| OpenMS 2.5.0

MarkerMower.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: Mathias Walzer $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/FILTERING/TRANSFORMERS/PeakMarker.h>
40
41 #include <OpenMS/KERNEL/MSSpectrum.h>
42 #include <OpenMS/KERNEL/MSExperiment.h>
43
44 #include <vector>
45 #include <map>
46
47 namespace OpenMS
48 {
54 class OPENMS_DLLAPI MarkerMower :
55 public DefaultParamHandler
56 {
57 public:
58
59 // @name Constructors and Destructors
60 // @{
62 MarkerMower();
64 ~MarkerMower() override;
65
67 MarkerMower(const MarkerMower & source);
69 MarkerMower & operator=(const MarkerMower & source);
70 // @}
71
72 // @name Accessors
73 // @{
75 template <typename SpectrumType>
76 void filterSpectrum(SpectrumType & spectrum)
77 {
78 typedef typename SpectrumType::Iterator Iterator;
79
80 std::map<double, int> marks;
81 for (std::vector<PeakMarker *>::const_iterator cvit = markers_.begin(); cvit != markers_.end(); ++cvit)
82 {
83 std::map<double, bool> marked;
84 (*cvit)->apply(marked, spectrum);
85 for (std::map<double, bool>::const_iterator cmit = marked.begin(); cmit != marked.end(); ++cmit)
86 {
87 if (cmit->second)
88 {
89 marks[cmit->first]++;
90 }
91 }
92 }
93
94 for (Iterator it = spectrum.begin(); it != spectrum.end(); )
95 {
96 if (marks[it->getMZ()] > 0)
97 {
98 ++it;
99 }
100 else
101 {
102 it = spectrum.erase(it);
103 }
104 }
105 }
106
107 void filterPeakSpectrum(PeakSpectrum & spectrum);
108
109 void filterPeakMap(PeakMap & exp);
110
111 static const String getProductName()
112 {
113 return "MarkerMower";
114 }
115
117 void insertmarker(PeakMarker * peak_marker);
118
119 //TODO reimplement DefaultParamHandler::updateMembers_()
120
121 // @}
122
123 private:
125 std::vector<PeakMarker *> markers_;
126
127 };
128 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MarkerMower::markers_
std::vector< PeakMarker * > markers_
used peak markers
Definition: MarkerMower.h:125
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::MSSpectrum::Iterator
ContainerType::iterator Iterator
Mutable iterator.
Definition: MSSpectrum.h:102
StandardTypes.h
OpenMS::PeakMarker
PeakMarker marks peaks that seem to fulfill some criterion.
Definition: PeakMarker.h:47
Iterator
PeakMarker.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::MarkerMower::getProductName
static const String getProductName()
Definition: MarkerMower.h:111
OpenMS::MarkerMower::filterSpectrum
void filterSpectrum(SpectrumType &spectrum)
Definition: MarkerMower.h:76
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
DefaultParamHandler.h
MSSpectrum.h
OpenMS::MarkerMower
MarkerMower uses PeakMarker to find peaks, those that are not marked get removed. ...
Definition: MarkerMower.h:54