public static void RunSimulationAndPostProcess(Experiment e) { Console.WriteLine("\nSimulating \"{0}\"", e.experimentName); PSMTSVReaderWriter.InitiatePSMWriter(Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, "NoExclusion_RealTimeCometSearchResult.tsv")); new DataReceiverSimulation().DoJob(e.exclusionProfile, ms2SpectraList); PSMTSVReaderWriter.ClosePSMWriter(); e.analysisTime = getCurrentTime() - e.experimentStartTime; PostExperimentProcessing(e); //WriteSpectralAndPeptideCountPerIdentifiedProtein(e); WriteUnusedSpectra(e); WriteUsedSpectra(e); //WriteUsedSpectra(e); WriteSpectralAndPeptideCountPerIdentifiedProtein(e); e.exclusionProfile.reset(); reset(); }
protected IDs performDatabaseSearch(Spectra spec) { IDs id = null; if (CometSingleSearch.Search(spec, out id)) { log.Debug("MS2 scan was identified."); log.Debug(id); performanceEvaluator.countMS2Identified(); PSMTSVReaderWriter.WritePSM(id); } else { // scan cannot be matched to a peptide log.Debug("MS2 scan {0} was not identified by a comet search", spec.getScanNum()); performanceEvaluator.countMS2Unidentified(); } return(id); }