OpenMS  3.0.0
NeutralLossDiffFilter.h
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31 // $Maintainer: Timo Sachsenberg $
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34 //
35 #pragma once
36 
38 
39 #include <map>
40 #include <cmath>
41 
42 namespace OpenMS
43 {
51  class OPENMS_DLLAPI NeutralLossDiffFilter :
52  public FilterFunctor
53  {
54 public:
55 
56  // @name Constructors and Destructors
57  // @{
60 
63 
65  ~NeutralLossDiffFilter() override;
66  // @}
67 
68  // @name Operators
69  // @{
71  NeutralLossDiffFilter & operator=(const NeutralLossDiffFilter & source);
72  // @}
73 
74  // @name Accessors
75  // @{
77  static FilterFunctor * create() { return new NeutralLossDiffFilter(); }
78 
80  template <typename SpectrumType>
81  double apply(SpectrumType & spectrum)
82  {
83  double tolerance = (double)param_.getValue("tolerance");
84  double isodiff = 0;
85  //iterate over all peaks
86  for (int i = 0; i < (int)spectrum.size(); ++i)
87  {
88  for (int j = 1; i - j >= 0; ++j)
89  {
90  double pos_diff = std::fabs(spectrum[i - j].getPosition()[0] - spectrum[i].getPosition()[0]);
91  if (std::fabs(pos_diff - 18) < tolerance || std::fabs(pos_diff - 17) < tolerance) // water and ammonium
92  {
93  isodiff += spectrum[i - j].getIntensity() + spectrum[i].getIntensity();
94  }
95  else
96  {
97  if (pos_diff > 18 + tolerance)
98  {
99  break;
100  }
101  }
102  }
103  }
104 
105  return isodiff;
106  }
107 
109  static const String getProductName()
110  {
111  return "NeutralLossDiffFilter";
112  }
113 
114  // @}
115 
116  };
117 }
double
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::NeutralLossDiffFilter::apply
double apply(SpectrumType &spectrum)
Definition: NeutralLossDiffFilter.h:81
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::NeutralLossDiffFilter
NeutralLossDiffFilter returns the total intensity ob peak pairs whose m/z difference can be explained...
Definition: NeutralLossDiffFilter.h:51
OpenMS::NeutralLossDiffFilter::getProductName
static const String getProductName()
Definition: NeutralLossDiffFilter.h:109
OpenMS::NeutralLossDiffFilter::create
static FilterFunctor * create()
Definition: NeutralLossDiffFilter.h:77
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66