private PeakListRemovePrecursorProcessorOptions GetPrecursorOptions()
{
var options = new PeakListRemovePrecursorProcessorOptions();
options.RemovePrecursor = cbRemovePrecursor.Checked;
if (options.RemovePrecursor)
{
options.NeutralLoss = txtNeutralLoss.Text;
options.RemoveChargeMinus1Precursor = cbRemovePrecursorMinus1ChargeIon.Checked;
options.RemoveIonLargerThanPrecursor = cbRemovePrecursorLargeIons.Checked;
options.RemoveIsotopicIons = cbRemovePrecursorIsotopicIons.Checked;
try
{
options.PPMTolerance = double.Parse(txtPrecursorPPM.Text);
}
catch (Exception)
{
throw new Exception("Input precursor PPM first!");
}
}
return(options);
}
public void Load(XElement parentNode)
{
TargetDirectory = parentNode.Element("TargetDirectory").Value;
RawFiles = (from file in parentNode.Element("RawFiles").Elements("File")
select file.Value).ToArray();
MascotTitleName = parentNode.Element("MascotTitleName").Value;
PrecursorMassRange = new MassRange(double.Parse(parentNode.Element("PrecursorMassRange").Attribute("From").Value), double.Parse(parentNode.Element("PrecursorMassRange").Attribute("To").Value));
MinimumIonIntensity = double.Parse(parentNode.Element("MinimumIonIntensity").Value);
MinimumIonCount = int.Parse(parentNode.Element("MinimumIonCount").Value);
MinimumTotalIonIntensity = int.Parse(parentNode.Element("MinimumTotalIonIntensity").Value);
DefaultCharges = new ChargeClass((from charge in parentNode.Element("DefaultCharges").Elements("Charge")
select int.Parse(charge.Value)).ToArray());
ProductIonPPM = double.Parse(parentNode.Element("ProductIonPPM").Value);
Deisotopic = bool.Parse(parentNode.Element("Deisotopic").Value);
ChargeDeconvolution = bool.Parse(parentNode.Element("ChargeDeconvolution").Value);
KeepTopX = bool.Parse(parentNode.Element("KeepTopX").Value);
TopX = int.Parse(parentNode.Element("TopX").Value);
GroupByMode = bool.Parse(parentNode.Element("GroupByMode").Value);
GroupByMsLevel = bool.Parse(parentNode.Element("GroupByMsLevel").Value);
ParallelMode = bool.Parse(parentNode.Element("ParallelMode").Value);
ExtractRawMS3 = bool.Parse(parentNode.Element("ExtractRawMS3").Value);
Overwrite = bool.Parse(parentNode.Element("Overwrite").Value);
OutputMzXmlFormat = bool.Parse(parentNode.Element("OutputMzXmlFormat").Value);
MzXmlNestedScan = bool.Parse(parentNode.Element("MzXmlNestedScan").Value);
RemoveIons = bool.Parse(parentNode.Element("RemoveIons").Value);
RemoveIonWindow = double.Parse(parentNode.Element("RemoveIonWindow").Value);
RemoveSpecialIons = bool.Parse(parentNode.Element("RemoveSpecialIons").Value);
SpecialIons = parentNode.Element("SpecialIons").Value;
RemoveIsobaricIons = bool.Parse(parentNode.Element("RemoveIsobaricIons").Value);
IsobaricType = IsobaricTypeFactory.Find(parentNode.Element("IsobaricType").Value);
ProteaseName = parentNode.Element("ProteaseName").Value;
RemoveIsobaricIonsReporters = bool.Parse(parentNode.Element("RemoveIsobaricIonsReporters").Value);
RemoveIsobaricIonsInLowRange = bool.Parse(parentNode.Element("RemoveIsobaricIonsInLowRange").Value);
RemoveIsobaricIonsInHighRange = bool.Parse(parentNode.Element("RemoveIsobaricIonsInHighRange").Value);
var precursorNode = parentNode.Element("Precursor");
PrecursorOptions = new PeakListRemovePrecursorProcessorOptions();
PrecursorOptions.RemovePrecursor = bool.Parse(precursorNode.Element("RemovePrecursor").Value);
PrecursorOptions.PPMTolerance = double.Parse(precursorNode.Element("PPMTolerance").Value);
PrecursorOptions.RemoveNeutralLoss = bool.Parse(precursorNode.Element("RemoveNeutralLoss").Value);
PrecursorOptions.NeutralLoss = precursorNode.Element("NeutralLoss").Value;
PrecursorOptions.RemoveChargeMinus1Precursor = bool.Parse(precursorNode.Element("RemoveChargeMinus1Precursor").Value);
PrecursorOptions.RemoveIsotopicIons = bool.Parse(precursorNode.Element("RemoveIsotopicIons").Value);
PrecursorOptions.RemoveIonLargerThanPrecursor = bool.Parse(precursorNode.Element("RemoveIonsLargerThanPrecursor").Value);
}
