| OpenMS 2.5.0

NLargest.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Mathias Walzer $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/KERNEL/StandardTypes.h>
40
41 #include <OpenMS/KERNEL/MSSpectrum.h>
42 #include <OpenMS/KERNEL/MSExperiment.h>
43
44 namespace OpenMS
45 {
46
54 class OPENMS_DLLAPI NLargest :
55 public DefaultParamHandler
56 {
57 public:
58
59 // @name Constructors and Destructors
60 // @{
61
63 NLargest();
65 NLargest(UInt n);
67 ~NLargest() override;
68
70 NLargest(const NLargest & source);
72 NLargest & operator=(const NLargest & source);
73
74 // @}
75
77 template <typename SpectrumType>
78 void filterSpectrum(SpectrumType & spectrum)
79 {
80 if (spectrum.size() <= peakcount_) return;
81
82 // sort by reverse intensity
83 spectrum.sortByIntensity(true);
84
85 // keep the n largest peaks if more than n are present
86 std::vector<Size> indices;
87 for (Size i = 0; i != peakcount_; ++i)
88 {
89 indices.push_back(i);
90 }
91 spectrum.select(indices);
92 }
93
94 void filterPeakSpectrum(PeakSpectrum & spectrum);
95
96 void filterPeakMap(PeakMap & exp);
97
98 //TODO reimplement DefaultParamHandler::updateMembers_()
99
100 // @}
101
102 protected:
103 void updateMembers_() override;
104 UInt peakcount_;
105
107 void init_();
108
109 };
110
111 }
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::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
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::NLargest
NLargest removes all but the n largest peaks.
Definition: NLargest.h:54
OpenMS::NLargest::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: NLargest.h:78
OpenMS::MSSpectrum::select
MSSpectrum & select(const std::vector< Size > &indices)
OpenMS::NLargest::peakcount_
UInt peakcount_
Definition: NLargest.h:104
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MSSpectrum::sortByIntensity
void sortByIntensity(bool reverse=false)
Lexicographically sorts the peaks by their intensity.