OpenMS  2.8.0
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 
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 
120  };
121 }
A container for features.
Definition: FeatureMap.h:106
Stores and handles combinations of enum values, e.g. a set of flags as bits flipped in an UInt64.
Definition: FlagSet.h:54
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
QC metric to determine the number of MS2 scans per MS1 scan over RT.
Definition: Ms2SpectrumStats.h:68
Status requires() const override
define the required input file: featureXML after FDR (=POSTFDRFEAT), MzML-file (MSExperiment) with al...
virtual ~Ms2SpectrumStats()=default
Destructor.
Ms2SpectrumStats()=default
Constructor.
static MSSpectrum::PeakType::IntensityType getBPI_(const MSSpectrum &spec)
calculate highest intensity (base peak intensity)
std::vector< PeptideIdentification > getUnassignedPeptideIdentifications_(const MSExperiment &exp)
return all unidentified MS2-Scans as unassignedPeptideIDs, these contain only Information about RT an...
std::vector< PeptideIdentification > compute(const MSExperiment &exp, FeatureMap &features, const QCBase::SpectraMap &map_to_spectrum)
Calculate the ScanEventNumber, find all unidentified MS2-Spectra and add them to unassigned PeptideId...
void setPresenceAndScanEventNumber_(PeptideIdentification &peptide_ID, const MSExperiment &exp, const QCBase::SpectraMap &map_to_spectrum)
set ms2_included_ bool to true, if PeptideID exist and set "ScanEventNumber" for every PeptideID
void setScanEventNumber_(const MSExperiment &exp)
compute "ScanEventNumber" for every spectrum: MS1=0, MS2=1-n, write into ms2_included_
const String & getName() const override
returns the name of the metric
float IntensityType
Intensity type.
Definition: Peak1D.h:62
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
Map to find a spectrum via its NativeID.
Definition: QCBase.h:90
This class serves as an abstract base class for all QC classes.
Definition: QCBase.h:55
A more convenient string class.
Definition: String.h:60
OPENMS_UINT32_TYPE UInt32
Unsigned integer type (32bit)
Definition: Types.h:63
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: Ms2SpectrumStats.h:71
ScanEvent(UInt32 sem, bool ms2)
Definition: Ms2SpectrumStats.h:72
bool ms2_presence
Definition: Ms2SpectrumStats.h:76
UInt32 scan_event_number
Definition: Ms2SpectrumStats.h:75