| OpenMS 2.5.0

SpectrumCheapDPCorr.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/KERNEL/StandardTypes.h>
38 #include <OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h>
39 #include <OpenMS/DATASTRUCTURES/Map.h>
40
41 #include <OpenMS/KERNEL/MSSpectrum.h>
42 #include <OpenMS/KERNEL/MSExperiment.h>
43
44 namespace OpenMS
45 {
46
60 class OPENMS_DLLAPI SpectrumCheapDPCorr :
61 public PeakSpectrumCompareFunctor
62 {
63 public:
64
65 // @name Constructors and Destructors
66 // @{
68 SpectrumCheapDPCorr();
69
71 SpectrumCheapDPCorr(const SpectrumCheapDPCorr & source);
72
74 ~SpectrumCheapDPCorr() override;
75 // @}
76
77 // @name Operators
78 // @{
80 SpectrumCheapDPCorr & operator=(const SpectrumCheapDPCorr & source);
81
82 double operator()(const PeakSpectrum & a, const PeakSpectrum & b) const override;
83
84 double operator()(const PeakSpectrum & a) const override;
85 // @}
86
87 // @name Accessors
88 // @{
90 static PeakSpectrumCompareFunctor * create() { return new SpectrumCheapDPCorr(); }
91
93 static const String getProductName()
94 {
95 return "SpectrumCheapDPCorr";
96 }
97
99 const PeakSpectrum & lastconsensus() const;
100
102 Map<UInt, UInt> getPeakMap() const;
103
105 void setFactor(double f);
106 // @}
107
108 private:
109
111 double dynprog_(const PeakSpectrum &, const PeakSpectrum &, int, int, int, int) const;
112
114 double comparepeaks_(double posa, double posb, double inta, double intb) const;
115
116 static const String info_;
117
119 mutable PeakSpectrum lastconsensus_;
120
122 bool keeppeaks_;
123
125 mutable double factor_;
126
128 mutable Map<UInt, UInt> peak_map_;
129 };
130
131 }
OpenMS::SpectrumCheapDPCorr::create
static PeakSpectrumCompareFunctor * create()
Definition: SpectrumCheapDPCorr.h:90
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SpectrumCheapDPCorr::lastconsensus_
PeakSpectrum lastconsensus_
consensus spectrum of the last comparison
Definition: SpectrumCheapDPCorr.h:119
StandardTypes.h
OpenMS::SpectrumCheapDPCorr
SpectrumCheapDPCorr calculates an optimal alignment on stick spectra.
Definition: SpectrumCheapDPCorr.h:60
OpenMS::SpectrumCheapDPCorr::info_
static const String info_
Definition: SpectrumCheapDPCorr.h:116
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::Map< UInt, UInt >
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::SpectrumCheapDPCorr::getProductName
static const String getProductName()
Definition: SpectrumCheapDPCorr.h:93
OpenMS::PeakSpectrumCompareFunctor
Base class for compare functors of spectra, that return a similarity value for two spectra...
Definition: PeakSpectrumCompareFunctor.h:52
PeakSpectrumCompareFunctor.h
Map.h
MSSpectrum.h
OpenMS::SpectrumCheapDPCorr::factor_
double factor_
weighting factor for the next consensus spectrum
Definition: SpectrumCheapDPCorr.h:125
OpenMS::SpectrumCheapDPCorr::keeppeaks_
bool keeppeaks_
should peaks with no alignment partner be kept in the consensus?
Definition: SpectrumCheapDPCorr.h:122
OpenMS::SpectrumCheapDPCorr::peak_map_
Map< UInt, UInt > peak_map_
last peak map
Definition: SpectrumCheapDPCorr.h:128