OpenMS  3.0.0
SwathQC.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
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34 
35 #pragma once
36 
38 #include <OpenMS/OpenMSConfig.h>
39 
40 #include <functional>
41 #include <map>
42 #include <vector>
43 
44 namespace OpenMS
45 {
46  class String;
47  class MSSpectrum;
48  class ExperimentalSettings;
49 
50 }
51 
52 namespace OpenSwath
53 {
54 
63  class OPENMS_DLLAPI SwathQC
64  {
65  public:
66  typedef std::map<int,int> ChargeDistribution;
67 
69  SwathQC() = delete;
70 
77  SwathQC(const size_t cd_spectra, const double decon_ms1_mz_tol);
78 
79 
86  std::function<void(const OpenMS::ExperimentalSettings& es)> getExpSettingsFunc();
87 
91  std::function<void (const OpenMS::MSSpectrum&)> getSpectraProcessingFunc();
92 
93 
112  static ChargeDistribution getChargeDistribution(const std::vector<SwathMap>& swath_maps, const size_t nr_samples, const double mz_tol);
113 
114 
118  void storeJSON(const OpenMS::String& filename);
119 
123  const ChargeDistribution& getChargeDistribution() const;
124 
132  void setNrMS1Spectra(size_t nr);
133 
134 
135  protected:
136 
151  static bool isSubsampledSpectrum_(const size_t total_spec_count, const size_t subsample_count, const size_t idx);
152 
153  private:
154 
157 
161  size_t cd_spectra_;
164 
167  };
168 
169 }
170 
SwathMap.h
OpenSwath
Definition: Scoring.h:43
OpenMS::ExperimentalSettings
Description of the experimental settings.
Definition: ExperimentalSettings.h:59
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenSwath::SwathQC
Quality Control function for OpenSwath.
Definition: SwathQC.h:63
OpenSwath::SwathQC::nr_ms1_spectra_
size_t nr_ms1_spectra_
number of MS1 spectra expected
Definition: SwathQC.h:159
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenSwath::SwathQC::ChargeDistribution
std::map< int, int > ChargeDistribution
Definition: SwathQC.h:66
OpenSwath::SwathQC::ms1_spectra_seen_
size_t ms1_spectra_seen_
keeps track of number of spectra passed to getSpectraProcessingFunc()
Definition: SwathQC.h:166
OpenSwath::SwathQC::cd_
ChargeDistribution cd_
internal ChargeDistribution which is augmented upon calling the corresponding member functions
Definition: SwathQC.h:156
OpenSwath::SwathQC::cd_spectra_
size_t cd_spectra_
number of spectra to inspect for charge distribution
Definition: SwathQC.h:161
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenSwath::SwathQC::decon_ms1_mz_tol_
double decon_ms1_mz_tol_
m/z tolerance for isotope deconvolution
Definition: SwathQC.h:163