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FeatureFinderAlgorithmIsotopeWavelet.h
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithm.h>
38
39 namespace OpenMS
40 {
59 class OPENMS_DLLAPI FeatureFinderAlgorithmIsotopeWavelet :
60 public FeatureFinderAlgorithm
61 {
62 public:
63
64 typedef FeatureFinderAlgorithm Base;
65 typedef Peak1D PeakType;
66
68 FeatureFinderAlgorithmIsotopeWavelet();
69
71 ~FeatureFinderAlgorithmIsotopeWavelet() override;
72
73 MSSpectrum* createHRData(const UInt i);
74
76 void run() override;
77
78 static const String getProductName();
79
80 static FeatureFinderAlgorithm* create();
81
82 protected:
83
85 struct BoxElement
86 {
87 double mz;
88 UInt c;
89 double score;
90 double intens;
91 double RT;
92 };
93
94 typedef std::map<UInt, BoxElement> Box;
95
96 UInt max_charge_;
97 double intensity_threshold_;
98 UInt RT_votes_cutoff_, real_RT_votes_cutoff_, RT_interleave_;
99 String use_gpus_, intensity_type_;
100 bool check_PPMs_, hr_data_;
101 std::vector<UInt> gpu_ids_;
102
103 Int progress_counter_;
104
105 void updateMembers_() override;
106
107 };
108
109 } //namespace
110
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::gpu_ids_
std::vector< UInt > gpu_ids_
A list of all GPU devices that can be used.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:101
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::Base
FeatureFinderAlgorithm Base
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:64
OpenMS::String
A more convenient string class.
Definition: String.h:58
FeatureFinderAlgorithm.h
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::score
double score
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:89
OpenMS::FeatureFinderAlgorithm
Abstract base class for FeatureFinder algorithms.
Definition: FeatureFinderAlgorithm.h:74
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::RT
double RT
The elution time (not the scan index)
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:91
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement
Internally used data structure for the sweep line algorithm.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:85
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::intens
double intens
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:90
OpenMS::FeatureFinderAlgorithmIsotopeWavelet
Implements the isotope wavelet feature finder.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:59
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::hr_data_
bool hr_data_
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:100
OpenMS::Peak1D
A 1-dimensional raw data point or peak.
Definition: Peak1D.h:54
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::mz
double mz
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:87
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::use_gpus_
String use_gpus_
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:99
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::PeakType
Peak1D PeakType
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:65
int
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::intensity_threshold_
double intensity_threshold_
The only parameter of the isotope wavelet.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:97
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::BoxElement::c
UInt c
Note, this is not the charge (it is charge-1!!!)
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:88
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::max_charge_
UInt max_charge_
The maximal charge state we will consider.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:96
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::Box
std::map< UInt, BoxElement > Box
Key: RT (index), value: BoxElement.
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:94
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::RT_votes_cutoff_
UInt RT_votes_cutoff_
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:98
OpenMS::FeatureFinderAlgorithmIsotopeWavelet::progress_counter_
Int progress_counter_
Definition: FeatureFinderAlgorithmIsotopeWavelet.h:103