PepNovoInfile.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Timo Sachsenberg $
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#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