OpenMS  3.0.0
PrecursorCorrection.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg, Oliver Alka $
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34 //
35 
36 #pragma once
37 
41 
44 
46 
47 #include <string>
48 #include <vector>
49 #include <set>
50 
51 namespace OpenMS
52 {
63 class OPENMS_DLLAPI PrecursorCorrection
64 {
65  public:
66 
67  static const std::string csv_header;
68 
77  static void getPrecursors(const MSExperiment & exp,
78  std::vector<Precursor> & precursors,
79  std::vector<double> & precursors_rt,
80  std::vector<Size> & precursor_scan_index);
81 
82 
97  static void writeHist(const String& out_csv,
98  const std::vector<double> & delta_mzs,
99  const std::vector<double> & mzs,
100  const std::vector<double> & rts);
115  static std::set<Size> correctToNearestMS1Peak(MSExperiment & exp,
116  double mz_tolerance,
117  bool ppm,
118  std::vector<double> & delta_mzs,
119  std::vector<double> & mzs,
120  std::vector<double> & rts);
121 
136  static std::set<Size> correctToHighestIntensityMS1Peak(MSExperiment & exp,
137  double mz_tolerance,
138  bool ppm,
139  std::vector<double> & delta_mzs,
140  std::vector<double> & mzs,
141  std::vector<double> & rts);
142 
143 
167  static std::set<Size> correctToNearestFeature(const FeatureMap& features,
168  MSExperiment & exp,
169  double rt_tolerance_s = 0.0,
170  double mz_tolerance = 0.0,
171  bool ppm = true,
172  bool believe_charge = false,
173  bool keep_original = false,
174  bool all_matching_features = false,
175  int max_trace = 2,
176  int debug_level = 0);
177 
178  protected:
179 
191  static bool overlaps_(const Feature& feature,
192  const double rt,
193  const double pc_mz,
194  const double rt_tolerance);
195 
208  static bool compatible_(const Feature& feature,
209  double pc_mz,
210  double mz_tolerance,
211  Size max_trace_number = 2,
212  int debug_level = 0);
213 
214 };
215 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Constants.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
FeatureMap.h
MathFunctions.h
Precursor.h
MSExperiment.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
StandardTypes.h
OpenMS::PrecursorCorrection
This class provides methods for precursor correction.
Definition: PrecursorCorrection.h:63
OpenMS::PrecursorCorrection::csv_header
static const std::string csv_header
Definition: PrecursorCorrection.h:67