OpenMS  2.4.0
PeakPickerHiRes.h
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31 // $Author: Erhan Kenar $
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34 
35 #pragma once
36 
38 
41 
42 #define DEBUG_PEAK_PICKING
43 #undef DEBUG_PEAK_PICKING
44 //#undef DEBUG_DECONV
45 namespace OpenMS
46 {
47  class MSChromatogram;
48  class OnDiscMSExperiment;
49 
73  class OPENMS_DLLAPI PeakPickerHiRes :
74  public DefaultParamHandler,
75  public ProgressLogger
76  {
77 public:
80 
82  ~PeakPickerHiRes() override;
83 
85  struct PeakBoundary
86  {
87  double mz_min;
88  double mz_max;
89  };
90 
99  void pick(const MSSpectrum& input, MSSpectrum& output) const;
100 
108  void pick(const MSChromatogram& input, MSChromatogram& output) const;
109 
120  void pick(const MSSpectrum& input, MSSpectrum& output, std::vector<PeakBoundary>& boundaries, bool check_spacings = true) const;
121 
122 
131  void pick(const MSChromatogram& input, MSChromatogram& output, std::vector<PeakBoundary>& boundaries) const;
132 
142  void pickExperiment(const PeakMap& input, PeakMap& output, const bool check_spectrum_type = true) const;
143 
155  void pickExperiment(const PeakMap& input, PeakMap& output, std::vector<std::vector<PeakBoundary> >& boundaries_spec, std::vector<std::vector<PeakBoundary> >& boundaries_chrom, const bool check_spectrum_type = true) const;
156 
164  void pickExperiment(/* const */ OnDiscMSExperiment& input, PeakMap& output, const bool check_spectrum_type = true) const;
165 
166 protected:
167  // signal-to-noise parameter
169 
170  // maximal spacing difference defining a large gap
172 
173  // maximal spacing difference defining a missing data point
175 
176  // maximum number of missing points
177  unsigned missing_;
178 
179  // MS levels to which peak picking is applied
180  std::vector<Int> ms_levels_;
181 
184 
187 
188  // docu in base class
189  void updateMembers_() override;
190 
191  }; // end PeakPickerHiRes
192 
193 } // namespace OpenMS
194 
bool report_FWHM_
add floatDataArray &#39;FWHM&#39;/&#39;FWHM_ppm&#39; to spectra with peak FWHM
Definition: PeakPickerHiRes.h:183
The representation of a chromatogram.
Definition: MSChromatogram.h:54
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool report_FWHM_as_ppm_
unit of &#39;FWHM&#39; float data array (can be absolute or ppm).
Definition: PeakPickerHiRes.h:186
double spacing_difference_gap_
Definition: PeakPickerHiRes.h:171
unsigned missing_
Definition: PeakPickerHiRes.h:177
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
std::vector< Int > ms_levels_
Definition: PeakPickerHiRes.h:180
double mz_min
Definition: PeakPickerHiRes.h:87
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
double signal_to_noise_
Definition: PeakPickerHiRes.h:168
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
double mz_max
Definition: PeakPickerHiRes.h:88
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:73
structure for peak boundaries
Definition: PeakPickerHiRes.h:85
double spacing_difference_
Definition: PeakPickerHiRes.h:174