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());
}