OpenMS  3.0.0
Ms2SpectrumStats.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Juliane Schmachtenberg, Chris Bielow $
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34 
35 #pragma once
36 
37 #include <OpenMS/QC/QCBase.h>
38 
39 #include <OpenMS/KERNEL/Peak1D.h>
41 
42 
43 namespace OpenMS
44 {
45  class FeatureMap;
46  class MSExperiment;
47  class PeptideIdentification;
48  class TransformationDescription;
49 
67  class OPENMS_DLLAPI Ms2SpectrumStats : public QCBase
68  {
69  public:
70  struct ScanEvent
71  {
72  ScanEvent(UInt32 sem, bool ms2)
73  : scan_event_number(sem), ms2_presence(ms2)
74  {}
77  };
78 
80  Ms2SpectrumStats() = default;
81 
83  virtual ~Ms2SpectrumStats() = default;
84 
95  std::vector<PeptideIdentification> compute(const MSExperiment& exp, FeatureMap& features, const QCBase::SpectraMap& map_to_spectrum);
96 
98  const String& getName() const override;
100  Status requires() const override;
101 
102  private:
104  const String name_ = "Ms2SpectrumStats";
105 
107  std::vector<ScanEvent> ms2_included_{};
108 
110  void setScanEventNumber_(const MSExperiment& exp);
111 
113  void setPresenceAndScanEventNumber_(PeptideIdentification& peptide_ID, const MSExperiment& exp, const QCBase::SpectraMap& map_to_spectrum);
114 
116  std::vector<PeptideIdentification> getUnassignedPeptideIdentifications_(const MSExperiment& exp);
117 
119  static MSSpectrum::PeakType::IntensityType getBPI_(const MSSpectrum& spec);
120  };
121 }
OpenMS::Ms2SpectrumStats::ScanEvent::scan_event_number
UInt32 scan_event_number
Definition: Ms2SpectrumStats.h:75
OpenMS::UInt32
OPENMS_UINT32_TYPE UInt32
Unsigned integer type (32bit)
Definition: Types.h:63
OpenMS::Ms2SpectrumStats::ScanEvent::ms2_presence
bool ms2_presence
Definition: Ms2SpectrumStats.h:76
OpenMS::Ms2SpectrumStats::ScanEvent
Definition: Ms2SpectrumStats.h:70
OpenMS::String
A more convenient string class.
Definition: String.h:58
Peak1D.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::QCBase::SpectraMap
Map to find a spectrum via its NativeID.
Definition: QCBase.h:89
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Ms2SpectrumStats::ScanEvent::ScanEvent
ScanEvent(UInt32 sem, bool ms2)
Definition: Ms2SpectrumStats.h:72
OpenMS::QCBase
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:54
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::FlagSet
Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64.
Definition: FlagSet.h:53
float
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
MSSpectrum.h
OpenMS::Ms2SpectrumStats
QC metric to determine the number of MS2 scans per MS1 scan over RT.
Definition: Ms2SpectrumStats.h:67
QCBase.h