| OpenMS 2.5.0

SwathQC.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
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
156 ChargeDistribution cd_;
157
159 size_t nr_ms1_spectra_;
161 size_t cd_spectra_;
163 double decon_ms1_mz_tol_;
164
166 size_t ms1_spectra_seen_;
167 };
168
169 }
170
OpenSwath::SwathQC
Quality Control function for OpenSwath.
Definition: SwathQC.h:63
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenSwath
Definition: MRMScoring.h:49
OpenSwath::SwathQC::decon_ms1_mz_tol_
double decon_ms1_mz_tol_
m/z tolerance for isotope deconvolution
Definition: SwathQC.h:163
OpenSwath::SwathQC::cd_
ChargeDistribution cd_
internal ChargeDistribution which is augmented upon calling the corresponding member functions ...
Definition: SwathQC.h:156
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::ChargeDistribution
std::map< int, int > ChargeDistribution
Definition: SwathQC.h:66
OpenSwath::SwathQC::cd_spectra_
size_t cd_spectra_
number of spectra to inspect for charge distribution
Definition: SwathQC.h:161
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
SwathMap.h
OpenSwath::SwathQC::nr_ms1_spectra_
size_t nr_ms1_spectra_
number of MS1 spectra expected
Definition: SwathQC.h:159