| OpenMS 2.5.0

FIAMSDataProcessor.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Svetlana Kutuzova, Douglas McCloskey $
32 // $Authors: Svetlana Kutuzova, Douglas McCloskey $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36 #include <OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h>
37 #include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
38 #include <OpenMS/FORMAT/MzTab.h>
39 #include <OpenMS/FORMAT/MzTabFile.h>
40 #include <OpenMS/FORMAT/MzMLFile.h>
41
42 namespace OpenMS
43 {
59 class OPENMS_DLLAPI FIAMSDataProcessor :
60 public DefaultParamHandler
61 {
62 public:
64 FIAMSDataProcessor();
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_;
177 SavitzkyGolayFilter sgfilter_;
178 PeakPickerHiRes picker_;
179 };
180 } // namespace OpenMS
OpenMS::String
A more convenient string class.
Definition: String.h:58
SavitzkyGolayFilter.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::SavitzkyGolayFilter
Computes the Savitzky-Golay filter coefficients using QR decomposition.
Definition: SavitzkyGolayFilter.h:101
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::FIAMSDataProcessor::mzs_
std::vector< float > mzs_
Definition: FIAMSDataProcessor.h:175
OpenMS::PeakPickerHiRes
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:73
PeakPickerHiRes.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::FIAMSDataProcessor
Data processing for FIA-MS data.
Definition: FIAMSDataProcessor.h:59
OpenMS::FIAMSDataProcessor::sgfilter_
SavitzkyGolayFilter sgfilter_
Definition: FIAMSDataProcessor.h:177
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MzTab.h
OpenMS::MzTab
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/.
Definition: MzTab.h:855
MzTabFile.h
OpenMS::FIAMSDataProcessor::picker_
PeakPickerHiRes picker_
Definition: FIAMSDataProcessor.h:178
MzMLFile.h
OpenMS::FIAMSDataProcessor::bin_sizes_
std::vector< float > bin_sizes_
Definition: FIAMSDataProcessor.h:176