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fasta_io_handler.hh
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1 //------------------------------------------------------------------------------
2 // This file is part of the OpenStructure project <www.openstructure.org>
3 //
4 // Copyright (C) 2008-2011 by the OpenStructure authors
5 //
6 // This library is free software; you can redistribute it and/or modify it under
7 // the terms of the GNU Lesser General Public License as published by the Free
8 // Software Foundation; either version 3.0 of the License, or (at your option)
9 // any later version.
10 // This library is distributed in the hope that it will be useful, but WITHOUT
11 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
13 // details.
14 //
15 // You should have received a copy of the GNU Lesser General Public License
16 // along with this library; if not, write to the Free Software Foundation, Inc.,
17 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
18 //------------------------------------------------------------------------------
19 #ifndef OST_IO_FASTA_HANDLER_HH
20 #define OST_IO_FASTA_HANDLER_HH
21 /*
22  Author: Marco Biasini
23  */
24 #include <ost/io/module_config.hh>
25 #include "sequence_io_handler.hh"
26 
27 namespace ost { namespace io {
28 
29 class DLLEXPORT_OST_IO FastaIOHandler : public SequenceIOHandler {
30 public:
31  virtual void Import(seq::SequenceList& aln,
32  const boost::filesystem::path& loc);
33 
34  virtual void Export(const seq::ConstSequenceList& aln,
35  const boost::filesystem::path& loc) const;
36 
37  virtual void Import(seq::SequenceList& aln,
38  std::istream& instream);
39 
40  virtual void Export(const seq::ConstSequenceList& aln,
41  std::ostream& ostream) const;
42 
43  static bool ProvidesImport(const boost::filesystem::path& loc,
44  const String& format="auto");
45  static bool ProvidesExport(const boost::filesystem::path& loc,
46  const String& format="auto");
47  static String GetFormatName() { return String("Fasta"); }
48  static String GetFormatDescription() { return String("Sequence format originally used by the Fasta suite of programs"); }
49 
50 private:
51 };
52 
53 typedef SequenceIOHandlerFactory<FastaIOHandler> FastaIOHandlerFactory;
54 }}
55 
56 #endif
SequenceIOHandlerFactory< FastaIOHandler > FastaIOHandlerFactory
std::string String
Definition: base.hh:54
static String GetFormatName()
static String GetFormatDescription()
std::vector< SequenceImplPtr > SequenceList
#define DLLEXPORT_OST_IO