| OpenMS 2.5.0

NeutralLossDiffFilter.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
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 // @{
59 NeutralLossDiffFilter();
60
62 NeutralLossDiffFilter(const NeutralLossDiffFilter & source);
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 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::NeutralLossDiffFilter::apply
double apply(SpectrumType &spectrum)
Definition: NeutralLossDiffFilter.h:81
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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
double
int
OpenMS::NeutralLossDiffFilter::create
static FilterFunctor * create()
Definition: NeutralLossDiffFilter.h:77
OpenMS::NeutralLossDiffFilter::getProductName
static const String getProductName()
Definition: NeutralLossDiffFilter.h:109
FilterFunctor.h