public static String DoJob(ProteinProphetResult ppr, ExclusionProfile exclusionProfile, int experimentNum)
{
String outputFile = Path.Combine(InputFileOrganizer.OutputFolderOfTheRun, "NumberOfPeptidesPerIdentifiedProtein_" + experimentNum + ".txt");
StreamWriter sw = new StreamWriter(outputFile);
sw.WriteLine("Accession\tNumberOfPeptides\tSpectralCount");
List <String> confidentlyIdentifiedProts = ppr.getProteinsIdentified();
foreach (String accession in confidentlyIdentifiedProts)
{
Protein prot = exclusionProfile.getDatabase().getProtein(accession);
HashSet <String> peptidesObserved = new HashSet <String>();
foreach (PeptideScore pepEvidence in prot.getPeptideScore())
{
peptidesObserved.Add(pepEvidence.getPeptideSequence());
}
sw.WriteLine("{0}\t{1}\t{2}", accession, peptidesObserved.Count, prot.getPeptideScore().Count);
}
sw.Close();
return(outputFile);
}
