| OpenMS 2.5.0

PrecursorCorrection.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 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg, Oliver Alka $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <OpenMS/KERNEL/StandardTypes.h>
39 #include <OpenMS/KERNEL/MSExperiment.h>
40 #include <OpenMS/KERNEL/FeatureMap.h>
41
42 #include <OpenMS/CONCEPT/Constants.h>
43 #include <OpenMS/MATH/MISC/MathFunctions.h>
44
45 #include <OpenMS/METADATA/Precursor.h>
46
47 #include <fstream>
48 #include <iostream>
49 #include <string>
50 #include <algorithm>
51
52 namespace OpenMS
53 {
64 class OPENMS_DLLAPI PrecursorCorrection
65 {
66 public:
67
68 static const std::string csv_header;
69
78 static void getPrecursors(const MSExperiment & exp,
79 std::vector<Precursor> & precursors,
80 std::vector<double> & precursors_rt,
81 std::vector<Size> & precursor_scan_index);
82
83
98 static void writeHist(const String& out_csv,
99 const std::vector<double> & delta_mzs,
100 const std::vector<double> & mzs,
101 const std::vector<double> & rts);
116 static std::set<Size> correctToNearestMS1Peak(MSExperiment & exp,
117 double mz_tolerance,
118 bool ppm,
119 std::vector<double> & delta_mzs,
120 std::vector<double> & mzs,
121 std::vector<double> & rts);
122
137 static std::set<Size> correctToHighestIntensityMS1Peak(MSExperiment & exp,
138 double mz_tolerance,
139 bool ppm,
140 std::vector<double> & delta_mzs,
141 std::vector<double> & mzs,
142 std::vector<double> & rts);
143
144
168 static std::set<Size> correctToNearestFeature(const FeatureMap& features,
169 MSExperiment & exp,
170 double rt_tolerance_s = 0.0,
171 double mz_tolerance = 0.0,
172 bool ppm = true,
173 bool believe_charge = false,
174 bool keep_original = false,
175 bool all_matching_features = false,
176 int max_trace = 2,
177 int debug_level = 0);
178
179 protected:
180
192 static bool overlaps_(const Feature& feature,
193 const double rt,
194 const double pc_mz,
195 const double rt_tolerance);
196
209 static bool compatible_(const Feature& feature,
210 double pc_mz,
211 double mz_tolerance,
212 Size max_trace_number = 2,
213 int debug_level = 0);
214
215 };
216 }
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
Constants.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
Precursor.h
MathFunctions.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
StandardTypes.h
FeatureMap.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::PrecursorCorrection::csv_header
static const std::string csv_header
Definition: PrecursorCorrection.h:68
OpenMS::PrecursorCorrection
This class provides methods for precursor correction.
Definition: PrecursorCorrection.h:64
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127