"
#include "../Sequence.h"
#include "AbstractOAlignment.h"
 
namespace bpp
{
class Stockholm :
  public AbstractOAlignment
{
private:
  bool checkNames_;
 
public:
  Stockholm(bool checkSequenceNames = true) : checkNames_(checkSequenceNames) {}
 
  // Class destructor
  virtual ~Stockholm() {}
 
public:
  void writeAlignment(std::ostream& output, const SiteContainerInterface& sc) const override;
  void writeAlignment(const std::string& path, const SiteContainerInterface& sc, bool overwrite = true) const override
  {
    AbstractOAlignment::writeAlignment(path, sc, overwrite);
  }
  const std::string getFormatName() const override { return "Stockholm file"; }
  const std::string getFormatDescription() const override
  {
    return "See http://en.wikipedia.org/wiki/Stockholm_format";
  }
  bool checkNames() const { return checkNames_; }
 
  void checkNames(bool yn) { checkNames_ = yn; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_IO_STOCKHOLM_H