C++ PeakSpectrum::isSorted方法代码示例

 PeptideHit AScore::compute(const PeptideHit & hit, PeakSpectrum & real_spectrum, double fragment_mass_tolerance, bool fragment_mass_unit_ppm, Size max_peptide_len, Size max_num_perm)
 {
   PeptideHit phospho = hit;
   
   //reset phospho
   phospho.setScore(-1);
   if (real_spectrum.empty())
   {
     return phospho;
   }
   
   String sequence_str = phospho.getSequence().toString();
   
   Size number_of_phosphorylation_events = numberOfPhosphoEvents_(sequence_str);
   AASequence seq_without_phospho = removePhosphositesFromSequence_(sequence_str);
   
   if (seq_without_phospho.toUnmodifiedString().size() > max_peptide_len)
   {
     LOG_DEBUG << "\tcalculation aborted: peptide too long: " << seq_without_phospho.toString() << std::endl;
     return phospho;
   }
   
   // determine all phospho sites
   vector<Size> sites(getSites_(seq_without_phospho));
   Size number_of_STY = sites.size();
   
   if (number_of_phosphorylation_events == 0 || number_of_STY == 0 || number_of_STY == number_of_phosphorylation_events)
   {
     return phospho;
   }
   
   vector<vector<Size> > permutations(computePermutations_(sites, (Int)number_of_phosphorylation_events));
   LOG_DEBUG << "\tnumber of permutations: " << permutations.size() << std::endl;
   
   // TODO: using a heuristic to calculate the best phospho sites if the number of permutations are exceeding the maximum.
   // A heuristic could be to calculate the best site for the first phosphorylation and based on this the best site for the second 
   // phosphorylation and so on until every site is determined
   if (permutations.size() > max_num_perm) 
   {
     LOG_DEBUG << "\tcalculation aborted: number of permutations exceeded" << std::endl;
     return phospho;
   }
     
   vector<PeakSpectrum> th_spectra(createTheoreticalSpectra_(permutations, seq_without_phospho));
   
   // prepare real spectrum windows
   if (!real_spectrum.isSorted())
   {
     real_spectrum.sortByPosition();
   }
   vector<PeakSpectrum> windows_top10(peakPickingPerWindowsInSpectrum_(real_spectrum));
   
   // calculate peptide score for each possible phospho site permutation
   vector<vector<double> > peptide_site_scores(calculatePermutationPeptideScores_(th_spectra, windows_top10, fragment_mass_tolerance, fragment_mass_unit_ppm));
   
   // rank peptide permutations ascending
   multimap<double, Size> ranking(rankWeightedPermutationPeptideScores_(peptide_site_scores));
   
   multimap<double, Size>::reverse_iterator rev = ranking.rbegin();
   String seq1 = th_spectra[rev->second].getName();
   phospho.setSequence(AASequence::fromString(seq1));
   phospho.setMetaValue("search_engine_sequence", hit.getSequence().toString());
   
   double peptide1_score = rev->first;
   phospho.setMetaValue("AScore_pep_score", peptide1_score); // initialize score with highest peptide score (aka highest weighted score)
   
   ++rev;
   String seq2 = th_spectra[rev->second].getName();
   double peptide2_score = rev->first;
   
   vector<ProbablePhosphoSites> phospho_sites;
   determineHighestScoringPermutations_(peptide_site_scores, phospho_sites, permutations, ranking);
   
   Int rank = 1;
   double best_Ascore = std::numeric_limits<double>::max(); // the lower the better
   for (vector<ProbablePhosphoSites>::iterator s_it = phospho_sites.begin(); s_it != phospho_sites.end(); ++s_it)
   {
     double Ascore = 0;
     if (peptide1_score == peptide2_score) // set Ascore = 0 for each phosphorylation site
     {
       LOG_DEBUG << "\tscore of best (" << seq1 << ") and second best peptide (" << seq2 << ") are equal (" << peptide1_score << ")" << std::endl;
     }
     else
     {
       vector<PeakSpectrum> site_determining_ions;
       
       computeSiteDeterminingIons_(th_spectra, *s_it, site_determining_ions, fragment_mass_tolerance, fragment_mass_unit_ppm);
       Size N = site_determining_ions[0].size(); // all possibilities have the same number so take the first one
       double p = static_cast<double>(s_it->peak_depth) / 100.0;
       
       Size n_first = 0; // number of matching peaks for first peptide
       for (Size window_idx = 0; window_idx != windows_top10.size(); ++window_idx) // for each 100 m/z window
       {
         n_first += numberOfMatchedIons_(site_determining_ions[0], windows_top10[window_idx], s_it->peak_depth, fragment_mass_tolerance, fragment_mass_unit_ppm);        
       }
       double P_first = computeCumulativeScore_(N, n_first, p);
       
       Size n_second = 0; // number of matching peaks for second peptide
       for (Size window_idx = 0; window_idx <  windows_top10.size(); ++window_idx) //each 100 m/z window
       {
//.........这里部分代码省略.........