OpenStructure
pssm_io_handler.hh
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1 //------------------------------------------------------------------------------
2 // This file is part of the OpenStructure project <www.openstructure.org>
3 //
4 // Copyright (C) 2008-2020 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
13 // details.
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17 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
18 //------------------------------------------------------------------------------
19 
20 /*
21  Author: Gerardo Tauriello
22  */
23 
24 #ifndef OST_PSSM_IO_HANDLER_HH
25 #define OST_PSSM_IO_HANDLER_HH
26 
27 #include <ost/io/module_config.hh>
28 #include "profile_io_handler.hh"
29 
30 namespace ost { namespace io {
31 
33 public:
34  virtual void Import(seq::ProfileHandle& prof,
35  const boost::filesystem::path& loc);
37  const String& data);
38  virtual void Export(const seq::ProfileHandle& prof,
39  const boost::filesystem::path& loc) const;
40 
41  static bool ProvidesImport(const boost::filesystem::path& loc,
42  const String& format="auto");
43  static bool ProvidesExport(const boost::filesystem::path& loc,
44  const String& format="auto");
45 
46  static String GetFormatName() { return String("PSSM"); }
48  return String("ASCII Table (PSSM) output of PSI-BLAST (flag -Q)");
49  }
50 private:
51  void Import(seq::ProfileHandle& prof, std::istream& in);
52 };
53 
55 
56 }}
57 
58 #endif
pure abstract base class for profile io handlers
virtual void ImportFromString(seq::ProfileHandle &prof, const String &data)
static bool ProvidesImport(const boost::filesystem::path &loc, const String &format="auto")
static String GetFormatName()
virtual void Import(seq::ProfileHandle &prof, const boost::filesystem::path &loc)
static bool ProvidesExport(const boost::filesystem::path &loc, const String &format="auto")
virtual void Export(const seq::ProfileHandle &prof, const boost::filesystem::path &loc) const
static String GetFormatDescription()
Provides a profile for a sequence.
#define DLLEXPORT_OST_IO
std::string String
Definition: base.hh:54
ProfileIOHandlerFactory< PssmIOHandler > PssmIOHandlerFactory
Definition: base.dox:1