InspectInfile.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: Andreas Bertsch $
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#ifndef OPENMS_FORMAT_INSPECTINFILE_H
#define OPENMS_FORMAT_INSPECTINFILE_H

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/Map.h>

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);

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

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

    Real getPeakMassTolerance() const;
    void setPeakMassTolerance(Real 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 Map<String, std::vector<String> > & getModifications() const;

private:

    String spectra_;         

    String db_;         

    String enzyme_;         

    Int modifications_per_peptide_;         

    UInt blind_;         


    Real maxptmsize_;         

    Real precursor_mass_tolerance_;         

    Real peak_mass_tolerance_;         

    UInt multicharge_;         


    String instrument_;         

    Int tag_count_;         

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

  };

} // namespace OpenMS

#endif // OPENMS_FORMAT_INSPECTINFILE_H