OpenMS  2.5.0
FIAMSDataProcessor.h
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31 // $Maintainer: Svetlana Kutuzova, Douglas McCloskey $
32 // $Authors: Svetlana Kutuzova, Douglas McCloskey $
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34 
35 #pragma once
38 #include <OpenMS/FORMAT/MzTab.h>
40 #include <OpenMS/FORMAT/MzMLFile.h>
41 
42 namespace OpenMS
43 {
59  class OPENMS_DLLAPI FIAMSDataProcessor :
60  public DefaultParamHandler
61  {
62 public:
65 
67  ~FIAMSDataProcessor() = default;
68 
70  FIAMSDataProcessor(const FIAMSDataProcessor& cp) = default;
71 
73  FIAMSDataProcessor& operator=(const FIAMSDataProcessor& fdp) = default;
74 
95  bool run(const MSExperiment& experiment, const float n_seconds, OpenMS::MzTab& output, const bool load_cached_spectrum = true);
96 
104  void cutForTime(const MSExperiment& experiment, const float n_seconds, std::vector<MSSpectrum>& output);
105 
116  MSSpectrum mergeAlongTime(const std::vector<OpenMS::MSSpectrum>& input);
117 
124  MSSpectrum extractPeaks(const MSSpectrum& input);
125 
134  FeatureMap convertToFeatureMap(const MSSpectrum& input);
135 
144  MSSpectrum trackNoise(const MSSpectrum& input);
145 
154  void runAccurateMassSearch(FeatureMap& input, OpenMS::MzTab& output);
155 
159  const std::vector<float>& getMZs();
160 
164  const std::vector<float>& getBinSizes();
165 
166 protected:
167  void updateMembers_() override;
168 
169 private:
173  void storeSpectrum_(const MSSpectrum& input, String filename);
174 
175  std::vector<float> mzs_;
176  std::vector<float> bin_sizes_;
179  };
180 } // namespace OpenMS
A more convenient string class.
Definition: String.h:58
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Computes the Savitzky-Golay filter coefficients using QR decomposition.
Definition: SavitzkyGolayFilter.h:101
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
A container for features.
Definition: FeatureMap.h:95
std::vector< float > mzs_
Definition: FIAMSDataProcessor.h:175
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:73
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Data processing for FIA-MS data.
Definition: FIAMSDataProcessor.h:59
SavitzkyGolayFilter sgfilter_
Definition: FIAMSDataProcessor.h:177
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.
Definition: MzTab.h:855
PeakPickerHiRes picker_
Definition: FIAMSDataProcessor.h:178
std::vector< float > bin_sizes_
Definition: FIAMSDataProcessor.h:176