OpenMS  2.8.0
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 
130  void pick(const MSChromatogram& input, MSChromatogram& output, std::vector<PeakBoundary>& boundaries, bool check_spacings = false) const;
131 
141  void pickExperiment(const PeakMap& input, PeakMap& output, const bool check_spectrum_type = true) const;
142 
154  void pickExperiment(const PeakMap& input,
155  PeakMap& output,
156  std::vector<std::vector<PeakBoundary> >& boundaries_spec,
157  std::vector<std::vector<PeakBoundary> >& boundaries_chrom,
158  const bool check_spectrum_type = true) const;
159 
167  void pickExperiment(/* const */ OnDiscMSExperiment& input, PeakMap& output, const bool check_spectrum_type = true) const;
168 
169 protected:
170 
171  template <typename ContainerType>
172  void pick_(const ContainerType& input, ContainerType& output, std::vector<PeakBoundary>& boundaries, bool check_spacings = true) const;
173 
174  // signal-to-noise parameter
176 
177  // maximal spacing difference defining a large gap
179 
180  // maximal spacing difference defining a missing data point
182 
183  // maximum number of missing points
184  unsigned missing_;
185 
186  // MS levels to which peak picking is applied
187  std::vector<Int> ms_levels_;
188 
191 
194 
195  // docu in base class
196  void updateMembers_() override;
197 
198  }; // end PeakPickerHiRes
199 
200 } // namespace OpenMS
201 
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:93
The representation of a chromatogram.
Definition: MSChromatogram.h:57
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:67
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:76
void pick(const MSSpectrum &input, MSSpectrum &output) const
Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are ...
unsigned missing_
Definition: PeakPickerHiRes.h:184
double spacing_difference_
Definition: PeakPickerHiRes.h:181
double signal_to_noise_
Definition: PeakPickerHiRes.h:175
double spacing_difference_gap_
Definition: PeakPickerHiRes.h:178
bool report_FWHM_
add floatDataArray 'FWHM'/'FWHM_ppm' to spectra with peak FWHM
Definition: PeakPickerHiRes.h:190
~PeakPickerHiRes() override
Destructor.
std::vector< Int > ms_levels_
Definition: PeakPickerHiRes.h:187
double mz_max
Definition: PeakPickerHiRes.h:88
PeakPickerHiRes()
Constructor.
void pick(const MSSpectrum &input, MSSpectrum &output, std::vector< PeakBoundary > &boundaries, bool check_spacings=true) const
Applies the peak-picking algorithm to a single spectrum (MSSpectrum). The resulting picked peaks are ...
void pick(const MSChromatogram &input, MSChromatogram &output) const
Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked pe...
double mz_min
Definition: PeakPickerHiRes.h:87
void pick(const MSChromatogram &input, MSChromatogram &output, std::vector< PeakBoundary > &boundaries, bool check_spacings=false) const
Applies the peak-picking algorithm to a single chromatogram (MSChromatogram). The resulting picked pe...
bool report_FWHM_as_ppm_
unit of 'FWHM' float data array (can be absolute or ppm).
Definition: PeakPickerHiRes.h:193
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
void pick_(const ContainerType &input, ContainerType &output, std::vector< PeakBoundary > &boundaries, bool check_spacings=true) const
void pickExperiment(OnDiscMSExperiment &input, PeakMap &output, const bool check_spectrum_type=true) const
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in ...
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
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in ...
void pickExperiment(const PeakMap &input, PeakMap &output, const bool check_spectrum_type=true) const
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in ...
structure for peak boundaries
Definition: PeakPickerHiRes.h:86
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47