C++ (Cpp) Peptide::parse_from_string Examples

Example #1

File: AdvancedScoreModel.cpp Project: pombredanne/BICEPS

void predict_fragmentation(AdvancedScoreModel* model, 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);
	}

	Config *config = model->get_config();
	DeNovoRankScorer *dnv_rank = (DeNovoRankScorer *)model->get_rank_model_ptr(1);
	PeakRankModel *prm = dnv_rank->get_peak_prediction_model(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.parse_from_string(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);
}