public PsmFromTsv(string line, char[] split, Dictionary <string, int> parsedHeader)
{
var spl = line.Split(split);
//Required properties
Filename = spl[parsedHeader[PsmTsvHeader.FileName]].Trim();
Ms2ScanNumber = int.Parse(spl[parsedHeader[PsmTsvHeader.Ms2ScanNumber]]);
PrecursorScanNum = int.Parse(spl[parsedHeader[PsmTsvHeader.PrecursorScanNum]].Trim());
PrecursorCharge = (int)double.Parse(spl[parsedHeader[PsmTsvHeader.PrecursorCharge]].Trim(), CultureInfo.InvariantCulture);
PrecursorMz = double.Parse(spl[parsedHeader[PsmTsvHeader.PrecursorMz]].Trim(), CultureInfo.InvariantCulture);
PrecursorMass = double.Parse(spl[parsedHeader[PsmTsvHeader.PrecursorMass]].Trim(), CultureInfo.InvariantCulture);
BaseSeq = RemoveParentheses(spl[parsedHeader[PsmTsvHeader.BaseSequence]].Trim());
FullSequence = spl[parsedHeader[PsmTsvHeader.FullSequence]];
PeptideMonoMass = spl[parsedHeader[PsmTsvHeader.PeptideMonoMass]].Trim();
Score = double.Parse(spl[parsedHeader[PsmTsvHeader.Score]].Trim(), CultureInfo.InvariantCulture);
DecoyContamTarget = spl[parsedHeader[PsmTsvHeader.DecoyContaminantTarget]].Trim();
QValue = double.Parse(spl[parsedHeader[PsmTsvHeader.QValue]].Trim(), CultureInfo.InvariantCulture);
MatchedIons = (spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].StartsWith("{")) ? ReadChildScanMatchedIons(spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].Trim(), BaseSeq).First().Value : ReadFragmentIonsFromString(spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].Trim(), BaseSeq);
//For general psms
TotalIonCurrent = (parsedHeader[PsmTsvHeader.TotalIonCurrent] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.TotalIonCurrent]].Trim(), CultureInfo.InvariantCulture);
DeltaScore = (parsedHeader[PsmTsvHeader.DeltaScore] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.DeltaScore]].Trim(), CultureInfo.InvariantCulture);
Notch = (parsedHeader[PsmTsvHeader.Notch] < 0) ? null : spl[parsedHeader[PsmTsvHeader.Notch]].Trim();
EssentialSeq = (parsedHeader[PsmTsvHeader.EssentialSequence] < 0) ? null : spl[parsedHeader[PsmTsvHeader.EssentialSequence]].Trim();
MissedCleavage = (parsedHeader[PsmTsvHeader.MissedCleavages] < 0) ? null : spl[parsedHeader[PsmTsvHeader.MissedCleavages]].Trim();
MassDiffDa = (parsedHeader[PsmTsvHeader.MassDiffDa] < 0) ? null : spl[parsedHeader[PsmTsvHeader.MassDiffDa]].Trim();
MassDiffPpm = (parsedHeader[PsmTsvHeader.MassDiffPpm] < 0) ? null : spl[parsedHeader[PsmTsvHeader.MassDiffPpm]].Trim();
ProteinAccession = (parsedHeader[PsmTsvHeader.ProteinAccession] < 0) ? null : spl[parsedHeader[PsmTsvHeader.ProteinAccession]].Trim();
ProteinName = (parsedHeader[PsmTsvHeader.ProteinName] < 0) ? null : spl[parsedHeader[PsmTsvHeader.ProteinName]].Trim();
GeneName = (parsedHeader[PsmTsvHeader.GeneName] < 0) ? null : spl[parsedHeader[PsmTsvHeader.GeneName]].Trim();
OrganismName = (parsedHeader[PsmTsvHeader.OrganismName] < 0) ? null : spl[parsedHeader[PsmTsvHeader.OrganismName]].Trim();
IntersectingSequenceVariations = (parsedHeader[PsmTsvHeader.IntersectingSequenceVariations] < 0) ? null : spl[parsedHeader[PsmTsvHeader.IntersectingSequenceVariations]].Trim();
IdentifiedSequenceVariations = (parsedHeader[PsmTsvHeader.IdentifiedSequenceVariations] < 0) ? null : spl[parsedHeader[PsmTsvHeader.IdentifiedSequenceVariations]].Trim();
SpliceSites = (parsedHeader[PsmTsvHeader.SpliceSites] < 0) ? null : spl[parsedHeader[PsmTsvHeader.SpliceSites]].Trim();
PeptideDesicription = (parsedHeader[PsmTsvHeader.PeptideDesicription] < 0) ? null : spl[parsedHeader[PsmTsvHeader.PeptideDesicription]].Trim();
StartAndEndResiduesInProtein = (parsedHeader[PsmTsvHeader.StartAndEndResiduesInProtein] < 0) ? null : spl[parsedHeader[PsmTsvHeader.StartAndEndResiduesInProtein]].Trim();
PreviousAminoAcid = (parsedHeader[PsmTsvHeader.PreviousAminoAcid] < 0) ? null : spl[parsedHeader[PsmTsvHeader.PreviousAminoAcid]].Trim();
NextAminoAcid = (parsedHeader[PsmTsvHeader.NextAminoAcid] < 0) ? null : spl[parsedHeader[PsmTsvHeader.NextAminoAcid]].Trim();
QValueNotch = (parsedHeader[PsmTsvHeader.QValueNotch] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.QValueNotch]].Trim(), CultureInfo.InvariantCulture);
RetentionTime = (parsedHeader[PsmTsvHeader.Ms2ScanRetentionTime] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.Ms2ScanRetentionTime]].Trim(), CultureInfo.InvariantCulture);
PEP = double.Parse(spl[parsedHeader[PsmTsvHeader.PEP]].Trim(), CultureInfo.InvariantCulture);
PEP_QValue = double.Parse(spl[parsedHeader[PsmTsvHeader.PEP_QValue]].Trim(), CultureInfo.InvariantCulture);
VariantCrossingIons = findVariantCrossingIons();
//For crosslinks
CrossType = (parsedHeader[PsmTsvHeader.CrossTypeLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.CrossTypeLabel]].Trim();
LinkResidues = (parsedHeader[PsmTsvHeader.LinkResiduesLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.LinkResiduesLabel]].Trim();
ProteinLinkSite = (parsedHeader[PsmTsvHeader.ProteinLinkSiteLabel] < 0) ? null : (spl[parsedHeader[PsmTsvHeader.ProteinLinkSiteLabel]] == "" ? null : (int?)int.Parse(spl[parsedHeader[PsmTsvHeader.ProteinLinkSiteLabel]].Trim()));
Rank = (parsedHeader[PsmTsvHeader.RankLabel] < 0) ? null : (int?)int.Parse(spl[parsedHeader[PsmTsvHeader.RankLabel]].Trim());
BetaPeptideProteinAccession = (parsedHeader[PsmTsvHeader.BetaPeptideProteinAccessionLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.BetaPeptideProteinAccessionLabel]].Trim();
BetaPeptideProteinLinkSite = (parsedHeader[PsmTsvHeader.BetaPeptideProteinLinkSiteLabel] < 0) ? null : (spl[parsedHeader[PsmTsvHeader.BetaPeptideProteinLinkSiteLabel]] == "" ? null : (int?)int.Parse(spl[parsedHeader[PsmTsvHeader.BetaPeptideProteinLinkSiteLabel]].Trim()));
BetaPeptideBaseSequence = (parsedHeader[PsmTsvHeader.BetaPeptideBaseSequenceLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.BetaPeptideBaseSequenceLabel]].Trim();
BetaPeptideFullSequence = (parsedHeader[PsmTsvHeader.BetaPeptideFullSequenceLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.BetaPeptideFullSequenceLabel]].Trim();
BetaPeptideTheoreticalMass = (parsedHeader[PsmTsvHeader.BetaPeptideTheoreticalMassLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.BetaPeptideTheoreticalMassLabel]].Trim();
BetaPeptideScore = (parsedHeader[PsmTsvHeader.BetaPeptideScoreLabel] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.BetaPeptideScoreLabel]].Trim(), CultureInfo.InvariantCulture);
BetaPeptideRank = (parsedHeader[PsmTsvHeader.BetaPeptideRankLabel] < 0) ? null : (int?)int.Parse(spl[parsedHeader[PsmTsvHeader.BetaPeptideRankLabel]].Trim());
BetaPeptideMatchedIons = (parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel] < 0) ? null :
((spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].StartsWith("{")) ? ReadChildScanMatchedIons(spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].Trim(), BetaPeptideBaseSequence).First().Value : ReadFragmentIonsFromString(spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].Trim(), BetaPeptideBaseSequence));
XLTotalScore = (parsedHeader[PsmTsvHeader.XLTotalScoreLabel] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.XLTotalScoreLabel]].Trim(), CultureInfo.InvariantCulture);
ParentIons = (parsedHeader[PsmTsvHeader.ParentIonsLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.ParentIonsLabel]].Trim();
// child scan matched ions (only for crosslinks for now, but in the future this will change)
ChildScanMatchedIons = (!spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].StartsWith("{")) ? null : ReadChildScanMatchedIons(spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].Trim(), BaseSeq);
if (ChildScanMatchedIons != null && ChildScanMatchedIons.ContainsKey(Ms2ScanNumber))
{
ChildScanMatchedIons.Remove(Ms2ScanNumber);
}
// beta peptide child scan matched ions (for crosslinks)
BetaPeptideChildScanMatchedIons = (parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel] < 0) ? null :
((!spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].StartsWith("{")) ? null : ReadChildScanMatchedIons(spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].Trim(), BetaPeptideBaseSequence));
if (BetaPeptideChildScanMatchedIons != null && BetaPeptideChildScanMatchedIons.ContainsKey(Ms2ScanNumber))
{
BetaPeptideChildScanMatchedIons.Remove(Ms2ScanNumber);
}
//For Glyco
GlycanMass = (parsedHeader[PsmTsvHeader_Glyco.GlycanMass] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader_Glyco.GlycanMass]]);
GlycanComposition = (parsedHeader[PsmTsvHeader_Glyco.GlycanComposition] < 0) ? null : spl[parsedHeader[PsmTsvHeader_Glyco.GlycanComposition]];
GlycanStructure = (parsedHeader[PsmTsvHeader_Glyco.GlycanStructure] < 0) ? null : spl[parsedHeader[PsmTsvHeader_Glyco.GlycanStructure]];
var localizationLevel = (parsedHeader[PsmTsvHeader_Glyco.GlycanLocalizationLevel] < 0) ? null : spl[parsedHeader[PsmTsvHeader_Glyco.GlycanLocalizationLevel]];
if (localizationLevel != null)
{
GlycanLocalizationLevel = (LocalizationLevel)Enum.Parse(typeof(LocalizationLevel), localizationLevel);
}
LocalizedGlycan = (parsedHeader[PsmTsvHeader_Glyco.LocalizedGlycan] < 0) ? null : spl[parsedHeader[PsmTsvHeader_Glyco.LocalizedGlycan]];
}
public PsmFromTsv(string line, char[] split, Dictionary <string, int> parsedHeader)
{
var spl = line.Split(split);
//Required properties
FileNameWithoutExtension = spl[parsedHeader[PsmTsvHeader.FileName]].Trim();
// remove file format, e.g., .raw, .mzML, .mgf
// this is more robust but slower than Path.GetFileNameWithoutExtension
if (FileNameWithoutExtension.Contains('.'))
{
foreach (var knownSpectraFileExtension in GlobalVariables.AcceptedSpectraFormats)
{
FileNameWithoutExtension = Path.GetFileName(FileNameWithoutExtension.Replace(knownSpectraFileExtension, string.Empty, StringComparison.InvariantCultureIgnoreCase));
}
}
Ms2ScanNumber = int.Parse(spl[parsedHeader[PsmTsvHeader.Ms2ScanNumber]]);
// this will probably not be known in an .mgf data file
if (int.TryParse(spl[parsedHeader[PsmTsvHeader.PrecursorScanNum]].Trim(), out int result))
{
PrecursorScanNum = result;
}
else
{
PrecursorScanNum = 0;
}
PrecursorCharge = (int)double.Parse(spl[parsedHeader[PsmTsvHeader.PrecursorCharge]].Trim(), CultureInfo.InvariantCulture);
PrecursorMz = double.Parse(spl[parsedHeader[PsmTsvHeader.PrecursorMz]].Trim(), CultureInfo.InvariantCulture);
PrecursorMass = double.Parse(spl[parsedHeader[PsmTsvHeader.PrecursorMass]].Trim(), CultureInfo.InvariantCulture);
BaseSeq = RemoveParentheses(spl[parsedHeader[PsmTsvHeader.BaseSequence]].Trim());
FullSequence = spl[parsedHeader[PsmTsvHeader.FullSequence]];
PeptideMonoMass = spl[parsedHeader[PsmTsvHeader.PeptideMonoMass]].Trim();
Score = double.Parse(spl[parsedHeader[PsmTsvHeader.Score]].Trim(), CultureInfo.InvariantCulture);
DecoyContamTarget = spl[parsedHeader[PsmTsvHeader.DecoyContaminantTarget]].Trim();
QValue = double.Parse(spl[parsedHeader[PsmTsvHeader.QValue]].Trim(), CultureInfo.InvariantCulture);
MatchedIons = (spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].StartsWith("{")) ? ReadChildScanMatchedIons(spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].Trim(), spl[parsedHeader[PsmTsvHeader.MatchedIonIntensities]].Trim(), BaseSeq).First().Value : ReadFragmentIonsFromString(spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].Trim(), spl[parsedHeader[PsmTsvHeader.MatchedIonIntensities]].Trim(), BaseSeq);
AmbiguityLevel = (parsedHeader[PsmTsvHeader.AmbiguityLevel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.AmbiguityLevel]].Trim();
//For general psms
TotalIonCurrent = (parsedHeader[PsmTsvHeader.TotalIonCurrent] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.TotalIonCurrent]].Trim(), CultureInfo.InvariantCulture);
DeltaScore = (parsedHeader[PsmTsvHeader.DeltaScore] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.DeltaScore]].Trim(), CultureInfo.InvariantCulture);
Notch = (parsedHeader[PsmTsvHeader.Notch] < 0) ? null : spl[parsedHeader[PsmTsvHeader.Notch]].Trim();
EssentialSeq = (parsedHeader[PsmTsvHeader.EssentialSequence] < 0) ? null : spl[parsedHeader[PsmTsvHeader.EssentialSequence]].Trim();
MissedCleavage = (parsedHeader[PsmTsvHeader.MissedCleavages] < 0) ? null : spl[parsedHeader[PsmTsvHeader.MissedCleavages]].Trim();
MassDiffDa = (parsedHeader[PsmTsvHeader.MassDiffDa] < 0) ? null : spl[parsedHeader[PsmTsvHeader.MassDiffDa]].Trim();
MassDiffPpm = (parsedHeader[PsmTsvHeader.MassDiffPpm] < 0) ? null : spl[parsedHeader[PsmTsvHeader.MassDiffPpm]].Trim();
ProteinAccession = (parsedHeader[PsmTsvHeader.ProteinAccession] < 0) ? null : spl[parsedHeader[PsmTsvHeader.ProteinAccession]].Trim();
ProteinName = (parsedHeader[PsmTsvHeader.ProteinName] < 0) ? null : spl[parsedHeader[PsmTsvHeader.ProteinName]].Trim();
GeneName = (parsedHeader[PsmTsvHeader.GeneName] < 0) ? null : spl[parsedHeader[PsmTsvHeader.GeneName]].Trim();
OrganismName = (parsedHeader[PsmTsvHeader.OrganismName] < 0) ? null : spl[parsedHeader[PsmTsvHeader.OrganismName]].Trim();
IntersectingSequenceVariations = (parsedHeader[PsmTsvHeader.IntersectingSequenceVariations] < 0) ? null : spl[parsedHeader[PsmTsvHeader.IntersectingSequenceVariations]].Trim();
IdentifiedSequenceVariations = (parsedHeader[PsmTsvHeader.IdentifiedSequenceVariations] < 0) ? null : spl[parsedHeader[PsmTsvHeader.IdentifiedSequenceVariations]].Trim();
SpliceSites = (parsedHeader[PsmTsvHeader.SpliceSites] < 0) ? null : spl[parsedHeader[PsmTsvHeader.SpliceSites]].Trim();
PeptideDescription = (parsedHeader[PsmTsvHeader.PeptideDesicription] < 0) ? null : spl[parsedHeader[PsmTsvHeader.PeptideDesicription]].Trim();
StartAndEndResiduesInProtein = (parsedHeader[PsmTsvHeader.StartAndEndResiduesInProtein] < 0) ? null : spl[parsedHeader[PsmTsvHeader.StartAndEndResiduesInProtein]].Trim();
PreviousAminoAcid = (parsedHeader[PsmTsvHeader.PreviousAminoAcid] < 0) ? null : spl[parsedHeader[PsmTsvHeader.PreviousAminoAcid]].Trim();
NextAminoAcid = (parsedHeader[PsmTsvHeader.NextAminoAcid] < 0) ? null : spl[parsedHeader[PsmTsvHeader.NextAminoAcid]].Trim();
QValueNotch = (parsedHeader[PsmTsvHeader.QValueNotch] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.QValueNotch]].Trim(), CultureInfo.InvariantCulture);
RetentionTime = (parsedHeader[PsmTsvHeader.Ms2ScanRetentionTime] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.Ms2ScanRetentionTime]].Trim(), CultureInfo.InvariantCulture);
PEP = double.Parse(spl[parsedHeader[PsmTsvHeader.PEP]].Trim(), CultureInfo.InvariantCulture);
PEP_QValue = double.Parse(spl[parsedHeader[PsmTsvHeader.PEP_QValue]].Trim(), CultureInfo.InvariantCulture);
VariantCrossingIons = findVariantCrossingIons();
//For crosslinks
CrossType = (parsedHeader[PsmTsvHeader.CrossTypeLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.CrossTypeLabel]].Trim();
LinkResidues = (parsedHeader[PsmTsvHeader.LinkResiduesLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.LinkResiduesLabel]].Trim();
ProteinLinkSite = (parsedHeader[PsmTsvHeader.ProteinLinkSiteLabel] < 0) ? null : (spl[parsedHeader[PsmTsvHeader.ProteinLinkSiteLabel]] == "" ? null : (int?)int.Parse(spl[parsedHeader[PsmTsvHeader.ProteinLinkSiteLabel]].Trim()));
Rank = (parsedHeader[PsmTsvHeader.RankLabel] < 0) ? null : (int?)int.Parse(spl[parsedHeader[PsmTsvHeader.RankLabel]].Trim());
BetaPeptideProteinAccession = (parsedHeader[PsmTsvHeader.BetaPeptideProteinAccessionLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.BetaPeptideProteinAccessionLabel]].Trim();
BetaPeptideProteinLinkSite = (parsedHeader[PsmTsvHeader.BetaPeptideProteinLinkSiteLabel] < 0) ? null : (spl[parsedHeader[PsmTsvHeader.BetaPeptideProteinLinkSiteLabel]] == "" ? null : (int?)int.Parse(spl[parsedHeader[PsmTsvHeader.BetaPeptideProteinLinkSiteLabel]].Trim()));
BetaPeptideBaseSequence = (parsedHeader[PsmTsvHeader.BetaPeptideBaseSequenceLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.BetaPeptideBaseSequenceLabel]].Trim();
BetaPeptideFullSequence = (parsedHeader[PsmTsvHeader.BetaPeptideFullSequenceLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.BetaPeptideFullSequenceLabel]].Trim();
BetaPeptideTheoreticalMass = (parsedHeader[PsmTsvHeader.BetaPeptideTheoreticalMassLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.BetaPeptideTheoreticalMassLabel]].Trim();
BetaPeptideScore = (parsedHeader[PsmTsvHeader.BetaPeptideScoreLabel] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.BetaPeptideScoreLabel]].Trim(), CultureInfo.InvariantCulture);
BetaPeptideRank = (parsedHeader[PsmTsvHeader.BetaPeptideRankLabel] < 0) ? null : (int?)int.Parse(spl[parsedHeader[PsmTsvHeader.BetaPeptideRankLabel]].Trim());
BetaPeptideMatchedIons = (parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel] < 0) ? null :
((spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].StartsWith("{")) ? ReadChildScanMatchedIons(spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].Trim(), spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonIntensitiesLabel]].Trim(), BetaPeptideBaseSequence).First().Value : ReadFragmentIonsFromString(spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].Trim(), spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonIntensitiesLabel]].Trim(), BetaPeptideBaseSequence));
XLTotalScore = (parsedHeader[PsmTsvHeader.XLTotalScoreLabel] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader.XLTotalScoreLabel]].Trim(), CultureInfo.InvariantCulture);
ParentIons = (parsedHeader[PsmTsvHeader.ParentIonsLabel] < 0) ? null : spl[parsedHeader[PsmTsvHeader.ParentIonsLabel]].Trim();
// child scan matched ions (only for crosslinks for now, but in the future this will change)
ChildScanMatchedIons = (!spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].StartsWith("{")) ? null : ReadChildScanMatchedIons(spl[parsedHeader[PsmTsvHeader.MatchedIonMzRatios]].Trim(), spl[parsedHeader[PsmTsvHeader.MatchedIonIntensities]].Trim(), BaseSeq);
if (ChildScanMatchedIons != null && ChildScanMatchedIons.ContainsKey(Ms2ScanNumber))
{
ChildScanMatchedIons.Remove(Ms2ScanNumber);
}
// beta peptide child scan matched ions (for crosslinks)
BetaPeptideChildScanMatchedIons = (parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel] < 0) ? null :
((!spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].StartsWith("{")) ? null : ReadChildScanMatchedIons(spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonsLabel]].Trim(), spl[parsedHeader[PsmTsvHeader.BetaPeptideMatchedIonIntensitiesLabel]].Trim(), BetaPeptideBaseSequence));
if (BetaPeptideChildScanMatchedIons != null && BetaPeptideChildScanMatchedIons.ContainsKey(Ms2ScanNumber))
{
BetaPeptideChildScanMatchedIons.Remove(Ms2ScanNumber);
}
//For Glyco
GlycanMass = (parsedHeader[PsmTsvHeader_Glyco.GlycanMass] < 0) ? null : (double?)double.Parse(spl[parsedHeader[PsmTsvHeader_Glyco.GlycanMass]], CultureInfo.InvariantCulture);
GlycanComposition = (parsedHeader[PsmTsvHeader_Glyco.GlycanComposition] < 0) ? null : spl[parsedHeader[PsmTsvHeader_Glyco.GlycanComposition]];
GlycanStructure = (parsedHeader[PsmTsvHeader_Glyco.GlycanStructure] < 0) ? null : spl[parsedHeader[PsmTsvHeader_Glyco.GlycanStructure]];
var localizationLevel = (parsedHeader[PsmTsvHeader_Glyco.GlycanLocalizationLevel] < 0) ? null : spl[parsedHeader[PsmTsvHeader_Glyco.GlycanLocalizationLevel]];
if (localizationLevel != null)
{
GlycanLocalizationLevel = (LocalizationLevel)Enum.Parse(typeof(LocalizationLevel), localizationLevel);
}
LocalizedGlycan = (parsedHeader[PsmTsvHeader_Glyco.LocalizedGlycan] < 0) ? null : spl[parsedHeader[PsmTsvHeader_Glyco.LocalizedGlycan]];
}