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/*****************************************************************************
* *
* PLAST : Parallel Local Alignment Search Tool *
* Version 2.3, released November 2015 *
* Copyright (c) 2009-2015 Inria-Cnrs-Ens *
* *
* PLAST is free software; you can redistribute it and/or modify it under *
* the Affero GPL ver 3 License, that is compatible with the GNU General *
* Public License *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* Affero GPL ver 3 License for more details. *
*****************************************************************************/
/** \file FastaSequenceOutput.hpp
* \brief Dump of sequences in a FASTA file
* \date 07/11/2011
* \author edrezen
*/
#ifndef _FASTA_SEQUENCE_OUTPUT_HPP_
#define _FASTA_SEQUENCE_OUTPUT_HPP_
/********************************************************************************/
#include <misc/api/types.hpp>
#include <designpattern/api/SmartPointer.hpp>
#include <os/api/IFile.hpp>
#include <database/api/ISequenceIterator.hpp>
#include <list>
#include <string>
/********************************************************************************/
namespace database {
/** \brief Implementation of concepts related to genomic databases. */
namespace impl {
/********************************************************************************/
/** \brief Dump sequences into a FASTA file
*
* This class is a small utility for dumping sequences into an output FASTA file.
*
* Note: by now, the length of the data lines is set to 60 and is not a parameter
* of the constructor, which could be improved.
*/
class FastaSequenceOutput : public dp::SmartPointer
{
public:
/** Constructor.
* \param[in] iterator : iteration of sequences to be dumped into the file
* \param[in] filename : uri of the dump file
* \param[in] comments : list of sequences comments; if not empty, it overrides the iterated comments
*/
FastaSequenceOutput (ISequenceIterator* iterator, const char* filename, const std::list<std::string>& comments);
/** Constructor.
* \param[in] iterator : iteration of sequences to be dumped into the file
* \param[in] filename : uri of the dump file
*/
FastaSequenceOutput (ISequenceIterator* iterator, const char* filename);
/** Destructor. */
virtual ~FastaSequenceOutput ();
/** Dump the sequences defined by the provided iterator in a file.
*/
void dump ();
private:
/** Iterator whose sequences have to be dumped into a file. */
ISequenceIterator* _iterator;
/** Smart setter for \ref _iterator attribute. */
void setIterator (ISequenceIterator* iterator) { SP_SETATTR(iterator); }
/** Callback to be called during sequences iteration.
* \param[in] seq : the currently iterated sequence
*/
void dumpSequence (const ISequence* seq);
/** File name */
std::string _filename;
/** File where the sequences are dumped. */
os::IFile* _file;
/** List of comments to be used for file dump. */
const std::list<std::string> _comments;
std::list<std::string>::const_iterator _itComments;
};
/********************************************************************************/
} } /* end of namespaces. */
/********************************************************************************/
#endif /* _FASTA_SEQUENCE_OUTPUT_HPP_ */
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