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// File: BppOAlphabetIndex2Format.h
// Created by: Julien Dutheil
// Created on: Thursday Februar 07th, 19:26
//
/*
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 _BPPOALPHABETINDEX2FORMAT_H_
#define _BPPOALPHABETINDEX2FORMAT_H_
#include <Bpp/Io/IoFormat.h>
#include "../AlphabetIndex/AlphabetIndex2.h"
// From the STL:
#include <string>
namespace bpp
{
/**
* @brief AlphabetIndex2 I/O in BppO format.
*
* Enables the instanciation of AlphabetIndex2 objects according to
* the BppO syntax (see the Bio++ Program Suite
* manual for a detailed description of this syntax).
*
*/
class BppOAlphabetIndex2Format:
public virtual IOFormat
{
private:
const Alphabet* alphabet_;
std::string message_;
bool verbose_;
public:
/**
* @param alphabet The alphabet for which indices should be built.
* The alphabet will be used to check that the instanciated index is compatible.
* @param message Some text describing what the index is intended for.
* @param verbose Tell if some messages should be printed while parsing.
*/
BppOAlphabetIndex2Format(const Alphabet* alphabet, const std::string& message, bool verbose = true):
alphabet_(alphabet), message_(message), verbose_(verbose) {}
BppOAlphabetIndex2Format(const BppOAlphabetIndex2Format& format):
alphabet_(format.alphabet_),
message_(format.message_),
verbose_(format.verbose_) {}
BppOAlphabetIndex2Format& operator=(const BppOAlphabetIndex2Format& format)
{
alphabet_ = format.alphabet_;
message_ = format.message_;
verbose_ = format.verbose_;
return *this;
}
virtual ~BppOAlphabetIndex2Format() {}
public:
const std::string getFormatName() const { return "BppO"; }
const std::string getFormatDescription() const { return "Bpp Options format."; }
const std::string getDataType() const { return "AlphabetIndex2"; }
/**
* @brief Read a AlphabetIndex1 object from a string.
*
* @param description A string describing the index in the keyval syntax.
* @return A new AlphabetIndex2 object according to options specified.
* @throw Exception if an error occured.
*/
AlphabetIndex2* read(const std::string& description) throw (Exception);
};
} //end of namespace bpp.
#endif //_BPPOALPHABETINDEX2FORMAT_H_
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