OpenMS  3.0.0
ChromatogramExtractorAlgorithm.h
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34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
42 
58  class OPENMS_DLLAPI ChromatogramExtractorAlgorithm :
59  public ProgressLogger
60  {
61 
62 public:
63 
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 
76  {
77  return left.mz < right.mz;
78  }
82  {
83  return left.mz > right.mz;
84  }
85  };
86 
103  void extractChromatograms(const OpenSwath::SpectrumAccessPtr input,
104  std::vector< OpenSwath::ChromatogramPtr >& output,
105  const std::vector<ExtractionCoordinates>& extraction_coordinates,
106  double mz_extraction_window,
107  bool ppm,
108  double im_extraction_window,
109  const String& filter);
110 
135  void extract_value_tophat(const std::vector<double>::const_iterator& mz_start,
136  std::vector<double>::const_iterator& mz_it,
137  const std::vector<double>::const_iterator& mz_end,
138  std::vector<double>::const_iterator& int_it,
139  const double mz,
140  double& integrated_intensity,
141  const double mz_extraction_window,
142  const bool ppm);
143 
172  void extract_value_tophat(const std::vector<double>::const_iterator& mz_start,
173  std::vector<double>::const_iterator& mz_it,
174  const std::vector<double>::const_iterator& mz_end,
175  std::vector<double>::const_iterator& int_it,
176  std::vector<double>::const_iterator& im_it,
177  const double mz,
178  const double im,
179  double& integrated_intensity,
180  const double mz_extraction_window,
181  const double im_extraction_window,
182  const bool ppm);
183 
184 private:
185 
186  int getFilterNr_(const String& filter);
187 
188  };
189 
190 }
191 
192 
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
OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates
Definition: ChromatogramExtractorAlgorithm.h:64
OpenMS::String
A more convenient string class.
Definition: String.h:58
ISpectrumAccess.h
OpenMS::ChromatogramExtractorAlgorithm
The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data.
Definition: ChromatogramExtractorAlgorithm.h:58
OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates::mz
double mz
m/z value around which should be extracted
Definition: ChromatogramExtractorAlgorithm.h:66
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:87
OpenMS::ChromatogramExtractorAlgorithm::ExtractionCoordinates::id
std::string id
identifier
Definition: ChromatogramExtractorAlgorithm.h:71