PepNovoInfile.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
#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