IoDAG.h

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// SPDX-FileCopyrightText: The Bio++ Development Group
//
// SPDX-License-Identifier: CECILL-2.1
 
#ifndef BPP_PHYL_IO_IODAGRAPH_H
#define BPP_PHYL_IO_IODAGRAPH_H
 
 
// From the STL:
#include <string>
#include <iostream>
#include <fstream>
#include <sstream>
#include <memory>
 
#include <Bpp/Exceptions.h>
#include <Bpp/Io/IoFormat.h>
 
namespace bpp
{
class IODAG :
  public virtual IOFormat
{
protected:
  struct Element
  {
public:
    std::string content;
    std::string length;
    std::string annotation;
    bool isLeaf;
 
public:
    Element() : content(),
      length(),
      annotation(),
      isLeaf(false) {}
  };
 
public:
  IODAG() {}
  virtual ~IODAG() {}
 
public:
  virtual const std::string getDataType() const { return "DAG"; }
};
 
class IPhyloDAG :
  public virtual IODAG
{
public:
  IPhyloDAG() {}
  virtual ~IPhyloDAG() {}
 
public:
  virtual std::unique_ptr<PhyloDAG> readPhyloDAG(const std::string& path) const = 0;
 
  virtual std::unique_ptr<PhyloDAG> readPhyloDAG(std::istream& in) const = 0;
};
 
 
 
class OPhyloDAG :
  public virtual IODAG
{
public:
  OPhyloDAG() {}
  virtual ~OPhyloDAG() {}
 
public:
  virtual void writePhyloDAG(const PhyloDAG& dag, const std::string& path, bool overwrite) const = 0;
 
  virtual void writePhyloDAG(const PhyloDAG& dag, std::ostream& out) const =  0;
};
 
class AbstractIPhyloDAG :
  public virtual IPhyloDAG
{
public:
  AbstractIPhyloDAG() {}
  virtual ~AbstractIPhyloDAG() {}
 
public:
  std::unique_ptr<PhyloDAG> readPhyloDAG(std::istream& in) const override = 0;
 
  std::unique_ptr<PhyloDAG> readPhyloDAG(const std::string& path) const override
  {
    std::ifstream input(path.c_str(), std::ios::in);
    if (!input)
      throw IOException ("AbstractIPhyloDAG::readPhyloDAG(path): failed to read from path " + path);
    auto dag = readPhyloDAG(input);
    input.close();
    return dag;
  }
 
  virtual Element getElement(const std::string& elt) const
  {
    return Element();
  }
};
 
class AbstractOPhyloDAG :
  public virtual OPhyloDAG
{
public:
  AbstractOPhyloDAG() {}
  virtual ~AbstractOPhyloDAG() {}
 
public:
  virtual void writePhyloDAG(const PhyloDAG& dag, std::ostream& out) const = 0;
  virtual void writePhyloDAG(const PhyloDAG& dag, const std::string& path, bool overwrite) const
  {
    try
    {
      // Open file in specified mode
 
      std::ofstream output(path.c_str(), overwrite ? (std::ios::out) : (std::ios::out | std::ios::app));
      if (!output)
        throw Exception("Problem opening file " + path + "in writePhyloDAG.");
      writePhyloDAG(dag, output);
      output.close();
    }
    catch (IOException& e)
    {
      std::stringstream ss;
      ss << e.what() << "\nProblem writing dag to file " << path << "\n Is the file path correct and do \
you have the proper authorizations? ";
      throw (IOException ( ss.str() ) );
    }
  }
};
 
 
class IMultiPhyloDAG :
  public virtual IODAG
{
public:
  IMultiPhyloDAG() {}
  virtual ~IMultiPhyloDAG() {}
 
public:
  virtual void readPhyloDAGs(const std::string& path, std::vector<std::unique_ptr<PhyloDAG>>& dags) const = 0;
 
  virtual void readPhyloDAGs(std::istream& in, std::vector<std::unique_ptr<PhyloDAG>>& dags) const = 0;
};
 
class OMultiPhyloDAG :
  public virtual IODAG
{
public:
  OMultiPhyloDAG() {}
  virtual ~OMultiPhyloDAG() {}
 
public:
  virtual void writePhyloDAGs(
      const std::vector<const PhyloDAG*>& dags,
      const std::string& path,
      bool overwrite) const = 0;
 
  virtual void writePhyloDAGs(
      const std::vector<const PhyloDAG*>& dags,
      std::ostream& out) const = 0;
};
 
class AbstractIMultiPhyloDAG :
  public virtual IMultiPhyloDAG
{
public:
  AbstractIMultiPhyloDAG() {}
  virtual ~AbstractIMultiPhyloDAG() {}
 
public:
  virtual void readPhyloDAGs(std::istream& in, std::vector<std::unique_ptr<PhyloDAG>>& dags) const override = 0;
 
  virtual void readPhyloDAGs(const std::string& path, std::vector<std::unique_ptr<PhyloDAG>>& dags) const override
  {
    std::ifstream input(path.c_str(), std::ios::in);
    readPhyloDAGs(input, dags);
    input.close();
  }
};
 
class AbstractOMultiPhyloDAG :
  public virtual OMultiPhyloDAG
{
public:
  AbstractOMultiPhyloDAG() {}
  virtual ~AbstractOMultiPhyloDAG() {}
 
public:
  virtual void writePhyloDAGs(const std::vector<const PhyloDAG*>& dags, std::ostream& out) const = 0;
 
  virtual void writePhyloDAGs(const std::vector<const PhyloDAG*>& dags, 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));
    writePhyloDAGs(dags, output);
    output.close();
  }
};
} // end of namespace bpp.
#endif // BPP_PHYL_IO_IODAGRAPH_H