OpenStructure
 All Data Structures Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Groups Pages
pssm_io_handler.hh
Go to the documentation of this file.
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)
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 
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 
32 class DLLEXPORT_OST_IO PssmIOHandler : public ProfileIOHandler {
33 public:
34  virtual void Import(seq::ProfileHandle& prof,
35  const boost::filesystem::path& loc);
36  virtual void ImportFromString(seq::ProfileHandle& prof,
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 
54 typedef ProfileIOHandlerFactory<PssmIOHandler> PssmIOHandlerFactory;
55 
56 }}
57 
58 #endif
std::string String
Definition: base.hh:54
Provides a profile for a sequence.
static String GetFormatDescription()
static String GetFormatName()
#define DLLEXPORT_OST_IO
ProfileIOHandlerFactory< PssmIOHandler > PssmIOHandlerFactory