public override string ToString()
{
StringBuilder spectrum = new StringBuilder();
spectrum.Append("Name: " + Name);
spectrum.Append("\nMW: " + PrecursorMz);
spectrum.Append("\nComment: ");
spectrum.Append("Parent=" + PrecursorMz);
spectrum.Append(" RT=" + RetentionTime);
spectrum.Append("\nNum peaks: " + MatchedFragmentIons.Count);
double maxIntensity = MatchedFragmentIons.Select(b => b.Intensity).Max();
foreach (MatchedFragmentIon matchedIon in MatchedFragmentIons)
{
double intensityFraction = matchedIon.Intensity / maxIntensity;
string neutralLoss = null;
if (matchedIon.NeutralTheoreticalProduct.NeutralLoss != 0)
{
neutralLoss = "-" + matchedIon.NeutralTheoreticalProduct.NeutralLoss;
}
spectrum.Append("\n" + matchedIon.Mz + "\t" + intensityFraction + "\t" + "\"" +
matchedIon.NeutralTheoreticalProduct.ProductType.ToString() +
matchedIon.NeutralTheoreticalProduct.FragmentNumber.ToString() + "^" +
matchedIon.Charge + neutralLoss + "/" + 0 + "ppm" + "\"");
}
return(spectrum.ToString());
}
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()
{
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");
sb.Append(ProteinAccession + "\t");
sb.Append(XlProteinPos + "\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");
foreach (var mid in MatchedIonDataDictionary(this.MatchedFragmentIons))
{
sb.Append(mid.Value);
sb.Append("\t");
}
StringBuilder childScanFragmentStringbuilder = new StringBuilder();
if (ChildMatchedFragmentIons != null)
{
foreach (var childScan in ChildMatchedFragmentIons)
{
int oneBasedScan = childScan.Key;
var matchedIonsDict = MatchedIonDataDictionary(childScan.Value);
childScanFragmentStringbuilder.Append("{" + oneBasedScan + "|" + matchedIonsDict[PsmTsvHeader.MatchedIonMzRatios] + "}");
}
}
sb.Append(childScanFragmentStringbuilder.ToString() + "\t");
if (BetaPeptide != null)
{
sb.Append("\t");
sb.Append(BetaPeptide.ProteinAccession + "\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");
foreach (var betamid in MatchedIonDataDictionary(this.BetaPeptide.MatchedFragmentIons))
{
sb.Append(betamid.Value);
sb.Append("\t");
}
StringBuilder childScanFragmentStringbuilderBeta = new StringBuilder();
if (BetaPeptide.ChildMatchedFragmentIons != null)
{
foreach (var childScan in BetaPeptide.ChildMatchedFragmentIons)
{
int oneBasedScan = childScan.Key;
var matchedIonsDict = MatchedIonDataDictionary(childScan.Value);
childScanFragmentStringbuilderBeta.Append("{" + oneBasedScan + "|" + matchedIonsDict[PsmTsvHeader.MatchedIonMzRatios] + "}");
}
}
sb.Append(childScanFragmentStringbuilderBeta.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());
}
