pssm_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
//------------------------------------------------------------------------------

/*
  Author: Gerardo Tauriello
 */

#ifndef OST_PSSM_IO_HANDLER_HH
#define OST_PSSM_IO_HANDLER_HH

#include <ost/io/module_config.hh>
#include "profile_io_handler.hh"

namespace ost { namespace io {

class DLLEXPORT_OST_IO PssmIOHandler : public ProfileIOHandler {
public:
  virtual void Import(seq::ProfileHandle& prof,
                      const boost::filesystem::path& loc);
  virtual void ImportFromString(seq::ProfileHandle& prof,
                                const String& data);
  virtual void Export(const seq::ProfileHandle& prof,
                      const boost::filesystem::path& loc) 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("PSSM"); }
  static String GetFormatDescription() {
    return String("ASCII Table (PSSM) output of PSI-BLAST (flag -Q)");
  }
private:
  void Import(seq::ProfileHandle& prof, std::istream& in);
};

typedef ProfileIOHandlerFactory<PssmIOHandler> PssmIOHandlerFactory; 

}}

#endif