| OpenMS 2.5.0

Normalizer.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: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34 //
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38
39 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
40
41 #include <OpenMS/KERNEL/MSSpectrum.h>
42 #include <OpenMS/KERNEL/MSExperiment.h>
43
44 #include <vector>
45
46 namespace OpenMS
47 {
57 class OPENMS_DLLAPI Normalizer :
58 public DefaultParamHandler
59 {
60 public:
61
62 // @name Constructors and Destructors
63 // @{
65 Normalizer();
67 ~Normalizer() override;
68
70 Normalizer & operator=(const Normalizer & source);
72 Normalizer(const Normalizer & source);
73
74 // @}
75
76 // @name Accessors
77 // @{
78
85 template <typename SpectrumType>
86 void filterSpectrum(SpectrumType& spectrum) const
87 {
88 if (spectrum.empty()) return;
89
90 typedef typename SpectrumType::Iterator Iterator;
91 typedef typename SpectrumType::ConstIterator ConstIterator;
92
93 double divisor(0);
94 // find divisor
95 if (method_ == "to_one")
96 { // normalizes the max peak to 1 and the remaining peaks to values relative to max
97 divisor = spectrum.begin()->getIntensity(); // safety measure: if all intensities are negative, divisor would stay 0 (as constructed)
98 for (ConstIterator it = spectrum.begin(); it != spectrum.end(); ++it)
99 {
100 if (divisor < it->getIntensity()) divisor = it->getIntensity();
101 }
102 }
103 else if (method_ == "to_TIC")
104 { // normalizes the peak intensities to the TIC
105 for (ConstIterator it = spectrum.begin(); it != spectrum.end(); ++it)
106 {
107 divisor += it->getIntensity();
108 }
109 }
110 // method unknown
111 else
112 {
113 throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Method not known", method_);
114 }
115
116 // normalize
117 for (Iterator it = spectrum.begin(); it != spectrum.end(); ++it)
118 {
119 it->setIntensity(it->getIntensity() / divisor);
120 }
121
122 return;
123
124 }
125
127 void filterPeakSpectrum(PeakSpectrum & spectrum) const;
129 void filterPeakMap(PeakMap & exp) const;
130
131 void updateMembers_() override;
132
133 // @}
134
135 private:
136 String method_;
137 };
138
139
140 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Normalizer
Normalizes the peak intensities spectrum-wise.
Definition: Normalizer.h:57
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::Normalizer::filterSpectrum
void filterSpectrum(SpectrumType &spectrum) const
Definition: Normalizer.h:86
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
Iterator
OpenMS::Normalizer::method_
String method_
Definition: Normalizer.h:136
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::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:335
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104