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PeakPickerMRM.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_PEAKPICKERMRM_H
36 #define OPENMS_ANALYSIS_OPENSWATH_PEAKPICKERMRM_H
37 
43 
44 #ifdef WITH_CRAWDAD
45 #include <CrawdadWrapper.h>
46 #endif
47 
48 namespace OpenMS
49 {
50 
63  class OPENMS_DLLAPI PeakPickerMRM :
64  public DefaultParamHandler
65  {
66 
67 public:
68 
70  PeakPickerMRM();
72 
76 
84  void pickChromatogram(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);
85 
86 protected:
87 
88  void pickChromatogramCrawdad_(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);
89 
90  void pickChromatogram_(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);
91 
95  void integratePeaks_(const MSChromatogram& chromatogram);
96 
105  Size findClosestPeak_(const MSChromatogram& chromatogram, double target_rt, Size current_peak = 0);
106 
111  void removeOverlappingPeaks_(const MSChromatogram& chromatogram, MSChromatogram& picked_chrom);
112 
113 
115  void updateMembers_();
116 
118  PeakPickerMRM& operator=(const PeakPickerMRM& rhs);
119 
120  // Members
126  double gauss_width_;
131 
133  double peak_width_;
136 
138  double sn_win_len_;
145 
147  std::vector<double> integrated_intensities_;
149  std::vector<int> left_width_;
151  std::vector<int> right_width_;
152 
153  };
154 }
155 
156 #endif // OPENMS_ANALYSIS_OPENSWATH_PEAKPICKERMRM_H
157 
A more convenient string class.
Definition: String.h:57
bool use_gauss_
Whether to use Gaussian smoothing.
Definition: PeakPickerMRM.h:128
UInt sn_bin_count_
Signal to noise bin count.
Definition: PeakPickerMRM.h:140
The representation of a chromatogram.
Definition: MSChromatogram.h:55
double peak_width_
Forced peak with.
Definition: PeakPickerMRM.h:133
unsigned int UInt
Unsigned integer type.
Definition: Types.h:95
bool write_sn_log_messages_
Whether to write out log messages of the SN estimator.
Definition: PeakPickerMRM.h:142
The PeakPickerMRM finds peaks a single chromatogram.
Definition: PeakPickerMRM.h:63
double gauss_width_
Width of the Gaussian smoothing.
Definition: PeakPickerMRM.h:126
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< int > right_width_
Temporary vector to hold the peak right widths.
Definition: PeakPickerMRM.h:151
String method_
Peak picker method.
Definition: PeakPickerMRM.h:144
double sn_win_len_
Signal to noise window length.
Definition: PeakPickerMRM.h:138
std::vector< int > left_width_
Temporary vector to hold the peak left widths.
Definition: PeakPickerMRM.h:149
bool remove_overlapping_
Whether to resolve overlapping peaks.
Definition: PeakPickerMRM.h:130
std::vector< double > integrated_intensities_
Temporary vector to hold the integrated intensities.
Definition: PeakPickerMRM.h:147
UInt sgolay_frame_length_
Frame length for the SGolay smoothing.
Definition: PeakPickerMRM.h:122
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
~PeakPickerMRM()
Destructor.
Definition: PeakPickerMRM.h:74
double signal_to_noise_
Signal to noise threshold.
Definition: PeakPickerMRM.h:135
UInt sgolay_polynomial_order_
Polynomial order for the SGolay smoothing.
Definition: PeakPickerMRM.h:124
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:03 using doxygen 1.8.13