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PeakPickerMRM.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/CONCEPT/ProgressLogger.h>
39 #include <OpenMS/KERNEL/MSSpectrum.h>
40 #include <OpenMS/KERNEL/MSChromatogram.h>
41 #include <OpenMS/KERNEL/ChromatogramPeak.h>
42
43 #include <OpenMS/FILTERING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.h>
44 #include <OpenMS/FILTERING/SMOOTHING/SavitzkyGolayFilter.h>
45 #include <OpenMS/FILTERING/SMOOTHING/GaussFilter.h>
46
47 #include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerHiRes.h>
48
49 #ifdef WITH_CRAWDAD
50 #include <CrawdadWrapper.h>
51 #endif
52
53 namespace OpenMS
54 {
55
68 class OPENMS_DLLAPI PeakPickerMRM :
69 public DefaultParamHandler
70 {
71
72 public:
73
75 PeakPickerMRM();
77
79 ~PeakPickerMRM() override {}
81
83 enum FLOATINDICES { IDX_FWHM = 0, IDX_ABUNDANCE = 1, IDX_LEFTBORDER = 2, IDX_RIGHTBORDER = 3, SIZE_OF_FLOATINDICES };
84
92 void pickChromatogram(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);
93
94
102 void pickChromatogram(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom, MSChromatogram& smoothed_chrom);
103
104 protected:
105
106 void pickChromatogramCrawdad_(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);
107
108 void pickChromatogram_(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);
109
113 void integratePeaks_(const MSChromatogram& chromatogram);
114
123 Size findClosestPeak_(const MSChromatogram& chromatogram, double target_rt, Size current_peak = 0);
124
129 void removeOverlappingPeaks_(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);
130
131
133 void updateMembers_() override;
134
136 PeakPickerMRM& operator=(const PeakPickerMRM& rhs);
137
138 // Members
140 UInt sgolay_frame_length_;
142 UInt sgolay_polynomial_order_;
144 double gauss_width_;
146 bool use_gauss_;
148 bool remove_overlapping_;
149
151 double peak_width_;
153 double signal_to_noise_;
154
156 double sn_win_len_;
158 UInt sn_bin_count_;
160 bool write_sn_log_messages_;
162 String method_;
163
165 std::vector<double> integrated_intensities_;
167 std::vector<int> left_width_;
169 std::vector<int> right_width_;
170
171 PeakPickerHiRes pp_;
172 SavitzkyGolayFilter sgolay_;
173 GaussFilter gauss_;
174 SignalToNoiseEstimatorMedian<MSChromatogram > snt_;
175 };
176 }
177
178
OpenMS::PeakPickerMRM::right_width_
std::vector< int > right_width_
Temporary vector to hold the peak right widths.
Definition: PeakPickerMRM.h:169
OpenMS::String
A more convenient string class.
Definition: String.h:58
SavitzkyGolayFilter.h
OpenMS::PeakPickerMRM::peak_width_
double peak_width_
Forced peak with.
Definition: PeakPickerMRM.h:151
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:54
GaussFilter.h
OpenMS::PeakPickerMRM::snt_
SignalToNoiseEstimatorMedian< MSChromatogram > snt_
Definition: PeakPickerMRM.h:174
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::PeakPickerMRM::integrated_intensities_
std::vector< double > integrated_intensities_
Temporary vector to hold the integrated intensities.
Definition: PeakPickerMRM.h:165
SignalToNoiseEstimatorMedian.h
OpenMS::PeakPickerMRM::gauss_
GaussFilter gauss_
Definition: PeakPickerMRM.h:173
OpenMS::PeakPickerHiRes
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:73
OpenMS::PeakPickerMRM::use_gauss_
bool use_gauss_
Whether to use Gaussian smoothing.
Definition: PeakPickerMRM.h:146
OpenMS::PeakPickerMRM
The PeakPickerMRM finds peaks a single chromatogram.
Definition: PeakPickerMRM.h:68
OpenMS::GaussFilter
This class represents a Gaussian lowpass-filter which works on uniform as well as on non-uniform prof...
Definition: GaussFilter.h:74
OpenMS::SignalToNoiseEstimatorMedian
Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram ba...
Definition: SignalToNoiseEstimatorMedian.h:80
OpenMS::PeakPickerMRM::sn_bin_count_
UInt sn_bin_count_
Signal to noise bin count.
Definition: PeakPickerMRM.h:158
OpenMS::PeakPickerMRM::sgolay_
SavitzkyGolayFilter sgolay_
Definition: PeakPickerMRM.h:172
PeakPickerHiRes.h
OpenMS::PeakPickerMRM::~PeakPickerMRM
~PeakPickerMRM() override
Destructor.
Definition: PeakPickerMRM.h:79
OpenMS::PeakPickerMRM::FLOATINDICES
FLOATINDICES
indices into FloatDataArrays of resulting picked chromatograms
Definition: PeakPickerMRM.h:83
OpenMS::PeakPickerMRM::write_sn_log_messages_
bool write_sn_log_messages_
Whether to write out log messages of the SN estimator.
Definition: PeakPickerMRM.h:160
OpenMS::PeakPickerMRM::left_width_
std::vector< int > left_width_
Temporary vector to hold the peak left widths.
Definition: PeakPickerMRM.h:167
OpenMS::PeakPickerMRM::method_
String method_
Peak picker method.
Definition: PeakPickerMRM.h:162
OpenMS::PeakPickerMRM::sgolay_polynomial_order_
UInt sgolay_polynomial_order_
Polynomial order for the SGolay smoothing.
Definition: PeakPickerMRM.h:142
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DefaultParamHandler.h
OpenMS::PeakPickerMRM::pp_
PeakPickerHiRes pp_
Definition: PeakPickerMRM.h:171
OpenMS::PeakPickerMRM::remove_overlapping_
bool remove_overlapping_
Whether to resolve overlapping peaks.
Definition: PeakPickerMRM.h:148
MSSpectrum.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::PeakPickerMRM::signal_to_noise_
double signal_to_noise_
Signal to noise threshold.
Definition: PeakPickerMRM.h:153
OpenMS::PeakPickerMRM::sn_win_len_
double sn_win_len_
Signal to noise window length.
Definition: PeakPickerMRM.h:156
MSChromatogram.h
ChromatogramPeak.h
OpenMS::PeakPickerMRM::sgolay_frame_length_
UInt sgolay_frame_length_
Frame length for the SGolay smoothing.
Definition: PeakPickerMRM.h:140
OpenMS::PeakPickerMRM::gauss_width_
double gauss_width_
Width of the Gaussian smoothing.
Definition: PeakPickerMRM.h:144
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127