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AScore.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: David Wojnar, Timo Sachsenberg $
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34 
35 #ifndef OPENMS_ANALYSIS_ID_ASCORE_H
36 #define OPENMS_ANALYSIS_ID_ASCORE_H
37 
38 #include <OpenMS/CONCEPT/Types.h>
40 #include <vector>
41 
42 namespace OpenMS
43 {
44 class PeptideHit;
45 class AASequence;
47 {
50  Size seq_1; // index of best permutation with site in phosphorylated state
51  Size seq_2; // index of permutation with site in unphosphorylated state
52  Size peak_depth; // filtering level that gave rise to maximum discriminatory score
54 };
62 class OPENMS_DLLAPI AScore
63 {
64  public:
66  AScore();
67 
69  ~AScore();
70 
81  PeptideHit compute(PeptideHit & hit, RichPeakSpectrum &real_spectrum, double fragment_mass_tolerance, bool fragment_mass_unit_ppm) const;
82 
84  void computeSiteDeterminingIons(std::vector<RichPeakSpectrum> & th_spectra, ProbablePhosphoSites & candidates, Int charge, std::vector<RichPeakSpectrum> & site_determining_ions) const;
85 
87  std::vector<Size> getSites(AASequence & without_phospho) const;
88 
90  std::vector<std::vector<Size> > computePermutations(std::vector<Size> sites, Int n_phosphorylation_events) const;
91 
93  Size numberOfMatchedIons(const RichPeakSpectrum & th, const RichPeakSpectrum & windows, Size depth, double fragment_mass_tolerance, bool fragment_mass_tolerance_ppm = false) const;
94 
96  double peptideScore(const std::vector<double> & scores) const;
97 
102  void determineHighestScoringPermutations(const std::vector<std::vector<double> > & peptide_site_scores, std::vector<ProbablePhosphoSites> & sites, const std::vector<std::vector<Size> > & permutations) const;
103 
105  double computeCumulativeScore(Size N, Size n, double p) const;
106 };
107 
108 } // namespace OpenMS
109 
110 #endif // OPENMS_ANALYSIS_ID_ASCORE_H
Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the mo...
Definition: AScore.h:62
Size first
Definition: AScore.h:48
Size second
Definition: AScore.h:49
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Size peak_depth
Definition: AScore.h:52
Representation of a peptide hit.
Definition: PeptideHit.h:55
Size seq_1
Definition: AScore.h:50
Definition: AScore.h:46
Size seq_2
Definition: AScore.h:51
int Int
Signed integer type.
Definition: Types.h:96
Size AScore
Definition: AScore.h:53

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:21 using doxygen 1.8.9.1