/// <summary>
/// Handle a single SpectrumIdentificationResult element and child nodes
/// Called by ReadSpectrumIdentificationList (xml hierarchy)
/// </summary>
/// <param name="result">PSM result</param>
/// <param name="psmResults"></param>
private void ProcessSpectrumIdentificationResult(SimpleMZIdentMLReader.SpectrumIdItem result, ICollection <IdentData> psmResults)
{
var data = new IdentData
{
NativeId = result.NativeId,
ScanId = (ulong)result.ScanNum,
ScanTimeSeconds = result.ScanTimeMinutes * 60,
CalcMz = result.CalMz,
ExperMz = result.ExperimentalMz,
Charge = result.Charge,
ThresholdValue = result.SpecEv // MS-GF:SpecEValue
};
//data.MassError = data.ExperMz - data.CalcMz;
//data.PpmError = (data.MassError / data.CalcMz) * 1.0e6;
if (IdentProg == IdentProgramType.MyriMatch &&
result.AllParamsDict.TryGetValue("MyriMatch:MVH", out var valueText) &&
double.TryParse(valueText, out var value))
{
data.ThresholdValue = value;
}
if (PassesThreshold(data) && PassesWindows(data))
{
psmResults.Add(data);
}
if (data.ScanTimeSeconds > 0)
{
HaveScanTimes = true;
}
}
private bool PassesThreshold(IdentData data)
{
if (IdentProg == IdentProgramType.MSGFPlus)
{
return(data.ThresholdValue <= _specEValueThreshold);
}
if (IdentProg == IdentProgramType.MyriMatch)
{
return(data.ThresholdValue >= _mvhThreshold);
}
// If neither, return everything
return(true);
}
private bool PassesWindows(IdentData data)
{
return(-IsotopeErrorFilterWindow < data.MassError && data.MassError < IsotopeErrorFilterWindow &&
-PpmErrorFilterWindow < data.PpmError && data.PpmError < PpmErrorFilterWindow);
}
