IoDistanceMatrix.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_IO_IODISTANCEMATRIX_H
#define BPP_PHYL_IO_IODISTANCEMATRIX_H
 
#include <Bpp/Io/IoFormat.h>
#include <Bpp/Seq/DistanceMatrix.h>
 
// From the STL:
#include <iostream>
#include <fstream>
 
namespace bpp
{
class IODistanceMatrix :
  public virtual IOFormat
{
public:
  IODistanceMatrix() {}
  virtual ~IODistanceMatrix() {}
 
public:
  virtual const std::string getDataType() const { return "Distance matrix"; }
};
 
class IDistanceMatrix :
  public virtual IODistanceMatrix
{
public:
  IDistanceMatrix() {}
  virtual ~IDistanceMatrix() {}
 
public:
  virtual std::unique_ptr<DistanceMatrix> readDistanceMatrix(const std::string& path) const = 0;
  virtual std::unique_ptr<DistanceMatrix> readDistanceMatrix(std::istream& in) const = 0;
};
 
class ODistanceMatrix :
  public virtual IODistanceMatrix
{
public:
  ODistanceMatrix() {}
  virtual ~ODistanceMatrix() {}
 
public:
  virtual void writeDistanceMatrix(const DistanceMatrix& dist, const std::string& path, bool overwrite) const = 0;
  virtual void writeDistanceMatrix(const DistanceMatrix& dist, std::ostream& out) const = 0;
};
 
class AbstractIDistanceMatrix :
  public virtual IDistanceMatrix
{
public:
  AbstractIDistanceMatrix() {}
  virtual ~AbstractIDistanceMatrix() {}
 
public:
  virtual std::unique_ptr<DistanceMatrix> readDistanceMatrix(const std::string& path) const
  {
    std::ifstream input(path.c_str(), std::ios::in);
    auto mat = readDistanceMatrix(input);
    input.close();
    return mat;
  }
  virtual std::unique_ptr<DistanceMatrix> readDistanceMatrix(std::istream& in) const = 0;
};
 
class AbstractODistanceMatrix :
  public virtual ODistanceMatrix
{
public:
  AbstractODistanceMatrix() {}
  virtual ~AbstractODistanceMatrix() {}
 
public:
  virtual void writeDistanceMatrix(const DistanceMatrix& dist, const std::string& path, bool overwrite) const
  {
    // Open file in specified mode
    std::ofstream output(path.c_str(), overwrite ? (std::ios::out) : (std::ios::out | std::ios::app));
    writeDistanceMatrix(dist, output);
    output.close();
  }
  virtual void writeDistanceMatrix(const DistanceMatrix& dist, std::ostream& out) const = 0;
};
} // end of namespace bpp.
#endif // BPP_PHYL_IO_IODISTANCEMATRIX_H