OpenMS  3.0.0
IsotopeDiffFilter.h
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31 // $Maintainer: Timo Sachsenberg $
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34 //
35 #pragma once
36 
38 #include <cmath>
39 
40 namespace OpenMS
41 {
49  class OPENMS_DLLAPI IsotopeDiffFilter :
50  public FilterFunctor
51  {
52 
53 public:
54 
55  // @name Constructors and Destructors
56  // @{
59 
61  IsotopeDiffFilter(const IsotopeDiffFilter & source);
62 
64  ~IsotopeDiffFilter() override;
65  // @}
66 
67  // @name Operators
68  // @{
70  IsotopeDiffFilter & operator=(const IsotopeDiffFilter & source);
71  // @}
72 
73  // @name Accessors
74  // @{
76  static FilterFunctor * create() { return new IsotopeDiffFilter(); }
77 
79  template <typename SpectrumType>
80  double apply(SpectrumType & spectrum)
81  {
82  double tolerance = (double)param_.getValue("tolerance");
83  double isodiff = 0;
84 
85  //iterate over all peaks
86  for (Size i = 0; i < spectrum.size(); ++i)
87  {
88  for (Size j = 1; i + j < spectrum.size(); ++j)
89  {
90  double pos_ij = spectrum[i + j].getPosition()[0];
91  double pos_i = spectrum[i].getPosition()[0];
92  if (std::fabs(pos_ij - pos_i + 1) < tolerance)
93  {
94  isodiff += spectrum[i].getIntensity() + spectrum[i + j].getIntensity();
95  }
96  else
97  {
98  if (std::fabs(spectrum[i + j].getPosition()[0] - spectrum[i].getPosition()[0]) > 1 + tolerance)
99  {
100  break;
101  }
102  }
103  }
104  }
105  return isodiff;
106  }
107 
109  static const String getProductName()
110  {
111  return "IsotopeDiffFilter";
112  }
113 
114  // @}
115 
116 private:
117  };
118 }
double
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::IsotopeDiffFilter::getProductName
static const String getProductName()
Definition: IsotopeDiffFilter.h:109
OpenMS::IsotopeDiffFilter
IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks.
Definition: IsotopeDiffFilter.h:49
FilterFunctor.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::FilterFunctor
A FilterFunctor extracts some spectrum characteristics for quality assessment.
Definition: FilterFunctor.h:44
OpenMS::IsotopeDiffFilter::create
static FilterFunctor * create()
Definition: IsotopeDiffFilter.h:76
OpenMS::IsotopeDiffFilter::apply
double apply(SpectrumType &spectrum)
Definition: IsotopeDiffFilter.h:80
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66