ExitCodes main_(int , const char**) { String in = getStringOption_("in"); String out_meta = getStringOption_("out"); String in_cached = in + ".cached"; String out_cached = out_meta + ".cached"; bool convert_back = getFlag_("convert_back"); if (!convert_back) { MapType exp; CachedmzML cacher; MzMLFile f; cacher.setLogType(log_type_); f.setLogType(log_type_); f.load(in,exp); cacher.writeMemdump(exp, out_cached); DataProcessing dp; std::set<DataProcessing::ProcessingAction> actions; actions.insert(DataProcessing::FORMAT_CONVERSION); dp.setProcessingActions(actions); dp.setMetaValue("cached_data", "true"); for (Size i=0; i<exp.size(); ++i) { exp[i].getDataProcessing().push_back(dp); } std::vector<MSChromatogram<ChromatogramPeak> > chromatograms = exp.getChromatograms(); for (Size i=0; i<chromatograms.size(); ++i) { chromatograms[i].getDataProcessing().push_back(dp); } exp.setChromatograms(chromatograms); cacher.writeMetadata(exp, out_meta); } else { MzMLFile f; MapType meta_exp; CachedmzML cacher; MapType exp_reading; cacher.setLogType(log_type_); f.setLogType(log_type_); f.load(in,meta_exp); cacher.readMemdump(exp_reading, in_cached); std::cout << " read back, got " << exp_reading.size() << " spectra " << exp_reading.getChromatograms().size() << " chromats " << std::endl; { for (Size i=0; i<meta_exp.size(); ++i) { for (Size j = 0; j < meta_exp[i].getDataProcessing().size(); j++) { DataProcessing& dp = meta_exp[i].getDataProcessing()[j]; if (dp.metaValueExists("cached_data")) { dp.removeMetaValue("cached_data"); } } } std::vector<MSChromatogram<ChromatogramPeak> > chromatograms = meta_exp.getChromatograms(); for (Size i=0; i<chromatograms.size(); ++i) { for (Size j = 0; j < chromatograms[i].getDataProcessing().size(); j++) { DataProcessing& dp = chromatograms[i].getDataProcessing()[j]; if (dp.metaValueExists("cached_data")) { dp.removeMetaValue("cached_data"); } } } } if (meta_exp.size() != exp_reading.size()) { std::cerr << " Both experiments need to have the same size!"; } for (Size i=0; i<exp_reading.size(); ++i) { for (Size j = 0; j < exp_reading[i].size(); j++) { meta_exp[i].push_back(exp_reading[i][j]); } } std::vector<MSChromatogram<ChromatogramPeak> > chromatograms = exp_reading.getChromatograms(); std::vector<MSChromatogram<ChromatogramPeak> > old_chromatograms = meta_exp.getChromatograms(); for (Size i=0; i<chromatograms.size(); ++i) { for (Size j = 0; j < chromatograms[i].size(); j++) { old_chromatograms[i].push_back(chromatograms[i][j]); } } meta_exp.setChromatograms(old_chromatograms); f.store(out_meta,meta_exp); } return EXECUTION_OK; }
void ChromatogramExtractor::return_chromatogram(std::vector< OpenSwath::ChromatogramPtr > & chromatograms, std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates, OpenMS::TargetedExperiment & transition_exp_used, SpectrumSettings settings, std::vector<OpenMS::MSChromatogram<> > & output_chromatograms, bool ms1) const { typedef std::map<String, const ReactionMonitoringTransition* > TransitionMapType; TransitionMapType trans_map; for (Size i = 0; i < transition_exp_used.getTransitions().size(); i++) { trans_map[transition_exp_used.getTransitions()[i].getNativeID()] = &transition_exp_used.getTransitions()[i]; } for (Size i = 0; i < chromatograms.size(); i++) { const OpenSwath::ChromatogramPtr & chromptr = chromatograms[i]; const ChromatogramExtractor::ExtractionCoordinates & coord = coordinates[i]; TargetedExperiment::Peptide pep; OpenMS::ReactionMonitoringTransition transition; OpenMS::MSChromatogram<> chrom; // copy data OpenSwathDataAccessHelper::convertToOpenMSChromatogram(chrom, chromptr); chrom.setNativeID(coord.id); // Create precursor and set // 1) the target m/z // 2) the isolation window (upper/lower) // 3) the peptide sequence Precursor prec; if (ms1) { pep = transition_exp_used.getPeptideByRef(coord.id); prec.setMZ(coord.mz); chrom.setChromatogramType(ChromatogramSettings::BASEPEAK_CHROMATOGRAM); } else { transition = (*trans_map[coord.id]); pep = transition_exp_used.getPeptideByRef(transition.getPeptideRef()); prec.setMZ(transition.getPrecursorMZ()); if (settings.getPrecursors().size() > 0) { prec.setIsolationWindowLowerOffset(settings.getPrecursors()[0].getIsolationWindowLowerOffset()); prec.setIsolationWindowUpperOffset(settings.getPrecursors()[0].getIsolationWindowUpperOffset()); } // Create product and set its m/z Product prod; prod.setMZ(transition.getProductMZ()); chrom.setProduct(prod); chrom.setChromatogramType(ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM); } prec.setMetaValue("peptide_sequence", pep.sequence); chrom.setPrecursor(prec); // Set the rest of the meta-data chrom.setInstrumentSettings(settings.getInstrumentSettings()); chrom.setAcquisitionInfo(settings.getAcquisitionInfo()); chrom.setSourceFile(settings.getSourceFile()); for (Size i = 0; i < settings.getDataProcessing().size(); ++i) { DataProcessing dp = settings.getDataProcessing()[i]; dp.setMetaValue("performed_on_spectra", "true"); chrom.getDataProcessing().push_back(dp); } output_chromatograms.push_back(chrom); } }