private void AddTransition(Library library, string[] line, double mzLastPeptide, int transMzIndex, int intensityIndex, double precursorMz)
{
var transition = new Library.Transition();
transition.Id = line[transMzIndex].Replace(",", ".");
transition.PeptideId = precursorMz.ToString().Replace(",", ".");
transition.PrecursorMz = precursorMz;
if (line[2].Length > 1)
{
transition.ProductMz = double.Parse(line[transMzIndex].Replace(",", "."), CultureInfo.InvariantCulture);
}
else
{
transition.ProductMz = mzLastPeptide;
}
transition.ProductIonIntensity = double.Parse(line[intensityIndex].Replace(",", "."), CultureInfo.InvariantCulture);
string keystring = transition.Id + "-" + transition.PrecursorMz;
if (library.TransitionList.Contains(keystring))
{
logger.Warn("Two of the same peptide - transition combinations were detected. The second entry was not added as a valid transition. Please check your file for duplication.");
}
else
{
library.TransitionList.Add(keystring, transition);
var correspondingPeptide = (Library.Peptide)(library.PeptideList[key : Convert.ToString(precursorMz).Replace(",", ".")]);
correspondingPeptide.AssociatedTransitions.Add(transition);
}
}
private void AddTransition(Library library, XmlReader reader)
{
var transition = new Library.Transition();
transition.PeptideId = reader.GetAttribute("peptideRef");
transition.Id = reader.GetAttribute("id");
Enums.IonType?ionType = null;
bool cvParamsRead = false;
while (reader.Read() && !cvParamsRead)
{
if (reader.IsStartElement())
{
if (reader.LocalName == "Precursor")
{
ionType = Enums.IonType.Precursor;
}
else if (reader.LocalName == "Product")
{
ionType = Enums.IonType.Product;
}
if (reader.LocalName == "cvParam")
{
switch (reader.GetAttribute("accession"))
{
case "MS:1000827":
if (ionType == Enums.IonType.Precursor)
{
transition.PrecursorMz = double.Parse(reader.GetAttribute("value"), System.Globalization.CultureInfo.InvariantCulture);
}
else if (ionType == Enums.IonType.Product)
{
transition.ProductMz = double.Parse(reader.GetAttribute("value"), System.Globalization.CultureInfo.InvariantCulture);
}
break;
case "MS:1000041":
transition.ProductIonChargeState = Convert.ToInt32(reader.GetAttribute("value"));
break;
case "MS:1000903":
transition.ProductIonSeriesOrdinal = Convert.ToInt32(reader.GetAttribute("value"));
break;
case "MS:1000926":
transition.ProductInterpretationRank = Convert.ToInt32(reader.GetAttribute("value"));
break;
case "MS:1001220":
transition.IonType = reader.GetAttribute("value");
break;
case "MS:1001226":
transition.ProductIonIntensity = double.Parse(reader.GetAttribute("value"), System.Globalization.CultureInfo.InvariantCulture);
break;
}
}
}
else if (reader.NodeType == XmlNodeType.EndElement && reader.LocalName == "Transition")
{
if (reader.LocalName == "Precursor" || reader.LocalName == "Product")
{
ionType = null;
}
if (reader.LocalName == "Transition")
{
cvParamsRead = true;
}
}
}
library.TransitionList.Add(transition.Id, transition);
var correspondingPeptide = (Library.Peptide)(library.PeptideList[transition.PeptideId]);
correspondingPeptide.AssociatedTransitionIds.Add(transition.Id);
correspondingPeptide.AssociatedTransitions.Add(transition);
}