OpenMS  3.0.0
ElutionPeakDetection.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Erhan Kenar, Holger Franken $
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34 
35 
36 #pragma once
37 
42 
43 namespace OpenMS
44 {
76  class OPENMS_DLLAPI ElutionPeakDetection :
77  public DefaultParamHandler, public ProgressLogger
78  {
79 public:
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) const;
146 
148  void smoothData(MassTrace& mt, int win_size) const;
149 
150 protected:
151  void updateMembers_() override;
152 
153 private:
154  double chrom_fwhm_;
156 
157  double min_fwhm_;
158  double max_fwhm_;
159 
162 
165 
167  void detectElutionPeaks_(MassTrace&, std::vector<MassTrace>&);
168  };
169 
170 } // namespace OpenMS
171 
DefaultParamHandler.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ElutionPeakDetection::pw_filtering_
String pw_filtering_
Type of width filtering.
Definition: ElutionPeakDetection.h:161
OpenMS::MassTrace
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:61
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
MassTrace.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ElutionPeakDetection
Extracts chromatographic peaks from a mass trace.
Definition: ElutionPeakDetection.h:76
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::ElutionPeakDetection::chrom_peak_snr_
double chrom_peak_snr_
Definition: ElutionPeakDetection.h:155
OpenMS::ElutionPeakDetection::max_fwhm_
double max_fwhm_
Definition: ElutionPeakDetection.h:158
MSExperiment.h
OpenMS::ElutionPeakDetection::mt_snr_filtering_
bool mt_snr_filtering_
Whether to apply S/N filtering.
Definition: ElutionPeakDetection.h:164
OpenMS::ElutionPeakDetection::chrom_fwhm_
double chrom_fwhm_
Definition: ElutionPeakDetection.h:154
OpenMS::ElutionPeakDetection::min_fwhm_
double min_fwhm_
Definition: ElutionPeakDetection.h:157