private void AddPeptide(Library library, string[] line, int sequenceIndex, int pepMzIndex)
{
var peptide = new Library.Peptide();
peptide.Id = line[pepMzIndex].Replace(",", ".");
peptide.Sequence = line[sequenceIndex];
peptide.AssociatedTransitions = new List <Library.Transition>();
library.PeptideList.Add(peptide.Id, peptide);
}
private void AddPeptide(Library library, XmlReader reader)
{
var peptide = new Library.Peptide();
peptide.Id = reader.GetAttribute("id");
peptide.Sequence = reader.GetAttribute("sequence");
peptide.AssociatedTransitionIds = new List <string>();
bool cvParamsRead = false;
while (reader.Read() && !cvParamsRead)
{
if (reader.IsStartElement())
{
if (reader.LocalName == "cvParam")
{
switch (reader.GetAttribute("accession"))
{
case "MS:1000041":
peptide.ChargeState = Convert.ToInt32(reader.GetAttribute("value"));
break;
case "MS:1000893":
peptide.GroupLabel = reader.GetAttribute("value");
break;
case "MS:1000896":
peptide.RetentionTime = double.Parse(reader.GetAttribute("value"), System.Globalization.CultureInfo.InvariantCulture);
break;
}
}
}
else if (reader.NodeType == XmlNodeType.EndElement && reader.LocalName == "Peptide")
{
cvParamsRead = true;
}
}
library.PeptideList.Add(peptide.Id, peptide);
}