/// <summary>
/// Handle PeptideEvidence element
/// Called by ReadSequenceCollection (xml hierarchy)
/// </summary>
/// <param name="reader">XmlReader that is only valid for the scope of the single PeptideEvidence element</param>
private void ReadPeptideEvidence(XmlReader reader)
{
reader.MoveToContent();
var pepEvidence = new PeptideEvidence
{
IsDecoy = Convert.ToBoolean(reader.GetAttribute("isDecoy")),
Post = reader.GetAttribute("post"),
Pre = reader.GetAttribute("pre"),
End = Convert.ToInt32(reader.GetAttribute("end")),
Start = Convert.ToInt32(reader.GetAttribute("start")),
PeptideRef = m_peptides[reader.GetAttribute("peptide_ref")],
DbSeq = m_database[reader.GetAttribute("dBSequence_ref")]
};
m_evidences.Add(reader.GetAttribute("id"), pepEvidence);
reader.Close();
}
private void ComputeTerminusState(PeptideEvidence evidence, short numTrypticEnds, ProteinInformation protein)
{
if (evidence.Pre[0] == '-')
{
if (evidence.Post[0] == '-')
{
protein.TerminusState =
clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.ProteinNandCCTerminus;
protein.CleavageState = clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.Full;
}
else
{
protein.TerminusState = clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.ProteinNTerminus;
}
}
else if (evidence.Post[0] == '-')
{
protein.TerminusState = clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.ProteinCTerminus;
}
else
{
protein.TerminusState = clsPeptideCleavageStateCalculator.ePeptideTerminusStateConstants.None;
}
switch (numTrypticEnds)
{
case 0:
protein.CleavageState = clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.NonSpecific;
break;
case 1:
protein.CleavageState =
clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.Partial;
break;
case 2:
protein.CleavageState = clsPeptideCleavageStateCalculator.ePeptideCleavageStateConstants.Full;
break;
}
}
