OpenMS  3.0.0
BernNorm.h
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31 // $Maintainer: Mathias Walzer $
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35 #pragma once
36 
38 
40 
41 #include <map>
42 
43 namespace OpenMS
44 {
56  class OPENMS_DLLAPI BernNorm :
57  public DefaultParamHandler
58  {
59 public:
60 
61  // @name Constructors and Destructors
63  BernNorm();
65 
67  BernNorm(const BernNorm & source);
68 
70  ~BernNorm() override;
72 
73  // @name Operators
74  // @{
76  BernNorm & operator=(const BernNorm & source);
78 
79  // @name Accessors
80  // @{
81 
83  template <typename SpectrumType>
84  void filterSpectrum(SpectrumType & spectrum)
85  {
86  typedef typename SpectrumType::Iterator Iterator;
87  typedef typename SpectrumType::ConstIterator ConstIterator;
88 
89  c1_ = (double)param_.getValue("C1");
90  c2_ = (double)param_.getValue("C2");
91  th_ = (double)param_.getValue("threshold");
92 
93  spectrum.sortByPosition();
94 
95  // find highest peak and ranking
96  double maxint = 0;
97  std::map<double, Size> peakranks;
98  for (ConstIterator it = spectrum.begin(); it != spectrum.end(); ++it)
99  {
100  peakranks[it->getIntensity()] = 0;
101  if (it->getIntensity() > maxint)
102  {
103  maxint = it->getIntensity();
104  }
105  }
106  UInt rank = 0;
107  for (std::map<double, Size>::reverse_iterator mit = peakranks.rbegin(); mit != peakranks.rend(); ++mit)
108  {
109  mit->second = ++rank;
110  }
111 
112  // find maxmz i.e. significant (> threshold * maxpeak) peak with highest m/z
113  double maxmz = 0;
114  for (SignedSize i = spectrum.size() - 1; i >= 0; --i)
115  {
116  if (spectrum[i].getIntensity() > maxint * th_)
117  {
118  maxmz = spectrum[i].getMZ();
119  break;
120  }
121  }
122 
123  // rank
124  for (Iterator it = spectrum.begin(); it != spectrum.end(); )
125  {
126  double newint = c1_ - (c2_ / maxmz) * peakranks[it->getIntensity()];
127  if (newint < 0)
128  {
129  it = spectrum.erase(it);
130  }
131  else
132  {
133  it->setIntensity(newint);
134  ++it;
135  }
136  }
137  return;
138  }
139 
140  void filterPeakSpectrum(PeakSpectrum & spectrum);
141 
142  void filterPeakMap(PeakMap & exp);
143  //TODO reimplement DefaultParamHandler::updateMembers_()
144 
145 private:
146  double c1_;
147  double c2_;
148  double th_;
149 
150  // @}
151 
152  };
153 
154 } // namespace OpenMS
155 
DefaultParamHandler.h
double
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::BernNorm::c1_
double c1_
Definition: BernNorm.h:146
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::BernNorm::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: BernNorm.h:84
OpenMS::BernNorm::c2_
double c2_
Definition: BernNorm.h:147
OpenMS::BernNorm::th_
double th_
Definition: BernNorm.h:148
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Iterator
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::MSSpectrum::Iterator
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:128
OpenMS::BernNorm
BernNorm scales the peaks by ranking them and then scaling them according to rank.
Definition: BernNorm.h:56
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