InspectInfile.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/StringUtils.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 std::string& filename);
 
    void handlePTMs(const std::string& modification_line, const std::string& modifications_filename, const bool monoisotopic);
 
    const std::string& getSpectra() const;
    void setSpectra(const std::string& spectra);
 
    const std::string& getDb() const;
    void setDb(const std::string& db);
 
    const std::string& getEnzyme() const;
    void setEnzyme(const std::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 std::string& getInstrument() const;
    void setInstrument(const std::string& instrument);
 
    Int getTagCount() const;
    void setTagCount(Int TagCount);
 
    const std::map<std::string, std::vector<std::string> >& getModifications() const;
 
private:
 
    std::string spectra_; 
 
    std::string db_; 
 
    std::string enzyme_; 
 
    Int modifications_per_peptide_; 
 
    UInt blind_; 
 
    float maxptmsize_; 
 
    float precursor_mass_tolerance_; 
 
    float peak_mass_tolerance_; 
 
    UInt multicharge_; 
 
    std::string instrument_; 
 
    Int tag_count_; 
 
    std::map<std::string, std::vector<std::string> > PTMname_residues_mass_type_; 
 
  };
 
} // namespace OpenMS