OpenMS  3.0.0
Normalizer.h
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31 // $Maintainer: Mathias Walzer $
32 // $Authors: Andreas Bertsch $
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34 //
35 #pragma once
36 
38 
40 
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:
137  };
138 
139 
140 }
DefaultParamHandler.h
OpenMS::Normalizer
Normalizes the peak intensities spectrum-wise.
Definition: Normalizer.h:57
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:327
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Normalizer::filterSpectrum
void filterSpectrum(SpectrumType &spectrum) const
Workhorse of this class.
Definition: Normalizer.h:86
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Iterator
OpenMS::Normalizer::method_
String method_
Definition: Normalizer.h:136
MSExperiment.h
OpenMS::MSSpectrum::Iterator
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:128
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:130
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
StandardTypes.h
MSSpectrum.h