/usr/include/Bpp/PopGen/PopgenlibIO.h is in libbpp-popgen-dev 2.1.0-1ubuntu2.
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// File PopgenlibIO.h
// Created by: Sylvain Gaillard
// Created on: Thursday July 29 2004
//
/*
Copyright or © or Copr. CNRS, (November 17, 2004)
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 _POPULIBIO_H_
#define _POPULIBIO_H_
#include <Bpp/Exceptions.h>
#include <Bpp/Text/TextTools.h>
#include <Bpp/Io/FileTools.h>
// From Seq
#include <Bpp/Seq/Io/Fasta.h>
#include <Bpp/Seq/Container/VectorSequenceContainer.h>
// From local Pop
#include "AbstractIDataSet.h"
#include "AbstractODataSet.h"
#include "BasicAlleleInfo.h"
namespace bpp
{
/**
* @brief The native I/O format for popgenlib.
*
* @author Sylvain Gaillard
*/
class PopgenlibIO :
public AbstractIDataSet,
public AbstractODataSet
{
public:
// Constantes
static const std::string WHITESPACE;
static const std::string TAB;
static const std::string COMA;
static const std::string SEMICOLON;
static const std::string DIPLOID;
static const std::string HAPLOID;
static const std::string HAPLODIPLOID;
static const std::string UNKNOWN;
private:
char data_separator_;
char missing_data_symbol_;
std::vector<std::string> getValues_(std::string& param_line, const std::string& delim);
void parseGeneral_(const std::vector<std::string>& in, DataSet& data_set);
void parseLocality_(const std::vector<std::string>& in, DataSet& data_set);
void parseSequence_(const std::vector<std::string>& in, VectorSequenceContainer& vsc);
void parseLoci_(const std::vector<std::string>& in, std::vector<LocusInfo>& locus_info);
void parseIndividual_(const std::vector<std::string>& in, DataSet& data_set, const VectorSequenceContainer& vsc);
public:
// Constructor and destructor
PopgenlibIO();
PopgenlibIO(const std::string& missing_data_symbol, const std::string& data_separator) throw (Exception);
~PopgenlibIO();
public:
/**
* @brief Get the code for missing data.
*/
std::string getMissingDataSymbol() const;
/**
* @brief Get the code for data separator.
*/
std::string getDataSeparator() const;
/**
* @brief Get the character for missing data.
*/
char getMissingDataChar() const;
/**
* @brief Get the data separator char.
*/
char getDataSeparatorChar() const;
/**
* @brief Set the code for missing data.
*
* The character used to code missing data can be every single non numerical
* character and can't be the same used as data separator or a white space
* or a tabulation.
* The default value is '$'.
*
* @throw Excpetion if missing_data_symbol is a not allowed character.
* @throw Exception if missing_data_symbol contains more than one character.
*/
void setMissingDataSymbol(const std::string& missing_data_symbol)
throw (Exception);
/**
* @brief Set the code for data separator.
*
* The character used to separate data can be every single non numerical
* character and can't be the same used for coding missing data.
* Most common characters used are:
* <ul><li>the white space: "WHITESPACE"</li>
* <li>the tabulation: "TAB"</li>
* <li>the coma: "COMA"</li>
* <li>the semicolon: "SEMICOLON"</li></ul>
* The default value is "WHITESPACE".
*
* @throw Exception if data_separator is a not allowed character.
* @throw Exception if data_separator containes more than one character other than the two codes defined upper.
*/
void setDataSeparator(const std::string& data_separator)
throw (Exception);
/**
* @name The IDataSet interface.
* @{
*/
void read(std::istream& is, DataSet& data_set) throw (Exception);
void read(const std::string& path, DataSet& data_set) throw (Exception);
DataSet* read(std::istream& is) throw (Exception);
DataSet* read(const std::string& path) throw (Exception);
/**
* @}
*/
/**
* @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
* @{
*/
const std::string getFormatName() const
{
return "PopgenlibIO ver 0.1";
}
const std::string getFormatDescription() const
{
return "IO format used to store DataSets inspired from Arlequin and Fasta";
}
/**
* @}
*/
};
} // end of namespace bpp;
#endif // _POPULIBIO_H_
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