| OpenMS 2.5.0

Scaler.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: 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/MSSpectrum.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41
42 #include <map>
43
44 namespace OpenMS
45 {
51 class OPENMS_DLLAPI Scaler :
52 public DefaultParamHandler
53 {
54 public:
55
56 // @name Constructors and Destructors
57 // @{
59 Scaler();
61 ~Scaler() override;
62
64 Scaler(const Scaler & source);
66 Scaler & operator=(const Scaler & source);
67
68 // @}
69
70 // @name Accessors
71 // @{
72
73 template <typename SpectrumType>
74 void filterSpectrum(SpectrumType & spectrum)
75 {
76 if (spectrum.empty()) return;
77
78 spectrum.sortByIntensity();
79 typename SpectrumType::size_type count = spectrum.size();
80 ++count;
81 typename SpectrumType::PeakType::IntensityType last_int = 0.0;
82 typename SpectrumType::Iterator it = spectrum.end();
83 do
84 {
85 --it;
86 if (it->getIntensity() != last_int)
87 {
88 --count;
89 }
90 last_int = it->getIntensity();
91 it->setIntensity(count);
92 }
93 while (it != spectrum.begin());
94 }
95
96 void filterPeakSpectrum(PeakSpectrum & spectrum);
97
98 void filterPeakMap(PeakMap & exp);
99
100 //TODO reimplement DefaultParamHandler::updateMembers_() when introducing member variables
101
102 // @}
103
104 };
105
106 }
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::Peak1D::IntensityType
float IntensityType
Intensity type.
Definition: Peak1D.h:63
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MSSpectrum::Iterator
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:102
StandardTypes.h
OpenMS::Scaler::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: Scaler.h:74
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::Scaler
Scaler scales the peak by ranking the peaks and assigning intensity according to rank.
Definition: Scaler.h:51
DefaultParamHandler.h
MSSpectrum.h
OpenMS::MSSpectrum::sortByIntensity
void sortByIntensity(bool reverse=false)
Lexicographically sorts the peaks by their intensity.