Clustal.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_IO_CLUSTAL_H
#define BPP_SEQ_IO_CLUSTAL_H
 
 
#include "../Container/SiteContainer.h"
#include "AbstractIAlignment.h"
#include "AbstractOAlignment.h"
 
// From the STL:
#include <iostream>
 
namespace bpp
{
class Clustal :
  public AbstractIAlignment2,
  public AbstractOAlignment
{
private:
  bool checkNames_;
  unsigned int nbSpacesBeforeSeq_;
  unsigned int charsByLine_;
 
public:
  Clustal(bool checkSequenceNames = true, unsigned int nbExtraSpacesBeforeSeq = 5, unsigned int charsByLine = 100) :
    checkNames_(checkSequenceNames),
    nbSpacesBeforeSeq_(nbExtraSpacesBeforeSeq + 1),
    charsByLine_(charsByLine)
  {}
 
  virtual ~Clustal() {}
 
public:
  void appendAlignmentFromStream(std::istream& input, SequenceContainerInterface& sc) const override;
  std::unique_ptr<SequenceContainerInterface> readSequences(std::istream& input, std::shared_ptr<const Alphabet> alpha) const override
  {
    return readAlignment(input, alpha);
  }
 
  std::unique_ptr<SequenceContainerInterface> readSequences(const std::string& path, std::shared_ptr<const Alphabet> alpha) const override
  {
    return readAlignment(path, alpha);
  }
  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 "Clustal"; }
 
  const std::string getFormatDescription() const override { return "The Clustal alignment tool output format."; }
 
  bool checkNames() const { return checkNames_; }
 
  void checkNames(bool yn) { checkNames_ = yn; }
};
} // end of namespace bpp.
#endif // BPP_SEQ_IO_CLUSTAL_H