| OpenMS 2.5.0

IsotopeMarker.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 #include <OpenMS/CHEMISTRY/ISOTOPEDISTRIBUTION/CoarseIsotopePatternGenerator.h>
39
40 #include <map>
41 #include <vector>
42 #include <cmath>
43 #include <utility>
44
45 namespace OpenMS
46 {
47
57 class OPENMS_DLLAPI IsotopeMarker :
58 public PeakMarker
59 {
60 public:
61
62 // @name Constructors and Destructors
63 // @{
65 IsotopeMarker();
66
68 IsotopeMarker(const IsotopeMarker & source);
69
71 ~IsotopeMarker() override;
72 // @}
73
74 // @name Operators
75 // @{
77 IsotopeMarker & operator=(const IsotopeMarker & source);
78 // @}
79
80 // @name Accessors
81 // @{
83 static PeakMarker * create() { return new IsotopeMarker(); }
84
86 template <typename SpectrumType>
87 void apply(std::map<double, bool> & marked, SpectrumType & spectrum)
88 {
89 double mzvariation = (double)param_.getValue("mz_variation");
90 double invariation = (double)param_.getValue("in_variation");
91 Size marks = param_.getValue("marks");
92
93 spectrum.sortByPosition();
94
95 std::map<double, Size> isotopemarks; // possible isotopes
96
97 for (Size i = 0; i < spectrum.size(); ++i)
98 {
99 double mz = spectrum[i].getPosition()[0];
100 double intensity = spectrum[i].getIntensity();
101 Size j = i + 1;
102
103 //std::vector<std::pair<double, double> > isotopes = SpectrumGenerator::instance()->isotopepeaks(mz, intensity);
104 CoarseIsotopePatternGenerator solver;
105 auto id = solver.estimateFromPeptideWeight(mz);
106
107 while (j < spectrum.size() && spectrum[j].getPosition()[0] <= mz + 3 + mzvariation)
108 {
109 double curmz = spectrum[j].getPosition()[0];
110 double curIntensity = spectrum[j].getIntensity();
111 UInt iso = (UInt)(curmz - mz + 0.499999);
112 if (iso > 0 && curmz - mz - iso > mzvariation)
113 {
114 ++j;
115 continue;
116 }
117 if (std::fabs(id.begin()->getIntensity() * intensity - curIntensity) < invariation * id.begin()->getIntensity() * intensity)
118 {
119 isotopemarks[mz]++;
120 isotopemarks[curmz]++;
121 }
122 ++j;
123 }
124 }
125
126 for (std::map<double, Size>::const_iterator cmit = isotopemarks.begin(); cmit != isotopemarks.end(); ++cmit)
127 {
128 if (cmit->second >= marks)
129 {
130 marked.insert(std::pair<double, bool>(cmit->first, true));
131 }
132 }
133 return;
134 }
135
137 static const String getProductName()
138 {
139 return "IsotopeMarker";
140 }
141
142 // @}
143
144 };
145
146 }
147
OpenMS::IsotopeMarker::apply
void apply(std::map< double, bool > &marked, SpectrumType &spectrum)
Definition: IsotopeMarker.h:87
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::PeakMarker
PeakMarker marks peaks that seem to fulfill some criterion.
Definition: PeakMarker.h:47
PeakMarker.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
CoarseIsotopePatternGenerator.h
OpenMS::IsotopeMarker::getProductName
static const String getProductName()
Definition: IsotopeMarker.h:137
OpenMS::CoarseIsotopePatternGenerator::estimateFromPeptideWeight
IsotopeDistribution estimateFromPeptideWeight(double average_weight)
Estimate Peptide Isotopedistribution from weight and number of isotopes that should be reported...
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
double
OpenMS::MSSpectrum::sortByPosition
void sortByPosition()
Lexicographically sorts the peaks by their position.
OpenMS::IsotopeMarker::create
static PeakMarker * create()
Definition: IsotopeMarker.h:83
OpenMS::CoarseIsotopePatternGenerator
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:96
OpenMS::IsotopeMarker
IsotopeMarker marks peak pairs which could represent an ion and its isotope.
Definition: IsotopeMarker.h:57
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127