public static Dictionary <string, string> MatchedIonDataDictionary(List <MatchedFragmentIon> matchedFragmentIons)
{
Dictionary <string, string> s = new Dictionary <string, string>();
PsmTsvWriter.AddMatchedIonsData(s, matchedFragmentIons);
return(s);
}
public override string ToString()
{
string position = "";
switch (CrossType)
{
case PsmCrossType.Single:
break;
case PsmCrossType.Loop:
position = "(" + LinkPositions[0].ToString() + "-" + LinkPositions[1].ToString() + ")";
break;
default:
position = "(" + LinkPositions[0].ToString() + ")";
break;
}
var sb = new StringBuilder();
sb.Append(FullFilePath + "\t");
sb.Append(ScanNumber + "\t");
sb.Append(PrecursorScanNumber + "\t");
sb.Append(ScanPrecursorMonoisotopicPeakMz + "\t");
sb.Append(ScanPrecursorCharge + "\t");
sb.Append(ScanPrecursorMass + "\t");
sb.Append(CrossType.ToString() + "\t");
if (LinkPositions != null)
{
if (CrossType == PsmCrossType.Loop)
{
sb.Append(BaseSequence[LinkPositions[0] - 1] + ";" + BaseSequence[LinkPositions[1] - 1] + "\t");
}
else if (CrossType == PsmCrossType.Inter || CrossType == PsmCrossType.Intra)
{
sb.Append(BaseSequence[LinkPositions[0] - 1] + ";" + BetaPeptide.BaseSequence[BetaPeptide.LinkPositions[0] - 1] + "\t");
}
else
{
// deadend
sb.Append(BaseSequence[LinkPositions[0] - 1] + "\t");
}
}
else
{
sb.Append("\t");
}
sb.Append("\t");
List <PeptideWithSetModifications> pepsWithMods = BestMatchingPeptides.Select(p => p.Peptide).ToList();
var proteinAccessionString = ProteinAccession != null ? ProteinAccession : PsmTsvWriter.Resolve(pepsWithMods.Select(b => b.Protein.Accession), FullSequence).ResolvedString;
sb.Append(proteinAccessionString + "\t");
sb.Append(XlProteinPos + (XlProteinPosLoop.HasValue? "~" + XlProteinPosLoop.Value : null) + "\t");
sb.Append(BaseSequence + "\t");
sb.Append(FullSequence + position + "\t");
sb.Append((PeptideMonisotopicMass.HasValue ? PeptideMonisotopicMass.Value.ToString() : "---")); sb.Append("\t");
sb.Append(Score + "\t");
sb.Append(XlRank[0] + "\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");
}
}
if (BetaPeptide != null)
{
sb.Append("\t");
List <PeptideWithSetModifications> betaPepsWithMods = BetaPeptide.BestMatchingPeptides.Select(p => p.Peptide).ToList();
var betaProteinAccessionString = BetaPeptide.ProteinAccession != null ? BetaPeptide.ProteinAccession : PsmTsvWriter.Resolve(betaPepsWithMods.Select(b => b.Protein.Accession), FullSequence).ResolvedString;
sb.Append(betaProteinAccessionString + "\t");
sb.Append(BetaPeptide.XlProteinPos + "\t");
sb.Append(BetaPeptide.BaseSequence + "\t");
sb.Append(BetaPeptide.FullSequence + "(" + BetaPeptide.LinkPositions[0].ToString() + ")" + "\t");
sb.Append(BetaPeptide.PeptideMonisotopicMass.ToString() + "\t");
sb.Append(BetaPeptide.Score + "\t");
sb.Append(XlRank[1] + "\t");
if (BetaPeptide.ChildMatchedFragmentIons == null)
{
foreach (var betamid in MatchedIonDataDictionary(this.BetaPeptide.MatchedFragmentIons))
{
sb.Append(betamid.Value);
sb.Append("\t");
}
}
else
{
StringBuilder[] scanFragmentStringbuilder = new StringBuilder[6];
int i = 0;
foreach (var betamid in MatchedIonDataDictionary(this.BetaPeptide.MatchedFragmentIons))
{
scanFragmentStringbuilder[i] = new StringBuilder();
scanFragmentStringbuilder[i].Append("{" + ScanNumber + "@" + betamid.Value + "}");
i++;
}
foreach (var betaChildScan in BetaPeptide.ChildMatchedFragmentIons)
{
int j = 0;
int betaOneBasedScan = betaChildScan.Key;
foreach (var betamid in MatchedIonDataDictionary(betaChildScan.Value))
{
scanFragmentStringbuilder[j].Append("{" + betaOneBasedScan + "@" + betamid.Value + "}");
j++;
}
}
foreach (var s in scanFragmentStringbuilder)
{
sb.Append(s.ToString() + "\t");
}
}
sb.Append("\t");
sb.Append(XLTotalScore + "\t");
// mass of crosslinker
sb.Append(((PeptideMonisotopicMass.HasValue) ? (ScanPrecursorMass - BetaPeptide.PeptideMonisotopicMass - PeptideMonisotopicMass.Value).ToString() : "---")); sb.Append("\t");
int alphaNumParentIons = MatchedFragmentIons.Count(p => p.NeutralTheoreticalProduct.ProductType == ProductType.M);
int betaNumParentIons = BetaPeptide.MatchedFragmentIons.Count(p => p.NeutralTheoreticalProduct.ProductType == ProductType.M);
sb.Append(alphaNumParentIons + ";" + betaNumParentIons + "\t");
sb.Append(alphaNumParentIons + betaNumParentIons + "\t");
sb.Append(((ParentIonMaxIntensityRanks != null) && (ParentIonMaxIntensityRanks.Any()) ? ParentIonMaxIntensityRanks.Min().ToString() : "-")); sb.Append("\t");
}
if (BetaPeptide == null)
{
sb.Append((IsDecoy) ? "D" : (IsContaminant) ? "C" : "T");
sb.Append("\t");
}
else
{
sb.Append((IsDecoy || BetaPeptide.IsDecoy) ? "D" : (IsContaminant || BetaPeptide.IsContaminant) ? "C" : "T");
sb.Append("\t");
}
sb.Append(FdrInfo.QValue.ToString());
sb.Append("\t");
return(sb.ToString());
}
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());
}
