| OpenMS 2.5.0

SpectraSTSimilarityScore.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: David Wojnar $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/COMPARISON/SPECTRA/PeakSpectrumCompareFunctor.h>
38 #include <OpenMS/COMPARISON/SPECTRA/BinnedSpectrum.h>
39
40 namespace OpenMS
41 {
42
62 class OPENMS_DLLAPI SpectraSTSimilarityScore :
63 public PeakSpectrumCompareFunctor
64 {
65 public:
66
67 // @name Constructors and Destructors
68 // @{
70 SpectraSTSimilarityScore();
71
73 SpectraSTSimilarityScore(const SpectraSTSimilarityScore & source);
74
76 ~SpectraSTSimilarityScore() override;
77 // @}
78
80 SpectraSTSimilarityScore & operator=(const SpectraSTSimilarityScore & source);
81
85 double operator()(const PeakSpectrum & spec1, const PeakSpectrum & spec2) const override;
89 double operator()(const BinnedSpectrum & bin1, const BinnedSpectrum & bin2) const;
93 double operator()(const PeakSpectrum & spec) const override;
94
103 bool preprocess(PeakSpectrum & spec, float remove_peak_intensity_threshold = 2.01, UInt cut_peaks_below = 1000, Size min_peak_number = 5, Size max_peak_number = 150);
104
105
107 BinnedSpectrum transform(const PeakSpectrum & spec);
108
116 double dot_bias(const BinnedSpectrum & bin1, const BinnedSpectrum & bin2, double dot_product = -1) const;
117
128 double delta_D(double top_hit, double runner_up);
129
138 double compute_F(double dot_product, double delta_D, double dot_bias);
139
140
141
143 static PeakSpectrumCompareFunctor * create() { return new SpectraSTSimilarityScore(); }
144
146 static const String getProductName()
147 {
148 return "SpectraSTSimilarityScore";
149 }
150
151 protected:
152
153
154 };
155
156 }
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeakSpectrumCompareFunctor
Base class for compare functors of spectra, that return a similarity value for two spectra...
Definition: PeakSpectrumCompareFunctor.h:52
PeakSpectrumCompareFunctor.h
BinnedSpectrum.h
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::BinnedSpectrum
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:75
OpenMS::SpectraSTSimilarityScore::getProductName
static const String getProductName()
Reimplemented from PeakSpectrumCompareFunctor.
Definition: SpectraSTSimilarityScore.h:146
OpenMS::SpectraSTSimilarityScore
Similarity score of SpectraST.
Definition: SpectraSTSimilarityScore.h:62
OpenMS::SpectraSTSimilarityScore::create
static PeakSpectrumCompareFunctor * create()
Definition: SpectraSTSimilarityScore.h:143
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127