Phylip.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_IO_PHYLIP_H
#define BPP_SEQ_IO_PHYLIP_H
 
 
#include "../Container/AlignedSequenceContainer.h"
#include "../Container/SequenceContainer.h"
#include "../Container/VectorSequenceContainer.h"
#include "../Sequence.h"
#include "AbstractIAlignment.h"
#include "AbstractOAlignment.h"
 
// From the STL:
#include <iostream>
 
namespace bpp
{
class Phylip :
  public AbstractIAlignment2,
  public AbstractOAlignment
{
private:
  /* this class allows two kinds of Phylip format:
   * traditional, with names limited to 10 chars,
   * and 'extended', defined by PAML, with names separated from sequences by at least 6 white spaces.
   */
  bool extended_;
  /* tells if sequences are in the seuqential or the interleave format/
   */
  bool sequential_;
 
  unsigned int charsByLine_;
 
  std::string namesSplit_;
 
public:
  Phylip(bool extended = true, bool sequential = true, unsigned int charsByLine = 100, const std::string& split = "  ") :
    extended_(extended), sequential_(sequential), charsByLine_(charsByLine), namesSplit_(split) {}
 
  virtual ~Phylip() {}
 
public:
  void appendAlignmentFromStream(std::istream& input, SequenceContainerInterface& sc) const override;
  virtual std::unique_ptr<SequenceContainerInterface> readSequences(std::istream& input, std::shared_ptr<const Alphabet> alpha) const override
  {
    return readAlignment(input, alpha);
  }
  virtual std::unique_ptr<SequenceContainerInterface> readSequences(const std::string& path, std::shared_ptr<const Alphabet> alpha) const override
  {
    return readAlignment(path, alpha);
  }
  unsigned int getNumberOfSequences(const std::string& path) const;
 
  void writeAlignment(std::ostream& output, const SiteContainerInterface& sc) const override;
  void writeAlignment(const std::string& path, const SiteContainerInterface& sc, bool overwrite) const override
  {
    AbstractOAlignment::writeAlignment(path, sc, overwrite);
  }
  const std::string getFormatName() const override;
  const std::string getFormatDescription() const override;
  const std::string& getSplit() const { return namesSplit_; }
 
  void setSplit(const std::string& split) { namesSplit_ = split; }
 
protected:
  // Reading tools:
  const std::vector<std::string> splitNameAndSequence(const std::string& s) const;
  void readSequential (std::istream& in, SequenceContainerInterface& asc) const;
  void readInterleaved(std::istream& in, SequenceContainerInterface& asc) const;
  // Writing tools:
  std::vector<std::string> getSizedNames(const std::vector<std::string>& names) const;
  void writeSequential(std::ostream& out, const SiteContainerInterface& sc) const;
  void writeInterleaved(std::ostream& out, const SiteContainerInterface& sc) const;
};
} // end of namespace bpp.
#endif // BPP_SEQ_IO_PHYLIP_H