OpenMS
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 
87  void updateIterativeWeightedMeanMZ(const double &, const double &, double &, double &, double &);
88 
93  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
127 
133 
135  };
136 }
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Forward iterator for an area of peaks in an experiment.
Definition: AreaIterator.h:62
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
A mass trace extraction method that gathers peaks similar in m/z and moving along retention time.
Definition: MassTraceDetection.h:75
double noise_threshold_int_
Definition: MassTraceDetection.h:124
String trace_termination_criterion_
Definition: MassTraceDetection.h:128
double mass_error_da_
Definition: MassTraceDetection.h:123
void updateIterativeWeightedMeanMZ(const double &, const double &, double &, double &, double &)
Allows the iterative computation of the intensity-weighted mean of a mass trace's centroid m/z.
double chrom_peak_snr_
Definition: MassTraceDetection.h:125
MassTrace::MT_QUANTMETHOD quant_method_
Definition: MassTraceDetection.h:126
MassTraceDetection()
Default constructor.
Size trace_termination_outliers_
Definition: MassTraceDetection.h:129
double min_trace_length_
Definition: MassTraceDetection.h:131
void run_(const std::vector< Apex > &chrom_apices, const Size peak_count, const PeakMap &work_exp, const std::vector< Size > &spec_offsets, std::vector< MassTrace > &found_masstraces, const Size max_traces=0)
The internal run method.
double min_sample_rate_
Definition: MassTraceDetection.h:130
void run(const PeakMap &, std::vector< MassTrace > &, const Size max_traces=0)
Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vec...
~MassTraceDetection() override
Default destructor.
double mass_error_ppm_
Definition: MassTraceDetection.h:122
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
double max_trace_length_
Definition: MassTraceDetection.h:132
bool reestimate_mt_sd_
Definition: MassTraceDetection.h:134
void run(PeakMap::ConstAreaIterator &begin, PeakMap::ConstAreaIterator &end, std::vector< MassTrace > &found_masstraces)
Invokes the run method (see above) on merely a subregion of a MSExperiment map.
MT_QUANTMETHOD
Definition: MassTrace.h:66
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Definition: MassTraceDetection.h:106
Size scan_idx
Definition: MassTraceDetection.h:109
Apex(double intensity, Size scan_idx, Size peak_idx)
double intensity
Definition: MassTraceDetection.h:108
Size peak_idx
Definition: MassTraceDetection.h:110