| OpenMS 2.5.0

ComplementMarker.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/PeakMarker.h>
38
39 #include <map>
40 #include <cmath>
41
42 namespace OpenMS
43 {
51 class OPENMS_DLLAPI ComplementMarker :
52 public PeakMarker
53 {
54 public:
55
56 // @name Constructors and Destructors
58 ComplementMarker();
60
62 ComplementMarker(const ComplementMarker & source);
63
65 ~ComplementMarker() override;
67
68 // @name Operators
70 ComplementMarker & operator=(const ComplementMarker & source);
73
74 // @name Accessors
76 static PeakMarker * create() { return new ComplementMarker(); }
78
80 template <typename SpectrumType>
81 void apply(std::map<double, bool> marked, SpectrumType & spectrum)
82 {
83 if (spectrum.size() < 2)
84 {
85 return;
86 }
87
88 // how often a peak needs to be marked to be returned
89 double marks = (double)param_.getValue("marks");
90 double parentmass = 0.0;
91 if (!spectrum.getPrecursors().empty()) parentmass = spectrum.getPrecursors()[0].getMZ();
92 double tolerance = (double)param_.getValue("tolerance");
93 std::map<double, int> matching_b_y_ions;
94
95 spectrum.sortByPosition();
96
97 SignedSize j = spectrum.size() - 1;
98 for (Size i = 0; i < spectrum.size(); ++i)
99 {
100 while (j >= 0 && spectrum[j].getPosition()[0] > (parentmass - spectrum[i].getPosition()[0]) + tolerance)
101 {
102 j--;
103 }
104
105 // just takes the first matching ion; todo take all
106 if (j >= 0 && std::fabs(spectrum[i].getPosition()[0] + spectrum[j].getPosition()[0] - parentmass) < tolerance)
107 {
108 matching_b_y_ions[spectrum[i].getPosition()[0]]++;
109 matching_b_y_ions[spectrum[j].getPosition()[0]]++;
110 j--;
111 }
112 }
113
114 for (std::map<double, int>::const_iterator cmit = matching_b_y_ions.begin(); cmit != matching_b_y_ions.end(); ++cmit)
115 {
116 if (cmit->second >= marks)
117 {
118 marked.insert(std::pair<double, bool>(cmit->first, true));
119 }
120 }
121 }
122
124 static const String getProductName()
125 {
126 return "ComplementMarker";
127 }
128
130
131 };
132
133 }
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ComplementMarker::apply
void apply(std::map< double, bool > marked, SpectrumType &spectrum)
Definition: ComplementMarker.h:81
OpenMS::PeakMarker
PeakMarker marks peaks that seem to fulfill some criterion.
Definition: PeakMarker.h:47
OpenMS::SpectrumSettings::getPrecursors
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
PeakMarker.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ComplementMarker
ComplementMarker marks peak pairs which could represent y - b ion pairs.
Definition: ComplementMarker.h:51
double
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::ComplementMarker::getProductName
static const String getProductName()
returns the name to register at the factory
Definition: ComplementMarker.h:124
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127