/usr/include/Bpp/PopGen/DarwinVarSingle.h is in libbpp-popgen-dev 2.1.0-1.
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// File DarwinVarSingle.h
// Author : Sylvain Gaillard
// Last modification : April 7, 2008
//
/*
Copyright or © or Copr. Bio++ Development Team, (April 7, 2008)
This software is a computer program whose purpose is to provide classes
for population genetics 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 _DARWIN_VAR_SINGLE_H_
#define _DARWIN_VAR_SINGLE_H_
#include <Bpp/Exceptions.h>
#include <Bpp/Io/FileTools.h>
#include <Bpp/Text/TextTools.h>
#include <Bpp/Text/StringTokenizer.h>
// From local Pop
#include "AbstractODataSet.h"
namespace bpp
{
/**
* @brief The Darwin .don output format for popgenlib.
*
* @author Sylvain Gaillard
*/
class DarwinVarSingle :
public virtual AbstractODataSet
{
private:
size_t missingData_;
public:
// Constructor and destructor
DarwinVarSingle(size_t missingData = 999);
~DarwinVarSingle();
public:
/**
* @name The ODataSet interface.
* @{
*/
void write(std::ostream& os, const DataSet& data_set) const throw (Exception);
void write(const std::string& path, const DataSet& data_set, bool overwrite) const throw (Exception);
/**
* @}
*/
/**
* @name The IOFormat interface
* @{
*/
virtual const std::string getFormatName() const
{
return "Darwin .var single data";
}
virtual const std::string getFormatDescription() const
{
return "Darwin .var file store data for each marker in each individual (1 variable per allele).";
}
/**
* @}
*/
};
} // end of namespace bpp;
#endif // _DARWIN_VAR_SINGLE_H_
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