| OpenMS 2.5.0

MassTraceDetection.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Erhan Kenar, Holger Franken $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/KERNEL/MassTrace.h>
39 #include <OpenMS/KERNEL/MSExperiment.h>
40 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
41 #include <OpenMS/CONCEPT/ProgressLogger.h>
42
43 namespace OpenMS
44 {
45
72 class OPENMS_DLLAPI MassTraceDetection :
73 public DefaultParamHandler,
74 public ProgressLogger
75 {
76 public:
78 MassTraceDetection();
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 typedef std::multimap<double, std::pair<Size, Size> > MapIdxSortedByInt;
106
108 void run_(const MapIdxSortedByInt& chrom_apices,
109 const Size peak_count,
110 const PeakMap & work_exp,
111 const std::vector<Size>& spec_offsets,
112 std::vector<MassTrace> & found_masstraces,
113 const Size max_traces = 0);
114
115 // parameter stuff
116 double mass_error_ppm_;
117 double noise_threshold_int_;
118 double chrom_peak_snr_;
119 MassTrace::MT_QUANTMETHOD quant_method_;
120
121 String trace_termination_criterion_;
122 Size trace_termination_outliers_;
123 double min_sample_rate_;
124 double min_trace_length_;
125 double max_trace_length_;
126
127 bool reestimate_mt_sd_;
128 };
129 }
MassTrace.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MassTraceDetection::reestimate_mt_sd_
bool reestimate_mt_sd_
Definition: MassTraceDetection.h:127
OpenMS::MassTraceDetection::trace_termination_criterion_
String trace_termination_criterion_
Definition: MassTraceDetection.h:121
OpenMS::MassTraceDetection::quant_method_
MassTrace::MT_QUANTMETHOD quant_method_
Definition: MassTraceDetection.h:119
OpenMS::MassTraceDetection::chrom_peak_snr_
double chrom_peak_snr_
Definition: MassTraceDetection.h:118
OpenMS::MassTraceDetection
A mass trace extraction method that gathers peaks similar in m/z and moving along retention time...
Definition: MassTraceDetection.h:72
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::MassTraceDetection::min_trace_length_
double min_trace_length_
Definition: MassTraceDetection.h:124
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MassTraceDetection::min_sample_rate_
double min_sample_rate_
Definition: MassTraceDetection.h:123
StandardTypes.h
OpenMS::MassTraceDetection::MapIdxSortedByInt
std::multimap< double, std::pair< Size, Size > > MapIdxSortedByInt
Definition: MassTraceDetection.h:105
OpenMS::MassTraceDetection::max_trace_length_
double max_trace_length_
Definition: MassTraceDetection.h:125
OpenMS::MassTraceDetection::mass_error_ppm_
double mass_error_ppm_
Definition: MassTraceDetection.h:116
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
DefaultParamHandler.h
OpenMS::MassTraceDetection::trace_termination_outliers_
Size trace_termination_outliers_
Definition: MassTraceDetection.h:122
OpenMS::MassTrace::MT_QUANTMETHOD
MT_QUANTMETHOD
Definition: MassTrace.h:66
OpenMS::Internal::AreaIterator
Forward iterator for an area of peaks in an experiment.
Definition: AreaIterator.h:57
OpenMS::MassTraceDetection::noise_threshold_int_
double noise_threshold_int_
Definition: MassTraceDetection.h:117
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127