libbpp-phyl-dev 2.2.0-1+b1 / usr / include / Bpp / Phyl / Io / IoTree.h

//
// File: IOTree.h
// Created by: Julien Dutheil
// Created on: Thu Oct 23 15:19:06 2003
//

/*
Copyright or © or Copr. CNRS, (November 16, 2004)

This software is a computer program whose purpose is to provide classes
for phylogenetic data analysis.

This software is governed by the CeCILL  license under French law and
abiding by the rules of distribution of free software.  You can  use, 
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info". 

As a counterpart to the access to the source code and  rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty  and the software's author,  the holder of the
economic rights,  and the successive licensors  have only  limited
liability. 

In this respect, the user's attention is drawn to the risks associated
with loading,  using,  modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean  that it is complicated to manipulate,  and  that  also
therefore means  that it is reserved for developers  and  experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or 
data to be ensured and,  more generally, to use and operate it in the 
same conditions as regards security. 

The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
*/

#ifndef _IOTREE_H_
#define _IOTREE_H_

#include "../Tree.h"

// From the STL:
#include <string>
#include <iostream>
#include <fstream>
#include <sstream>

#include <Bpp/Exceptions.h>
#include <Bpp/Io/IoFormat.h>

namespace bpp
{

/**
 * @brief General interface for tree I/O.
 */
class IOTree:
  public virtual IOFormat
{
	public:
		IOTree() {}
		virtual ~IOTree() {}

	public:
		virtual const std::string getDataType() const { return "Tree"; }
};

/**
 * @brief General interface for tree readers.
 */
class ITree:
  public virtual IOTree
{
	public:
		ITree() {}
		virtual ~ITree() {}

	public:
    /**
     * @brief Read a tree from a file.
     *
     * @param path The file path.
     * @return A new tree object.
     * @throw Exception If an error occured.
     */
		virtual Tree* read(const std::string& path) const throw (Exception) = 0;
    /**
     * @brief Read a tree from a stream.
     *
     * @param in The input stream.
     * @return A new tree object.
     * @throw Exception If an error occured.
     */
		virtual Tree* read(std::istream& in) const throw (Exception) = 0;
};

/**
 * @brief General interface for tree writers.
 */
class OTree:
  public virtual IOTree
{
	public:
		OTree() {}
		virtual ~OTree() {}

	public:
    /**
     * @brief Write a tree to a file.
     *
     * @param tree A tree object.
     * @param path The file path.
     * @param overwrite Tell if existing file must be overwritten.
     * Otherwise append to the file.
     * @throw Exception If an error occured.
     */
		virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception) = 0;
    /**
     * @brief Write a tree to a stream.
     *
     * @param tree A tree object.
     * @param out The output stream.
     * @throw Exception If an error occured.
     */
		virtual void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
};

/**
 * @brief Partial implementation of the ITree interface.
 */
class AbstractITree:
  public virtual ITree
{
	public:
		AbstractITree() {}
		virtual ~AbstractITree() {}

	public:
		virtual Tree* read(std::istream& in) const throw (Exception) = 0;
		virtual Tree* read(const std::string& path) const throw (Exception)
		{
      std::ifstream input(path.c_str(), std::ios::in);
			Tree* tree = read(input);
			input.close();
			return tree;
		}

};

/**
 * @brief Partial implementation of the OTree interface.
 */
class AbstractOTree:
  public virtual OTree
{
	public:
		AbstractOTree() {}
		virtual ~AbstractOTree() {}

	public:
		void write(const Tree& tree, std::ostream& out) const throw (Exception) = 0;
		virtual void write(const Tree& tree, const std::string& path, bool overwrite) const throw (Exception)
		{
		  try {
			// Open file in specified mode
		    std::ofstream output(path.c_str(), overwrite ? (std::ios::out) : (std::ios::out|std::ios::app));
		    write(tree, output);
		    output.close();
		  }
		  catch (IOException e)
		    {
		      std::stringstream ss ;
		      ss << e.what() <<"\nProblem writing tree to file "<< path <<"\n Is the file path correct and do \
you have the proper authorizations? ";
		      throw (IOException ( ss.str() ) );
		    }

		}
};







/**
 * @brief General interface for multiple trees readers.
 */
class IMultiTree:
  public virtual IOTree
{
	public:
		IMultiTree() {}
		virtual ~IMultiTree() {}

	public:
    /**
     * @brief Read trees from a file.
     *
     * @param path The file path.
     * @param trees The output trees container.
     * @throw Exception If an error occured.
     */
		virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception) = 0;
    /**
     * @brief Read trees from a stream.
     *
     * @param in The input stream.
     * @param trees The output trees container.
     * @throw Exception If an error occured.
     */
		virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
};

/**
 * @brief General interface for tree writers.
 */
class OMultiTree:
  public virtual IOTree
{
	public:
		OMultiTree() {}
		virtual ~OMultiTree() {}

	public:
    /**
     * @brief Write trees to a file.
     *
     * @param trees A vector of tree objects.
     * @param path The file path.
     * @param overwrite Tell if existing file must be overwritten.
     * Otherwise append to the file.
     * @throw Exception If an error occured.
     */
		virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception) = 0;
    /**
     * @brief Write trees to a stream.
     *
     * @param trees A vector of tree objects.
     * @param out The output stream.
     * @throw Exception If an error occured.
     */
		virtual void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
};

/**
 * @brief Partial implementation of the IMultiTree interface.
 */
class AbstractIMultiTree:
  public virtual IMultiTree
{
	public:
		AbstractIMultiTree() {}
		virtual ~AbstractIMultiTree() {}

	public:
		virtual void read(std::istream& in, std::vector<Tree*>& trees) const throw (Exception) = 0;
		virtual void read(const std::string& path, std::vector<Tree*>& trees) const throw (Exception)
		{
      std::ifstream input(path.c_str(), std::ios::in);
			read(input, trees);
			input.close();
		}

};

/**
 * @brief Partial implementation of the OTree interface.
 */
class AbstractOMultiTree:
  public virtual OMultiTree
{
	public:
		AbstractOMultiTree() {}
		virtual ~AbstractOMultiTree() {}

	public:
		void write(const std::vector<Tree*>& trees, std::ostream& out) const throw (Exception) = 0;
		virtual void write(const std::vector<Tree*>& trees, const std::string& path, bool overwrite) const throw (Exception)
		{
			// Open file in specified mode
      std::ofstream output(path.c_str(), overwrite ? (std::ios::out) : (std::ios::out|std::ios::app));
			write(trees, output);
			output.close();
		}
};

} //end of namespace bpp.

#endif	//_IOTREE_H_