public static void GlyTest_GetKindString() { byte[] kind = new byte[] { 3, 4, 0, 0, 1, 0, 0, 0, 0, 0 }; string kindString = Glycan.GetKindString(kind); Assert.AreEqual("H3N4F1", kindString); }
public override string ToString() { var sb = new StringBuilder(); sb.Append(FullFilePath + "\t"); sb.Append(ScanNumber + "\t"); sb.Append(ScanRetentionTime + "\t"); sb.Append(PrecursorScanNumber + "\t"); sb.Append(ScanPrecursorMonoisotopicPeakMz + "\t"); sb.Append(ScanPrecursorCharge + "\t"); sb.Append(ScanPrecursorMass + "\t"); var proteinAccessionString = ProteinAccession ?? PsmTsvWriter.Resolve(BestMatchingPeptides.Select(p => p.Peptide.Protein.Accession), FullSequence).ResolvedString; sb.Append(proteinAccessionString + "\t"); sb.Append(Organism + "\t"); sb.Append(PsmTsvWriter.Resolve(BestMatchingPeptides.Select(b => b.Peptide.Protein.FullName), FullSequence).ResolvedString + "\t"); int _FirstOneBasedStartResidueInProtein = OneBasedStartResidueInProtein.HasValue ? OneBasedStartResidueInProtein.Value : BestMatchingPeptides.First().Peptide.OneBasedStartResidueInProtein; int _FirstOneBasedEndResidueInProtein = OneBasedEndResidueInProtein.HasValue ? OneBasedEndResidueInProtein.Value : BestMatchingPeptides.First().Peptide.OneBasedEndResidueInProtein;; if (OneBasedStartResidueInProtein.HasValue) { sb.Append("[" + OneBasedStartResidueInProtein.Value.ToString() + " to " + OneBasedEndResidueInProtein.Value.ToString() + "]" + '\t'); } else { sb.Append("\t"); } sb.Append(BaseSequence + "\t"); sb.Append(BestMatchingPeptides.First().Peptide.PreviousAminoAcid + "," + BestMatchingPeptides.First().Peptide.NextAminoAcid + "\t"); sb.Append(FullSequence + "\t"); sb.Append(BestMatchingPeptides.First().Peptide.AllModsOneIsNterminus.Count + "\t"); sb.Append((PeptideMonisotopicMass.HasValue ? PeptideMonisotopicMass.Value.ToString() : "---")); sb.Append("\t"); sb.Append(Score + "\t"); sb.Append(Rank + "\t"); if (ChildMatchedFragmentIons == null) { foreach (var mid in MatchedIonDataDictionary(this.MatchedFragmentIons)) { sb.Append(mid.Value); sb.Append("\t"); } } else { StringBuilder[] scanFragmentStringbuilder = new StringBuilder[6]; int i = 0; foreach (var mid in MatchedIonDataDictionary(this.MatchedFragmentIons)) { scanFragmentStringbuilder[i] = new StringBuilder(); scanFragmentStringbuilder[i].Append("{" + ScanNumber + "@" + mid.Value + "}"); i++; } foreach (var childScan in ChildMatchedFragmentIons) { int j = 0; int oneBasedScan = childScan.Key; foreach (var mid in MatchedIonDataDictionary(childScan.Value)) { scanFragmentStringbuilder[j].Append("{" + oneBasedScan + "@" + mid.Value + "}"); j++; } } foreach (var s in scanFragmentStringbuilder) { sb.Append(s.ToString() + "\t"); } } sb.Append((IsDecoy) ? "D" : (IsContaminant) ? "C" : "T"); sb.Append("\t"); sb.Append(FdrInfo != null? FdrInfo.QValue.ToString() : "-1"); sb.Append("\t"); sb.Append("0" + "\t"); sb.Append("0" + "\t"); if (NGlycan != null) { sb.Append(PeptideScore + "\t"); sb.Append(GlycanScore + "\t"); sb.Append(DiagnosticIonScore + "\t"); sb.Append((double)NGlycan.First().Mass / 1E5); sb.Append("\t"); sb.Append(Glycan.GetKindString(NGlycan.First().Kind)); sb.Append("\t"); sb.Append(R138vs144.ToString()); sb.Append("\t"); if (NGlycan.First().Struc != null) { sb.Append(NGlycan.First().Struc); sb.Append("\t"); } } if (Routes != null) { sb.Append(LocalizationGraphs.First().TotalScore + "\t"); sb.Append(GlycanScore + "\t"); sb.Append(DiagnosticIonScore + "\t"); var glycanBox = GlycanBox.OGlycanBoxes[Routes.First().ModBoxId]; sb.Append(glycanBox.NumberOfMods + "\t"); sb.Append(LocalizationGraphs.First().ModPos.Length + "\t"); sb.Append(glycanBox.Mass + "\t"); sb.Append(Glycan.GetKindString(glycanBox.Kind)); sb.Append("\t"); var NSiteExist = MotifExist(BaseSequence, new string[] { "Nxt", "Nxs" }); sb.Append(NSiteExist); sb.Append("\t"); sb.Append(R138vs144.ToString()); sb.Append("\t"); //Get glycans var glycans = new Glycan[glycanBox.NumberOfMods]; for (int i = 0; i < glycanBox.NumberOfMods; i++) { glycans[i] = GlycanBox.GlobalOGlycans[glycanBox.ModIds[i]]; } if (glycans.First().Struc != null) { sb.Append(string.Join(",", glycans.Select(p => p.Struc.ToString()).ToArray())); } sb.Append("\t"); sb.Append(CorrectLocalizationLevel(SiteSpeciLocalProb, LocalizationGraphs.First(), Routes.First(), LocalizedGlycan, LocalizationLevel)); sb.Append("\t"); //string localizedGlycan = LocalizedGlycan.Where(p=>p.Item3).Count() > 0 ? "[" + string.Join(",", LocalizedGlycan.Where(p => p.Item3).Select(p => p.Item1.ToString() + "-" + p.Item2.ToString())) + "]" : ""; //sb.Append(localizedGlycan); sb.Append("\t"); string local_peptide = ""; string local_protein = ""; LocalizedSiteSpeciLocalInfo(SiteSpeciLocalProb, LocalizedGlycan, OneBasedStartResidueInProtein, ref local_peptide, ref local_protein); sb.Append(local_peptide); sb.Append("\t"); sb.Append(local_protein); sb.Append("\t"); sb.Append(AllLocalizationInfo(Routes)); sb.Append("\t"); sb.Append(SiteSpeciLocalInfo(SiteSpeciLocalProb)); } return(sb.ToString()); }