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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 
69  // this is the type in which we store the chromatograms for this analysis
71 
73  PeakPickerMRM();
75 
79 
87  void pickChromatogram(const RichPeakChromatogram& chromatogram, RichPeakChromatogram& picked_chrom);
88 
89 protected:
90 
91  void pickChromatogramCrawdad_(const RichPeakChromatogram& chromatogram, RichPeakChromatogram& picked_chrom);
92 
93  void pickChromatogram_(const RichPeakChromatogram& chromatogram, RichPeakChromatogram& picked_chrom);
94 
98  void integratePeaks_(const RichPeakChromatogram& chromatogram);
99 
108  Size findClosestPeak_(const RichPeakChromatogram& chromatogram, double target_rt, Size current_peak = 0);
109 
114  void removeOverlappingPeaks_(const RichPeakChromatogram& chromatogram, RichPeakChromatogram& picked_chrom);
115 
116 
118  void updateMembers_();
119 
121  PeakPickerMRM& operator=(const PeakPickerMRM& rhs);
122 
123  // Members
126  double gauss_width_;
129 
130  double peak_width_;
132 
133  double sn_win_len_;
136 
137  std::vector<double> integrated_intensities_;
138  std::vector<int> left_width_;
139  std::vector<int> right_width_;
140 
141  };
142 }
143 
144 #endif
A more convenient string class.
Definition: String.h:57
bool use_gauss_
Definition: PeakPickerMRM.h:127
UInt sn_bin_count_
Definition: PeakPickerMRM.h:134
double peak_width_
Definition: PeakPickerMRM.h:130
The PeakPickerMRM finds peaks a single chromatogram.
Definition: PeakPickerMRM.h:63
double gauss_width_
Definition: PeakPickerMRM.h:126
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< int > right_width_
Definition: PeakPickerMRM.h:139
String method_
Definition: PeakPickerMRM.h:135
double sn_win_len_
Definition: PeakPickerMRM.h:133
std::vector< int > left_width_
Definition: PeakPickerMRM.h:138
bool remove_overlapping_
Definition: PeakPickerMRM.h:128
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
std::vector< double > integrated_intensities_
Definition: PeakPickerMRM.h:137
MSSpectrum< ChromatogramPeak > RichPeakChromatogram
Definition: PeakPickerMRM.h:70
UInt sgolay_frame_length_
Definition: PeakPickerMRM.h:124
~PeakPickerMRM()
Destructor.
Definition: PeakPickerMRM.h:77
double signal_to_noise_
Definition: PeakPickerMRM.h:131
UInt sgolay_polynomial_order_
Definition: PeakPickerMRM.h:125
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92

OpenMS / TOPP release 2.0.0 Documentation generated on Sat May 16 2015 16:13:30 using doxygen 1.8.9.1