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Normalizer.h
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35 #ifndef OPENMS_FILTERING_TRANSFORMERS_NORMALIZER_H
36 #define OPENMS_FILTERING_TRANSFORMERS_NORMALIZER_H
37 
39 
41 
42 #include <vector>
43 
44 namespace OpenMS
45 {
53  class OPENMS_DLLAPI Normalizer :
54  public DefaultParamHandler
55  {
56 public:
57 
58  // @name Constructors and Destructors
59  // @{
61  Normalizer();
63  virtual ~Normalizer();
64 
66  Normalizer & operator=(const Normalizer & source);
68  Normalizer(const Normalizer & source);
69 
70  // @}
71 
72  // @name Accessors
73  // @{
74 
76  template <typename SpectrumType>
77  void filterSpectrum(SpectrumType & spectrum)
78  {
79  typedef typename SpectrumType::Iterator Iterator;
80  typedef typename SpectrumType::ConstIterator ConstIterator;
81 
82  method_ = param_.getValue("method");
83 
84  // normalizes the max peak to 1 and the rest of the peaks to values relative to max
85  if (method_ == "to_one")
86  {
87  double max(0);
88  for (ConstIterator it = spectrum.begin(); it != spectrum.end(); ++it)
89  {
90  if (max < it->getIntensity())
91  {
92  max = it->getIntensity();
93  }
94  }
95  for (Iterator it = spectrum.begin(); it != spectrum.end(); ++it)
96  {
97  it->setIntensity(it->getIntensity() / max);
98  }
99  }
100  // normalizes the peak intensities to the TIC
101  else if (method_ == "to_TIC")
102  {
103  double sum(0);
104  for (ConstIterator it = spectrum.begin(); it != spectrum.end(); ++it)
105  {
106  sum += it->getIntensity();
107  }
108 
109  for (Iterator it = spectrum.begin(); it != spectrum.end(); ++it)
110  {
111  it->setIntensity(it->getIntensity() / sum);
112  }
113  }
114  // method unknown
115  else
116  {
117  throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Method not known", method_);
118  }
119  return;
120 
121  }
122 
124  void filterPeakSpectrum(PeakSpectrum & spectrum);
126  void filterPeakMap(PeakMap & exp);
127 
128  //TODO reimplement DefaultParamHandler::updateMembers_()
129 
130  // @}
131 
132 private:
134 
135  };
136 
137 
138 }
139 #endif //OPENMS_FILTERING_TRANSFORMERS_NORMALIZER_H
A more convenient string class.
Definition: String.h:57
static double sum(IteratorType begin, IteratorType end)
Calculates the sum of a range of values.
Definition: StatisticFunctions.h:118
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Invalid value exception.
Definition: Exception.h:336
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Normalizer normalizes the peak intensities.
Definition: Normalizer.h:53
void filterSpectrum(SpectrumType &spectrum)
Definition: Normalizer.h:77
String method_
Definition: Normalizer.h:133

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11