OpenMS  2.4.0
HyperScore.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
38 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/CONCEPT/Macros.h>
40 #include <vector>
41 
42 namespace OpenMS
43 {
44 
49 struct OPENMS_DLLAPI HyperScore
50 {
51  typedef std::pair<Size, double> IndexScorePair;
52 
53  /* @brief compute the (ln transformed) X!Tandem HyperScore
54  * 1. the dot product of peak intensities between matching peaks in experimental and theoretical spectrum is calculated
55  * 2. the HyperScore is calculated from the dot product by multiplying by factorials of matching b- and y-ions
56  * @note Peak intensities of the theoretical spectrum are typically 1 or TIC normalized, but can also be e.g. ion probabilities
57  * @param fragment_mass_tolerance mass tolerance applied left and right of the theoretical spectrum peak position
58  * @param fragment_mass_tolerance_unit_ppm Unit of the mass tolerance is: Thomson if false, ppm if true
59  * @param exp_spectrum measured spectrum
60  * @param theo_spectrum theoretical spectrum Peaks need to contain an ion annotation as provided by TheoreticalSpectrumGenerator.
61  */
62 // static double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const RichPeakSpectrum& theo_spectrum);
63 
64  static double compute(double fragment_mass_tolerance, bool fragment_mass_tolerance_unit_ppm, const PeakSpectrum& exp_spectrum, const PeakSpectrum& theo_spectrum);
65 
66  private:
67  // helper to compute the log factorial
68  static double logfactorial_(UInt x);
69 };
70 
71 }
72 
73 
An implementation of the X!Tandem HyperScore PSM scoring function.
Definition: HyperScore.h:49
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
std::pair< Size, double > IndexScorePair
Definition: HyperScore.h:51