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clustal_io_handler.hh
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1 //------------------------------------------------------------------------------
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3 //
4 // Copyright (C) 2008-2020 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)
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12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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18 //------------------------------------------------------------------------------
19 #ifndef OST_IO_CLUSTAL_HANDLER_HH
20 #define OST_IO_CLUSTAL_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 
30 public:
31  virtual void Import(seq::SequenceList& ali,
32  const boost::filesystem::path& loc);
33 
34  virtual void Export(const seq::ConstSequenceList& ent,
35  const boost::filesystem::path& loc) const;
36 
37  virtual void Import(seq::SequenceList& ent,
38  std::istream& instream);
39 
40  virtual void Export(const seq::ConstSequenceList& ent,
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("Clustal"); }
48  static String GetFormatDescription() { return String("Format used by the ClustalW2 software package"); }
49 
50 };
51 
53 
54 }}
55 
56 #endif
std::string String
Definition: base.hh:54
static String GetFormatDescription()
list of immutable sequences.
SequenceIOHandlerFactory< ClustalIOHandler > ClustalIOHandlerFactory
#define DLLEXPORT_OST_IO
list of sequences.
pure abstract base class for entity io handlers