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ChromatogramExtractorAlgorithm.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_CHROMATOGRAMEXTRACTORALGORITHM_H
36 #define OPENMS_ANALYSIS_OPENSWATH_CHROMATOGRAMEXTRACTORALGORITHM_H
37 
40 
41 namespace OpenMS
42 {
43 
59  class OPENMS_DLLAPI ChromatogramExtractorAlgorithm :
60  public ProgressLogger
61  {
62 
63 public:
64 
66  {
67  double mz;
68  double rt_start;
69  double rt_end;
70  std::string id;
71 
75  {
76  return left.mz < right.mz;
77  }
81  {
82  return left.mz > right.mz;
83  }
84  };
85 
101  void extractChromatograms(const OpenSwath::SpectrumAccessPtr input,
102  std::vector< OpenSwath::ChromatogramPtr >& output,
103  std::vector<ExtractionCoordinates> extraction_coordinates, double mz_extraction_window,
104  bool ppm, String filter);
105 
122  void extract_value_tophat(const std::vector<double>::const_iterator& mz_start, std::vector<double>::const_iterator& mz_it,
123  const std::vector<double>::const_iterator& mz_end, std::vector<double>::const_iterator& int_it,
124  const double& mz, double& integrated_intensity, const double& mz_extraction_window, bool ppm);
125 
126 private:
127 
128  int getFilterNr_(String filter);
129 
130  };
131 
132 }
133 
134 #endif
A more convenient string class.
Definition: String.h:57
The ChromatogramExtractorAlgorithm extracts chromatograms from a MS data.
Definition: ChromatogramExtractorAlgorithm.h:59
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:90
static bool SortExtractionCoordinatesReverseByMZ(const ChromatogramExtractorAlgorithm::ExtractionCoordinates &left, const ChromatogramExtractorAlgorithm::ExtractionCoordinates &right)
Definition: ChromatogramExtractorAlgorithm.h:78
double rt_end
rt start of extraction (in seconds)
Definition: ChromatogramExtractorAlgorithm.h:69
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: ChromatogramExtractorAlgorithm.h:65
double mz
Definition: ChromatogramExtractorAlgorithm.h:67
static bool SortExtractionCoordinatesByMZ(const ChromatogramExtractorAlgorithm::ExtractionCoordinates &left, const ChromatogramExtractorAlgorithm::ExtractionCoordinates &right)
identifier
Definition: ChromatogramExtractorAlgorithm.h:72
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
double rt_start
mz around which should be extracted
Definition: ChromatogramExtractorAlgorithm.h:68
std::string id
rt end of extraction (in seconds)
Definition: ChromatogramExtractorAlgorithm.h:70

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:22 using doxygen 1.8.9.1