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// File: IoFrequenciesSet.h
// Created by: Laurent Guéguen
// Created on: lundi 9 juillet 2012, à 12h 49
//
/*
Copyright or © or Copr. Bio++ Development 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 _IOFREQUENCIESSET_H_
#define _IOFREQUENCIESSET_H_
#include "../Model/FrequenciesSet/FrequenciesSet.h"
//From bpp-core:
#include <Bpp/Exceptions.h>
#include <Bpp/Io/IoFormat.h>
#include <Bpp/Io/OutputStream.h>
//From bpp-seq:
#include <Bpp/Seq/Container/SiteContainer.h>
namespace bpp
{
class FrequenciesSet;
/**
* @brief General interface for model I/O.
*/
class IoFrequenciesSet:
public virtual IOFormat
{
public:
IoFrequenciesSet() {}
virtual ~IoFrequenciesSet() {}
public:
virtual const std::string getDataType() const { return "Frequencies Set"; }
};
/**
* @brief General interface for distance matrix readers.
*/
class IFrequenciesSet:
public virtual IoFrequenciesSet
{
public:
IFrequenciesSet() {}
virtual ~IFrequenciesSet() {}
public:
/**
* @brief Read a frequencies set from a string.
*
* @param alphabet The alpabet to use in the model.
* @param freqDescription A string describing the frequencies set.
* @param data A SiteContainer with the data to use to initialize fequency parameters. Can be set to 0.
* @param parseArguments Attempt to parse function arguments. If not, only store them and use default values instead.
* @return A new FrequenciesSet object according to options specified.
* @throw Exception if an error occured.
*/
virtual FrequenciesSet* read(const Alphabet* alphabet, const std::string& freqDescription, const SiteContainer* data, bool parseArguments) = 0;
/**
* @return The arguments and their unparsed values from the last call of the read function, if there are any.
*/
virtual const std::map<std::string, std::string>& getUnparsedArguments() const = 0;
};
/**
* @brief General interface for distance matrix writers.
*/
class OFrequenciesSet:
public virtual IoFrequenciesSet
{
public:
OFrequenciesSet() {}
virtual ~OFrequenciesSet() {}
public:
/**
* @brief Write a substitution model to a stream.
*
* @param pfreqset A pointer towards a frequencies set object;
* @param out The output stream;
* @param writtenNames is the vector of the written
* parameters so far [in, out];
*/
virtual void write(const FrequenciesSet* pfreqset,
OutputStream& out,
std::vector<std::string>& writtenNames) const = 0;
};
} //end of namespace bpp.
#endif //_IOFREQUENCIESSET_H_
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