InspectInfile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// This software is released under a three-clause BSD license:
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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