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ElutionPeakDetection.h
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31 // $Maintainer: Erhan Kenar$
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 
45 namespace OpenMS
46 {
60  class OPENMS_DLLAPI ElutionPeakDetection :
61  public DefaultParamHandler, public ProgressLogger
62  {
63 public:
66 
68  virtual ~ElutionPeakDetection();
69 
71 
74  void detectPeaks(MassTrace& mt, std::vector<MassTrace>& single_mtraces);
76 
79  void detectPeaks(std::vector<MassTrace>& mt_vec, std::vector<MassTrace>& single_mtraces);
80 
81  void filterByPeakWidth(std::vector<MassTrace> &, std::vector<MassTrace> &);
82  double computeMassTraceNoise(const MassTrace&);
83  double computeMassTraceSNR(const MassTrace&);
84  double computeApexSNR(const MassTrace&);
85  void findLocalExtrema(const MassTrace&, const Size&, std::vector<Size>&, std::vector<Size>&);
86 
88  void smoothData(MassTrace& mt, int win_size) const;
89 
90 protected:
91  virtual void updateMembers_();
92 
93 private:
94  double chrom_fwhm_;
95  // double scan_time_;
98  //double sample_rate_;
99 
100  double min_fwhm_;
101  double max_fwhm_;
102  // double min_trace_length_;
103  // double max_trace_length_;
104 
107 
108  void detectElutionPeaks_(MassTrace &, std::vector<MassTrace> &);
109  };
110 } // namespace OpenMS
111 #endif // OPENMS_FILTERING_DATAREDUCTION_ELUTIONPEAKDETECTION_H
double max_fwhm_
Definition: ElutionPeakDetection.h:101
double min_fwhm_
Definition: ElutionPeakDetection.h:100
A more convenient string class.
Definition: String.h:57
double chrom_fwhm_
Definition: ElutionPeakDetection.h:94
double chrom_peak_snr_
Definition: ElutionPeakDetection.h:96
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
double noise_threshold_int_
Definition: ElutionPeakDetection.h:97
Extracts chromatographic peaks from a mass trace.
Definition: ElutionPeakDetection.h:60
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:59
bool mt_snr_filtering_
Definition: ElutionPeakDetection.h:106
String pw_filtering_
Definition: ElutionPeakDetection.h:105

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11