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);
}
