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ChromatogramExtractorAlgorithm.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/ProgressLogger.h>
38 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
39
40 namespace OpenMS
41 {
42
58 class OPENMS_DLLAPI ChromatogramExtractorAlgorithm :
59 public ProgressLogger
60 {
61
62 public:
63
64 struct ExtractionCoordinates
65 {
66 double mz = 0.0;
67 double ion_mobility = 0.0;
68 double mz_precursor = 0.0;
69 double rt_start = 0.0;
70 double rt_end = 0.0;
71 std::string id;
72
73 static bool SortExtractionCoordinatesByMZ(
74 const ChromatogramExtractorAlgorithm::ExtractionCoordinates& left,
75 const ChromatogramExtractorAlgorithm::ExtractionCoordinates& right)
76 {
77 return left.mz < right.mz;
78 }
79 static bool SortExtractionCoordinatesReverseByMZ(
80 const ChromatogramExtractorAlgorithm::ExtractionCoordinates& left,
81 const ChromatogramExtractorAlgorithm::ExtractionCoordinates& right)
82 {
83 return left.mz > right.mz;
84 }
85 };
86
102 void extractChromatograms(const OpenSwath::SpectrumAccessPtr input,
103 std::vector< OpenSwath::ChromatogramPtr >& output,
104 const std::vector<ExtractionCoordinates>& extraction_coordinates,
105 double mz_extraction_window,
106 bool ppm,
107 double im_extraction_window,
108 const String& filter);
109
134 void extract_value_tophat(const std::vector<double>::const_iterator& mz_start,
135 std::vector<double>::const_iterator& mz_it,
136 const std::vector<double>::const_iterator& mz_end,
137 std::vector<double>::const_iterator& int_it,
138 const double mz,
139 double& integrated_intensity,
140 const double mz_extraction_window,
141 const bool ppm);
142
171 void extract_value_tophat(const std::vector<double>::const_iterator& mz_start,
172 std::vector<double>::const_iterator& mz_it,
173 const std::vector<double>::const_iterator& mz_end,
174 std::vector<double>::const_iterator& int_it,
175 std::vector<double>::const_iterator& im_it,
176 const double mz,
177 const double im,
178 double& integrated_intensity,
179 const double mz_extraction_window,
180 const double im_extraction_window,
181 const bool ppm);
182
183 private:
184
185 int getFilterNr_(const String& filter);
186
187 };
188
189 }
190
191
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates
Definition: ChromatogramExtractorAlgorithm.h:64
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates::mz
double mz
m/z value around which should be extracted
Definition: ChromatogramExtractorAlgorithm.h:66
OpenMS::ChromatogramExtractorAlgorithm
The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data.
Definition: ChromatogramExtractorAlgorithm.h:58
OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates::id
std::string id
identifier
Definition: ChromatogramExtractorAlgorithm.h:71
OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates::SortExtractionCoordinatesByMZ
static bool SortExtractionCoordinatesByMZ(const ChromatogramExtractorAlgorithm::ExtractionCoordinates &left, const ChromatogramExtractorAlgorithm::ExtractionCoordinates &right)
Definition: ChromatogramExtractorAlgorithm.h:73
OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates::SortExtractionCoordinatesReverseByMZ
static bool SortExtractionCoordinatesReverseByMZ(const ChromatogramExtractorAlgorithm::ExtractionCoordinates &left, const ChromatogramExtractorAlgorithm::ExtractionCoordinates &right)
Definition: ChromatogramExtractorAlgorithm.h:79
ISpectrumAccess.h