OpenMS  3.0.0
AScore.h
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31 // $Maintainer: Petra Gutenbrunner $
32 // $Authors: David Wojnar, Timo Sachsenberg, Petra Gutenbrunner $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
43 
44 #include <limits>
45 #include <vector>
46 
47 namespace OpenMS
48 {
49  class PeptideHit;
50  class AASequence;
51 
53  {
54  public:
55 
62  };
63 
72  class OPENMS_DLLAPI AScore: public DefaultParamHandler
73  {
74  friend struct PScore;
75 
76  public:
78  AScore();
79 
81  ~AScore() override;
82 
91  PeptideHit compute(const PeptideHit& hit, PeakSpectrum& real_spectrum);
92 
93  protected:
94  int compareMZ_(double mz1, double mz2) const;
95 
99  template <class InputIterator1, class InputIterator2, class OutputIterator>
100  OutputIterator getSpectrumDifference_(InputIterator1 first1, InputIterator1 last1,
101  InputIterator2 first2, InputIterator2 last2, OutputIterator result) const
102  {
103  while (first1 != last1 && first2 != last2)
104  {
105  double mz1 = first1->getMZ();
106  double mz2 = first2->getMZ();
107  int val = compareMZ_(mz1, mz2);
108 
109  if (val == -1)
110  {
111  *result = *first1;
112  ++result;
113  ++first1;
114  }
115  else if (val == 1)
116  {
117  ++first2;
118  }
119  else // check if more ions are within the same tolerance. If so, these can not be site determining ions
120  {
121  //check mz2 until no match
122  ++first2;
123  if (first2 != last2)
124  {
125  int ret = compareMZ_(mz1, first2->getMZ());
126  while (ret == 0 && first2 != last2)
127  {
128  ++first2;
129  ret = compareMZ_(mz1, first2->getMZ());
130  }
131  }
132 
133  //check mz1 until no match
134  ++first1;
135  if (first1 != last1)
136  {
137  int ret = compareMZ_(first1->getMZ(), mz2);
138  while (ret == 0 && first1 != last1)
139  {
140  ++first1;
141  ret = compareMZ_(first1->getMZ(), mz2);
142  }
143  }
144  }
145  }
146  return std::copy(first1, last1, result);
147  }
148 
150  void computeSiteDeterminingIons_(const std::vector<PeakSpectrum>& th_spectra, const ProbablePhosphoSites& candidates, std::vector<PeakSpectrum>& site_determining_ions) const;
151 
153  std::vector<Size> getSites_(const AASequence& without_phospho) const;
154 
156  std::vector<std::vector<Size>> computePermutations_(const std::vector<Size>& sites, Int n_phosphorylation_events) const;
157 
159  Size numberOfMatchedIons_(const PeakSpectrum& th, const PeakSpectrum& windows, Size depth) const;
160 
162  double peptideScore_(const std::vector<double>& scores) const;
163 
168  void determineHighestScoringPermutations_(const std::vector<std::vector<double>>& peptide_site_scores, std::vector<ProbablePhosphoSites>& sites, const std::vector<std::vector<Size>>& permutations, std::multimap<double, Size>& ranking) const;
169 
171  double computeBaseProbability_(double ppm_reference_mz) const;
172 
174  double computeCumulativeScore_(Size N, Size n, double p) const;
175 
177  Size numberOfPhosphoEvents_(const String& sequence) const;
178 
180  AASequence removePhosphositesFromSequence_(const String& sequence) const;
181 
183  std::vector<PeakSpectrum> createTheoreticalSpectra_(const std::vector<std::vector<Size>>& permutations, const AASequence& seq_without_phospho) const;
184 
186  std::vector<PeakSpectrum> peakPickingPerWindowsInSpectrum_(PeakSpectrum& real_spectrum) const;
187 
189  std::vector<std::vector<double>> calculatePermutationPeptideScores_(std::vector<PeakSpectrum>& th_spectra, const std::vector<PeakSpectrum>& windows_top10) const;
190 
192  std::multimap<double, Size> rankWeightedPermutationPeptideScores_(const std::vector<std::vector<double>>& peptide_site_scores) const;
193 
195  void updateMembers_() override;
196 
197  // variables:
204  };
205 
206 } // namespace OpenMS
DefaultParamHandler.h
OpenMS::ProbablePhosphoSites::seq_2
Size seq_2
index of permutation with site in unphosphorylated state
Definition: AScore.h:59
OpenMS::PScore
Implementation of the PScore PSM scoring algorithm.
Definition: PScore.h:49
Types.h
OpenMS::AScore::getSpectrumDifference_
OutputIterator getSpectrumDifference_(InputIterator1 first1, InputIterator1 last1, InputIterator2 first2, InputIterator2 last2, OutputIterator result) const
Definition: AScore.h:100
OpenMS::ProbablePhosphoSites::AScore
Size AScore
Definition: AScore.h:61
OpenMS::AScore::max_permutations_
Size max_permutations_
Limit for number of sequence permutations that can be handled.
Definition: AScore.h:201
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::AScore
Implementation of the Ascore For a given peptide sequence and its MS/MS spectrum it identifies the mo...
Definition: AScore.h:72
PScore.h
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::AScore::max_peptide_length_
Size max_peptide_length_
Limit for peptide lengths that can be analyzed.
Definition: AScore.h:200
OpenMS::AScore::fragment_mass_tolerance_
double fragment_mass_tolerance_
Fragment mass tolerance for spectrum comparisons.
Definition: AScore.h:198
OpenMS::ProbablePhosphoSites
Definition: AScore.h:52
OpenMS::AScore::base_match_probability_
double base_match_probability_
Probability of a match at a peak depth of 1.
Definition: AScore.h:203
OpenMS::AScore::fragment_tolerance_ppm_
bool fragment_tolerance_ppm_
Is fragment mass tolerance given in ppm (or Da)?
Definition: AScore.h:199
OpenMS::ProbablePhosphoSites::peak_depth
Size peak_depth
filtering level that gave rise to maximum discriminatory score
Definition: AScore.h:60
String.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::ProbablePhosphoSites::second
Size second
Definition: AScore.h:57
OpenMS::ProbablePhosphoSites::seq_1
Size seq_1
index of best permutation with site in phosphorylated state
Definition: AScore.h:58
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::ProbablePhosphoSites::first
Size first
Definition: AScore.h:56
StandardTypes.h
OpenMS::AScore::unambiguous_score_
double unambiguous_score_
Score for unambiguous assignments (all sites phosphorylated)
Definition: AScore.h:202
MSSpectrum.h
OpenMS::PeptideHit
Representation of a peptide hit.
Definition: PeptideHit.h:55