| OpenMS 2.5.0

ThresholdMower.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
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: Mathias Walzer $
32 // $Authors: Timo Sachsenberg $
33 // --------------------------------------------------------------------------
34 //
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/KERNEL/MSSpectrum.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41
42 namespace OpenMS
43 {
51 class OPENMS_DLLAPI ThresholdMower :
52 public DefaultParamHandler
53 {
54 public:
55
56 // @name Constructors and Destructors
57 // @{
59 ThresholdMower();
61 ~ThresholdMower() override;
62
64 ThresholdMower(const ThresholdMower & source);
66 ThresholdMower & operator=(const ThresholdMower & source);
67 // @}
68
69 // @name Accessors
70 // @{
72
74 template <typename SpectrumType>
75 void filterSpectrum(SpectrumType & spectrum)
76 {
77 threshold_ = ((double)param_.getValue("threshold"));
78 std::vector<Size> indices;
79 for (Size i = 0; i != spectrum.size(); ++i)
80 {
81 if (spectrum[i].getIntensity() >= threshold_)
82 {
83 indices.push_back(i);
84 }
85 }
86 spectrum.select(indices);
87 }
88
89 void filterPeakSpectrum(PeakSpectrum & spectrum);
90
91 void filterPeakMap(PeakMap & exp);
92
93 //TODO reimplement DefaultParamHandler::updateMembers_()
94
95 private:
96 double threshold_;
97
98 // @}
99 };
100
101 }
102
OpenMS::ThresholdMower::threshold_
double threshold_
Definition: ThresholdMower.h:96
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
StandardTypes.h
OpenMS::ThresholdMower
ThresholdMower removes all peaks below a threshold.
Definition: ThresholdMower.h:51
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
DefaultParamHandler.h
MSSpectrum.h
double
OpenMS::MSSpectrum::select
MSSpectrum & select(const std::vector< Size > &indices)
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ThresholdMower::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: ThresholdMower.h:75