OpenMS  3.0.0
MassTraceDetection.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Erhan Kenar, Holger Franken $
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34 
35 #pragma once
36 
42 
43 namespace OpenMS
44 {
45 
72  class OPENMS_DLLAPI MassTraceDetection :
73  public DefaultParamHandler,
74  public ProgressLogger
75  {
76  public:
79 
81  ~MassTraceDetection() override;
82 
86  void updateIterativeWeightedMeanMZ(const double &, const double &, double &, double &, double &);
88 
92  void run(const PeakMap &, std::vector<MassTrace> &, const Size max_traces = 0);
94 
96  void run(PeakMap::ConstAreaIterator & begin, PeakMap::ConstAreaIterator & end, std::vector<MassTrace> & found_masstraces);
97 
100  protected:
101  void updateMembers_() override;
102 
103  private:
104 
105  struct Apex
106  {
107  Apex(double intensity, Size scan_idx, Size peak_idx);
108  double intensity;
111  };
112 
114  void run_(const std::vector<Apex>& chrom_apices,
115  const Size peak_count,
116  const PeakMap & work_exp,
117  const std::vector<Size>& spec_offsets,
118  std::vector<MassTrace> & found_masstraces,
119  const Size max_traces = 0);
120 
121  // parameter stuff
126 
132 
134  };
135 }
OpenMS::MassTraceDetection::trace_termination_outliers_
Size trace_termination_outliers_
Definition: MassTraceDetection.h:128
DefaultParamHandler.h
OpenMS::MassTraceDetection::min_sample_rate_
double min_sample_rate_
Definition: MassTraceDetection.h:129
OpenMS::MassTraceDetection
A mass trace extraction method that gathers peaks similar in m/z and moving along retention time.
Definition: MassTraceDetection.h:72
OpenMS::Internal::AreaIterator
Forward iterator for an area of peaks in an experiment.
Definition: AreaIterator.h:57
OpenMS::MassTraceDetection::Apex::peak_idx
Size peak_idx
Definition: MassTraceDetection.h:110
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
OpenMS::MassTraceDetection::reestimate_mt_sd_
bool reestimate_mt_sd_
Definition: MassTraceDetection.h:133
OpenMS::MassTraceDetection::trace_termination_criterion_
String trace_termination_criterion_
Definition: MassTraceDetection.h:127
OpenMS::MassTraceDetection::Apex
Definition: MassTraceDetection.h:105
OpenMS::MassTraceDetection::noise_threshold_int_
double noise_threshold_int_
Definition: MassTraceDetection.h:123
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
MassTrace.h
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
OpenMS::MassTraceDetection::quant_method_
MassTrace::MT_QUANTMETHOD quant_method_
Definition: MassTraceDetection.h:125
OpenMS::MassTraceDetection::mass_error_ppm_
double mass_error_ppm_
Definition: MassTraceDetection.h:122
MSExperiment.h
OpenMS::MassTraceDetection::min_trace_length_
double min_trace_length_
Definition: MassTraceDetection.h:130
OpenMS::MassTraceDetection::chrom_peak_snr_
double chrom_peak_snr_
Definition: MassTraceDetection.h:124
OpenMS::MassTraceDetection::Apex::scan_idx
Size scan_idx
Definition: MassTraceDetection.h:109
OpenMS::MassTraceDetection::Apex::intensity
double intensity
Definition: MassTraceDetection.h:108
StandardTypes.h
OpenMS::MassTrace::MT_QUANTMETHOD
MT_QUANTMETHOD
Definition: MassTrace.h:66
OpenMS::MassTraceDetection::max_trace_length_
double max_trace_length_
Definition: MassTraceDetection.h:131