fasta_io_handler.hh

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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library 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 GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//------------------------------------------------------------------------------
#ifndef OST_IO_FASTA_HANDLER_HH
#define OST_IO_FASTA_HANDLER_HH
/*
  Author: Marco Biasini
 */
#include <ost/io/module_config.hh>
#include "sequence_io_handler.hh"
 
namespace ost { namespace io {
 
class DLLEXPORT_OST_IO FastaIOHandler : public SequenceIOHandler {
public:
  virtual void Import(seq::SequenceList& aln,
                      const boost::filesystem::path& loc);
 
  virtual void Export(const seq::ConstSequenceList& aln,
                      const boost::filesystem::path& loc) const;
                      
  virtual void Import(seq::SequenceList& aln,
                      std::istream& instream);
 
  virtual void Export(const seq::ConstSequenceList& aln,
                      std::ostream& ostream) const;                      
 
  static bool ProvidesImport(const boost::filesystem::path& loc, 
                             const String& format="auto");
  static bool ProvidesExport(const boost::filesystem::path& loc, 
                             const String& format="auto");
  static String GetFormatName() { return String("Fasta"); }
  static String GetFormatDescription() { return String("Sequence format originally used by the Fasta suite of programs"); }
 
private:                             
};
 
typedef SequenceIOHandlerFactory<FastaIOHandler> FastaIOHandlerFactory; 
}}
 
#endif