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ElutionPeakDetection.h
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31 // $Maintainer: Timo Sachsenberg$
32 // $Authors: Erhan Kenar, Holger Franken $
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34 
35 
36 #ifndef OPENMS_FILTERING_DATAREDUCTION_ELUTIONPEAKDETECTION_H
37 #define OPENMS_FILTERING_DATAREDUCTION_ELUTIONPEAKDETECTION_H
38 
43 
44 namespace OpenMS
45 {
77  class OPENMS_DLLAPI ElutionPeakDetection :
78  public DefaultParamHandler, public ProgressLogger
79  {
80 public:
83 
85  virtual ~ElutionPeakDetection();
86 
96  void detectPeaks(MassTrace& mt, std::vector<MassTrace>& single_mtraces);
97 
107  void detectPeaks(std::vector<MassTrace>& mt_vec, std::vector<MassTrace>& single_mtraces);
108 
110  void filterByPeakWidth(std::vector<MassTrace>&, std::vector<MassTrace>&);
111 
113  double computeMassTraceNoise(const MassTrace&);
114 
116  double computeMassTraceSNR(const MassTrace&);
117 
119  double computeApexSNR(const MassTrace&);
120 
145  void findLocalExtrema(const MassTrace& tr, const Size& num_neighboring_peaks,
146  std::vector<Size>& chrom_maxes, std::vector<Size>& chrom_mins);
147 
149  void smoothData(MassTrace& mt, int win_size) const;
150 
151 protected:
152  virtual void updateMembers_();
153 
154 private:
155  double chrom_fwhm_;
157 
158  double min_fwhm_;
159  double max_fwhm_;
160 
163 
166 
168  void detectElutionPeaks_(MassTrace&, std::vector<MassTrace>&);
169  };
170 
171 } // namespace OpenMS
172 
173 #endif // OPENMS_FILTERING_DATAREDUCTION_ELUTIONPEAKDETECTION_H
double max_fwhm_
Definition: ElutionPeakDetection.h:159
double min_fwhm_
Definition: ElutionPeakDetection.h:158
A more convenient string class.
Definition: String.h:57
double chrom_fwhm_
Definition: ElutionPeakDetection.h:155
double chrom_peak_snr_
Definition: ElutionPeakDetection.h:156
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Extracts chromatographic peaks from a mass trace.
Definition: ElutionPeakDetection.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
A container type that gathers peaks similar in m/z and moving along retention time.
Definition: MassTrace.h:62
bool mt_snr_filtering_
Whether to apply S/N filtering.
Definition: ElutionPeakDetection.h:165
String pw_filtering_
Type of width filtering.
Definition: ElutionPeakDetection.h:162

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:00 using doxygen 1.8.13