| OpenMS 2.5.0

GoodDiffFilter.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <OpenMS/FILTERING/TRANSFORMERS/FilterFunctor.h>
39
40 #include <map>
41 #include <string>
42 #include <cmath>
43
44 namespace OpenMS
45 {
53 class OPENMS_DLLAPI GoodDiffFilter :
54 public FilterFunctor
55 {
56 public:
57
58 // @name Constructors and Destructors
59 // @{
61 GoodDiffFilter();
62
64 GoodDiffFilter(const GoodDiffFilter & source);
65
67 ~GoodDiffFilter() override;
68 // @}
69
70 // @name Operators
71 // @{
73 GoodDiffFilter & operator=(const GoodDiffFilter & source);
74 // @}
75
76 // @name Accessors
77 // @{
79 static FilterFunctor * create() { return new GoodDiffFilter(); }
80
82 template <typename SpectrumType>
83 double apply(SpectrumType & spectrum)
84 {
85 double tolerance = (double)param_.getValue("tolerance");
86 double gooddiff = 0;
87 //iterate over all peaks
88 double totaldiff = 0;
89 for (Size i = 0; i < spectrum.size(); ++i)
90 {
91 //look for each peakdifference that is in range of aa residuemasses (56/187), if it could be a aa (aamass)
92 for (Size j = i; i + j < spectrum.size(); ++j)
93 {
94 double diff = spectrum[i + j].getPosition()[0] - spectrum[i].getPosition()[0];
95 if (diff < 56)
96 {
97 continue;
98 }
99
100 if (diff > 187)
101 {
102 j = spectrum.size();
103 }
104 else
105 {
106 totaldiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
107 std::map<double, char>::const_iterator aait = aamass_.lower_bound(diff);
108 if (aait == aamass_.end())
109 {
110 continue;
111 }
112 //look for aamasses that fit diff
113 if (fabs(aait->first - diff) <= tolerance)
114 {
115 gooddiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
116 }
117 else
118 {
119 ++aait;
120 if ((aait) != aamass_.end() && fabs((aait)->first - diff) <= tolerance)
121 {
122 gooddiff += spectrum[i + j].getIntensity() + spectrum[i].getIntensity();
123 }
124 }
125 }
126 }
127 }
128
129 return gooddiff / totaldiff;
130 }
131
133 static const String getProductName()
134 {
135 return "GoodDiffFilter";
136 }
137
138 // @}
139
140
141 private:
142
144 std::map<double, char> aamass_;
145 };
146 }
147
OpenMS::GoodDiffFilter::aamass_
std::map< double, char > aamass_
list of unique amino acid masses
Definition: GoodDiffFilter.h:144
OpenMS::GoodDiffFilter::getProductName
static const String getProductName()
Definition: GoodDiffFilter.h:133
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::GoodDiffFilter::apply
double apply(SpectrumType &spectrum)
Definition: GoodDiffFilter.h:83
OpenMS::GoodDiffFilter
GoodDiffFilter counts the number ob peak pairs whose m/z difference can be explained by a amino acid ...
Definition: GoodDiffFilter.h:53
OpenMS::GoodDiffFilter::create
static FilterFunctor * create()
Definition: GoodDiffFilter.h:79
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
double
FilterFunctor.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127