| OpenMS 2.5.0

IsotopeDiffFilter.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 #pragma once
36
37 #include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
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 // @{
58 IsotopeDiffFilter();
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 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IsotopeDiffFilter::apply
double apply(SpectrumType &spectrum)
Definition: IsotopeDiffFilter.h:80
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::IsotopeDiffFilter
IsotopeDiffFilter returns total intensity of peak pairs that could result from isotope peaks...
Definition: IsotopeDiffFilter.h:49
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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
double
OpenMS::IsotopeDiffFilter::getProductName
static const String getProductName()
Definition: IsotopeDiffFilter.h:109
FilterFunctor.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127