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// File: PairedSiteLikelihoods.h
// Created by: Nicolas Rochette
// Created on: January 10, 2011
//
/*
Copyright or © or Copr. Bio++ Developent Team, (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 _IOPAIREDSITELIKELIHOODS_H_
#define _IOPAIREDSITELIKELIHOODS_H_
// From the STL:
#include <vector>
#include <string>
#include <sstream>
// From Bio++
#include <Bpp/Io/IoFormat.h>
#include "../Likelihood/PairedSiteLikelihoods.h"
namespace bpp
{
/**
* @brief Base class for I/O on paired-site likelihoods.
*
* @author Nicolas Rochette
*/
class IOPairedSiteLikelihoods : public virtual IOFormat
{};
/**
* @brief This class provides I/O for the Tree-Puzzle/RAxML (phylip-like) paired-site likelihoods format.
*
* @author Nicolas Rochette
*/
class IOTreepuzzlePairedSiteLikelihoods : public virtual IOPairedSiteLikelihoods
{
public:
/**
* @brief Read paired-site likelihoods from a Treepuzzle/RAxML-formatted stream.
*
* @throw Exception If the format is not recognized.
*/
static PairedSiteLikelihoods read(std::istream& is) throw (Exception);
/**
* @brief Read paired-site likelihoods from a Treepuzzle/RAxML-formatted file.
*
* @throw Exception If the format is not recognized.
*/
static PairedSiteLikelihoods read(const std::string& path) throw (Exception);
/**
* @brief Write paired-site likelihoods to a stream.
*
* @param psl The PairedSiteLikelihoods object to write.
* @param os The output stream.
* @param delim The delimiter between model names and likelihoods. The defaut is a tab but two spaces might be used.
*/
static void write(const PairedSiteLikelihoods& psl, std::ostream& os, const std::string& delim = "\t");
/**
* @brief Write paired-site likelihoods to a file.
*
* @param psl The PairedSiteLikelihoods object to write.
* @param path The path of the output file.
* @param delim The delimiter between model names and likelihoods. (The defaut is a tab but two spaces might be used.)
*/
static void write(const PairedSiteLikelihoods& psl, const std::string& path, const std::string& delim = "\t");
};
/**
* @brief This class provides input for the Phyml paired-site likelihoods format.
*
* @author Nicolas Rochette
*/
class IOPhymlPairedSiteLikelihoods : public virtual IOPairedSiteLikelihoods
{
public:
/**
* @brief Read paired-site likelihoods from a Phyml-formatted stream.
* @throw Exception If the format is not recognized.
*/
static std::vector<double> read(std::istream& is) throw (Exception);
/**
* @brief Read Phyml paired-site likelihoods from a Phyml-formatted file.
* @throw Exception If the format is not recognized.
*/
static std::vector<double> read(const std::string& path) throw (Exception);
};
} // namespace bpp
#endif
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