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ElutionPeakDetection.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Erhan Kenar, Holger Franken $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/CONCEPT/ProgressLogger.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41 #include <OpenMS/KERNEL/MassTrace.h>
42
43 namespace OpenMS
44 {
76 class OPENMS_DLLAPI ElutionPeakDetection :
77 public DefaultParamHandler, public ProgressLogger
78 {
79 public:
81 ElutionPeakDetection();
82
84 ~ElutionPeakDetection() override;
85
95 void detectPeaks(MassTrace& mt, std::vector<MassTrace>& single_mtraces);
96
106 void detectPeaks(std::vector<MassTrace>& mt_vec, std::vector<MassTrace>& single_mtraces);
107
109 void filterByPeakWidth(std::vector<MassTrace>&, std::vector<MassTrace>&);
110
112 double computeMassTraceNoise(const MassTrace&);
113
115 double computeMassTraceSNR(const MassTrace&);
116
118 double computeApexSNR(const MassTrace&);
119
144 void findLocalExtrema(const MassTrace& tr, const Size& num_neighboring_peaks,
145 std::vector<Size>& chrom_maxes, std::vector<Size>& chrom_mins);
146
148 void smoothData(MassTrace& mt, int win_size) const;
149
150 protected:
151 void updateMembers_() override;
152
153 private:
154 double chrom_fwhm_;
155 double chrom_peak_snr_;
156
157 double min_fwhm_;
158 double max_fwhm_;
159
161 String pw_filtering_;
162
164 bool mt_snr_filtering_;
165
167 void detectElutionPeaks_(MassTrace&, std::vector<MassTrace>&);
168 };
169
170 } // namespace OpenMS
171
MassTrace.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MassTrace
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:61
OpenMS::ElutionPeakDetection::chrom_peak_snr_
double chrom_peak_snr_
Definition: ElutionPeakDetection.h:155
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::ElutionPeakDetection
Extracts chromatographic peaks from a mass trace.
Definition: ElutionPeakDetection.h:76
ProgressLogger.h
OpenMS::ElutionPeakDetection::chrom_fwhm_
double chrom_fwhm_
Definition: ElutionPeakDetection.h:154
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ElutionPeakDetection::pw_filtering_
String pw_filtering_
Type of width filtering.
Definition: ElutionPeakDetection.h:161
MSExperiment.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::ElutionPeakDetection::max_fwhm_
double max_fwhm_
Definition: ElutionPeakDetection.h:158
DefaultParamHandler.h
OpenMS::ElutionPeakDetection::mt_snr_filtering_
bool mt_snr_filtering_
Whether to apply S/N filtering.
Definition: ElutionPeakDetection.h:164
OpenMS::ElutionPeakDetection::min_fwhm_
double min_fwhm_
Definition: ElutionPeakDetection.h:157
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127