void AllScoreModels::predict_fragmentation( const char* input_file, size_t num_peaks) { FILE* stream = fopen(input_file,"r"); if (! stream) { cout << "Error: couldn't open file for reading: " << input_file << endl; exit(1); } PeptideRankScorer *dnv_rank = (PeptideRankScorer *)get_rank_model_ptr(1); PeakRankModel *prm = this->get_peak_prediction_model_ptr(3); char buffer[128]; char pep_str[128]; while (fgets(buffer,128,stream)) { int charge; if (sscanf(buffer,"%s %d",pep_str,&charge) != 2) continue; cout << ">> " << pep_str << "\t" << charge << endl; if (charge<1 || charge>=prm->get_size_thresholds().size()) { cout << "Invalid charge!" << endl; continue; } Peptide pep; pep.parseFromString(&config_,static_cast<string>(pep_str)); PeptideSolution sol; sol.pep = pep; sol.reaches_n_terminal=true; sol.reaches_c_terminal=true; sol.charge = charge; sol.pm_with_19 = pep.get_mass_with_19(); PeptidePeakPrediction ppp; prm->calc_peptide_predicted_scores(sol, ppp); const size_t num_frags = ppp.frag_idxs.size(); vector< vector<int> > predicted_ranks; calc_combined_peak_ranks(ppp.rank_scores, predicted_ranks); vector<PeakTuple> tuples; for (size_t f=0; f<num_frags; f++) for (size_t i=0; i<ppp.rank_scores[f].size(); i++) if (predicted_ranks[f][i]<999) { PeakTuple pt; pt.frag_idx = f; pt.pos =i; pt.rank = predicted_ranks[f][i]; pt.score = ppp.rank_scores[f][i]; tuples.push_back(pt); } sort(tuples.begin(),tuples.end()); if (tuples.size()<1) continue; const size_t num_aas = pep.get_num_aas(); vector<mass_t> breakage_masses; pep.calc_expected_breakage_masses(&config_, breakage_masses); cout << fixed << "Rank\tIon\tm/z\tScore" << endl; for (size_t i=0; i<num_peaks && i<tuples.size(); i++) { PeakTuple pt = tuples[i]; cout << i+1 << "\t"; const FragmentType& ft = config_.get_fragment(ppp.frag_idxs[pt.frag_idx]); cout << ft.label << ":" << (ft.orientation == PREFIX ? pt.pos : num_aas - pt.pos) << "\t"; mass_t mz = ft.calc_expected_mass(breakage_masses[pt.pos],pep.get_mass_with_19()); cout << setprecision(2); if (mz<100) cout << " "; if (mz<1000) cout << " "; cout << mz << "\t"; cout << setprecision(3) << pt.score << endl; } cout << endl; } fclose(stream); }