PepNovoInfile.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_PEPNOVOINFILE_H
#define OPENMS_FORMAT_PEPNOVOINFILE_H

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
#include <OpenMS/FORMAT/TextFile.h>

#include <map>


namespace OpenMS
{
  class OPENMS_DLLAPI PepNovoInfile
  {
public:
    PepNovoInfile();

    PepNovoInfile(const PepNovoInfile & pepnovo_infile);

    virtual ~PepNovoInfile();

    PepNovoInfile & operator=(const PepNovoInfile & pepnovo_infile);

    bool operator==(const PepNovoInfile & pepnovo_infile) const;

    void store(const String & filename);

    void setModifications(const StringList & fixed_mods, const StringList & variable_mods);

    void getModifications(std::map<String, String> & modification_key_map) const;

private:
    ModificationDefinitionsSet mods_;
    std::map<String, String> mods_and_keys_;
    TextFile ptm_file_;


    String handlePTMs_(const String & modification, const bool variable);
  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_PEPNOVOINFILE_H