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// File IoSequenceFactory.h
// Created by: Julien Dutheil
// Created on: Tue 18/04/06 10:24
//
/*
Copyright or © or Copr. Bio++ Development Team, (November 17, 2004)
This software is a computer program whose purpose is to provide classes
for sequences 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 _IOSEQUENCEFACTORY_H_
#define _IOSEQUENCEFACTORY_H_
#include "ISequence.h"
#include "OSequence.h"
#include "../Alphabet/Alphabet.h"
namespace bpp
{
/**
* @brief Utilitary class for creating sequence readers and writers.
*/
class IoSequenceFactory
{
public:
static const std::string FASTA_FORMAT;
static const std::string MASE_FORMAT;
static const std::string CLUSTAL_FORMAT;
static const std::string DCSE_FORMAT;
static const std::string PHYLIP_FORMAT_INTERLEAVED;
static const std::string PHYLIP_FORMAT_SEQUENTIAL;
static const std::string PAML_FORMAT_INTERLEAVED;
static const std::string PAML_FORMAT_SEQUENTIAL;
static const std::string GENBANK_FORMAT;
static const std::string NEXUS_FORMAT;
public:
/**
* @brief Creates a new factory object.
*
* Example:
* @code
* Alphabet* alphabet = new DNA();
* ISequence* seqReader = IoSequenceFactory().createReader(IoSequenceFactory::FASTA_FORMAT);
* SequenceContainer* sequences = seqReader->read("file.fasta", alphabet);
* delete seqReader;
* @endcode
*/
IoSequenceFactory() {}
virtual ~IoSequenceFactory() {}
/**
* @brief Get a new dynamically created ISequence object.
*
* @param format The input file format.
* @return A pointer toward a new ISequence object.
* @throw Exception If the format name do not match any available format.
*/
virtual ISequence* createReader(const std::string& format) throw (Exception);
/**
* @brief Get a new dynamically created IAlignment object.
*
* @param format The input file format.
* @return A pointer toward a new IAlignment object.
* @throw Exception If the format name do not match any available format.
*/
virtual IAlignment* createAlignmentReader(const std::string& format) throw (Exception);
/**
* @brief Get a new dynamically created OSequence object.
*
* @param format The output file format.
* @return A pointer toward a new OSequence object.
* @throw Exception If the format name do not match any available format.
*/
virtual OSequence* createWriter(const std::string& format) throw (Exception);
/**
* @brief Get a new dynamically created OAlignment object.
*
* @param format The output file format.
* @return A pointer toward a new OAlignment object.
* @throw Exception If the format name do not match any available format.
*/
virtual OAlignment* createAlignmentWriter(const std::string& format) throw (Exception);
};
} //end of namespace bpp.
#endif //_IOSEQUENCEFACTORY_H_
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