Pasta.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_SEQ_IO_PASTA_H
#define BPP_SEQ_IO_PASTA_H
 
#include <Bpp/Numeric/Table.h>
 
#include "../Container/VectorSiteContainer.h"
#include "../ProbabilisticSequence.h"
#include "../Container/AlignmentData.h"
#include "AbstractIAlignment.h"
#include "AbstractISequence.h"
#include "AbstractOAlignment.h"
#include "AbstractOSequence.h"
 
namespace bpp
{
class Pasta :
  public AbstractIProbabilisticAlignment,
  public AbstractOProbabilisticAlignment,
  public AbstractOSequence2
{
protected:
  unsigned int charsByLine_; // Number of chars by line (output only)
 
  bool extended_;            // If using HUPO-PSI extensions
  bool strictNames_;         // If name is between '>' and first space
 
public:
  typedef Table<double> DataTable;
 
  Pasta(unsigned int charsByLine = 100, bool extended = false, bool strictSequenceNames = false) : charsByLine_(charsByLine), extended_(extended), strictNames_(strictSequenceNames) {}
 
  // class destructor
  virtual ~Pasta() {}
 
public:
  const std::string getFormatName() const override { return "PASTA file"; }
  const std::string getFormatDescription() const override
  {
    return "By rows: alphabet, then Sequence name (preceded by >) in one line, and rows of sequence content.";
  }
 
  bool nextSequence(std::istream& input, ProbabilisticSequence& seq, bool hasLabels, const std::vector<size_t>& permutationMap) const;
 
  void writeSequence(std::ostream& output, const ProbabilisticSequence& seq, bool header) const;
 
  void writeSequence(std::ostream& output, const Sequence& seq, bool header) const;
 
  void writeSequences(std::ostream& output, const SequenceContainerInterface& sc) const override
  {
    for (size_t i = 0; i < sc.getNumberOfSequences(); ++i)
    {
      writeSequence(output, sc.sequence(i), i == 0);
    }
  }
 
  using AbstractOSequence::writeSequences;
 
  void appendAlignmentFromStream(std::istream& input, ProbabilisticSequenceContainerInterface& psc) const override;
 
  void writeAlignment(std::ostream& output, const ProbabilisticSiteContainerInterface& psc) const override
  {
    if (!output)
      throw IOException("Pasta::write: can't write to ostream output");
 
    // Main loop : for all sequences in vector container
 
    bool first = true;
    for (size_t i = 0; i < psc.getNumberOfSequences(); ++i)
    {
      writeSequence(output, psc.sequence(i), first);
      first = false;
    }
  }
  using AbstractOSequence2::writeAlignment;
 
  const std::string getDataType() const override { return "(Probabilistic) sequence container"; }
};
} // end of namespace bpp
#endif // BPP_SEQ_IO_PASTA_H