OpenMS  2.8.0
SpectraSTSimilarityScore.h
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31 // $Maintainer: Timo Sachsenberg $
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34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
42 
62  class OPENMS_DLLAPI SpectraSTSimilarityScore :
64  {
65 public:
66 
67  // @name Constructors and Destructors
68  // @{
71 
74 
77  // @}
78 
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 
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 
144 
146  static const String getProductName()
147  {
148  return "SpectraSTSimilarityScore";
149  }
150 
151 protected:
152 
153 
154  };
155 
156 }
This is a binned representation of a PeakSpectrum.
Definition: BinnedSpectrum.h:81
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
Base class for compare functors of spectra, that return a similarity value for two spectra.
Definition: PeakSpectrumCompareFunctor.h:54
Similarity score of SpectraST.
Definition: SpectraSTSimilarityScore.h:64
SpectraSTSimilarityScore & operator=(const SpectraSTSimilarityScore &source)
assignment operator
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)
Preprocesses the spectrum.
double delta_D(double top_hit, double runner_up)
calculates the normalized distance between top_hit and runner_up.
~SpectraSTSimilarityScore() override
destructor
double dot_bias(const BinnedSpectrum &bin1, const BinnedSpectrum &bin2, double dot_product=-1) const
Calculates how much of the dot product is dominated by a few peaks.
double operator()(const BinnedSpectrum &bin1, const BinnedSpectrum &bin2) const
: calculates the dot product of the two spectra
SpectraSTSimilarityScore()
default constructor
double operator()(const PeakSpectrum &spec1, const PeakSpectrum &spec2) const override
: calculates the dot product of the two spectra
double operator()(const PeakSpectrum &spec) const override
: calculates the dot product of itself
SpectraSTSimilarityScore(const SpectraSTSimilarityScore &source)
copy constructor
BinnedSpectrum transform(const PeakSpectrum &spec)
spectrum is transformed into a binned spectrum with bin size 1 and spread 1 and the intensities are n...
static PeakSpectrumCompareFunctor * create()
Definition: SpectraSTSimilarityScore.h:143
double compute_F(double dot_product, double delta_D, double dot_bias)
computes the overall all score
static const String getProductName()
Reimplemented from PeakSpectrumCompareFunctor.
Definition: SpectraSTSimilarityScore.h:146
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47