InspectInfile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
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#pragma once

#include <OpenMS/DATASTRUCTURES/String.h>

#include <map>

namespace OpenMS
{
  class OPENMS_DLLAPI InspectInfile
  {
public:

    InspectInfile();

    InspectInfile(const InspectInfile& inspect_infile);

    virtual ~InspectInfile();

    InspectInfile& operator=(const InspectInfile& inspect_infile);

    bool operator==(const InspectInfile& inspect_infile) const;

    void store(const String& filename);

    void handlePTMs(const String& modification_line, const String& modifications_filename, const bool monoisotopic);

    const String& getSpectra() const;
    void setSpectra(const String& spectra);

    const String& getDb() const;
    void setDb(const String& db);

    const String& getEnzyme() const;
    void setEnzyme(const String& enzyme);

    Int getModificationsPerPeptide() const;
    void setModificationsPerPeptide(Int modifications_per_peptide);

    UInt getBlind() const;
    void setBlind(UInt blind);

    float getMaxPTMsize() const;
    void setMaxPTMsize(float maxptmsize);

    float getPrecursorMassTolerance() const;
    void setPrecursorMassTolerance(float precursor_mass_tolerance);

    float getPeakMassTolerance() const;
    void setPeakMassTolerance(float peak_mass_tolerance);

    UInt getMulticharge() const;
    void setMulticharge(UInt multicharge);

    const String& getInstrument() const;
    void setInstrument(const String& instrument);

    Int getTagCount() const;
    void setTagCount(Int TagCount);

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

private:

    String spectra_; 

    String db_; 

    String enzyme_; 

    Int modifications_per_peptide_; 

    UInt blind_; 

    float maxptmsize_; 

    float precursor_mass_tolerance_; 

    float peak_mass_tolerance_; 

    UInt multicharge_; 

    String instrument_; 

    Int tag_count_; 

    std::map<String, std::vector<String> > PTMname_residues_mass_type_; 

  };

} // namespace OpenMS