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AScore.h
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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  {
54  };
62  class OPENMS_DLLAPI AScore
63  {
64 public:
66  AScore();
68  ~AScore();
69 
80  PeptideHit compute(PeptideHit & hit, RichPeakSpectrum & real_spectrum, DoubleReal fmt, Int number_of_phospho_sites);
81 
83  DoubleReal computeCumulativeScore(UInt N, UInt n, DoubleReal p);
84 
89  void computeHighestPeptides(std::vector<std::vector<DoubleReal> > & peptide_site_scores, std::vector<ProbablePhosphoSites> & sites, std::vector<std::vector<Size> > & permutations);
91  void compute_site_determining_ions(std::vector<RichPeakSpectrum> & th_spectra, ProbablePhosphoSites & candidates, Int charge, std::vector<RichPeakSpectrum> & site_determining_ions);
92 private:
94  Int numberOfMatchedIons_(const RichPeakSpectrum & th, const RichPeakSpectrum & windows, Size depth, DoubleReal fmt);
96  DoubleReal peptideScore_(std::vector<DoubleReal> & scores);
97 public:
99  std::vector<Size> computeTupel_(AASequence & without_phospho);
101  std::vector<std::vector<Size> > computePermutations_(std::vector<Size> tupel, Int number_of_phospho_sites);
102  };
103 
104 } // namespace OpenMS
105 
106 #endif // OPENMS_ANALYSIS_ID_ASCORE_H
Implementation of the Ascore For a given peptide sequence and its MS^2 spectrum it is tried to identi...
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:84
Size peak_depth
Definition: AScore.h:52
Representation of a peptide hit.
Definition: PeptideHit.h:54
Size seq_1
Definition: AScore.h:50
Definition: AScore.h:46
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
Size seq_2
Definition: AScore.h:51
int Int
Signed integer type.
Definition: Types.h:100
Size AScore
Definition: AScore.h:53

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:11 using doxygen 1.8.5