private SrmTransition ElementToTransaction(XElement xElement)
{
if (xElement == null)
{
return(null);
}
SrmTransition result = new SrmTransition(0, 0);
if (xElement.Element("Noise") != null)
{
result.Noise = MyConvert.ToDouble(xElement.Element("Noise").Value);
}
if (xElement.Element("SignalToNoise") != null)
{
result.SignalToNoise = MyConvert.ToDouble(xElement.Element("SignalToNoise").Value);
}
result.Intensities = (from a in xElement.Descendants("Scan")
select SrmScanFileFormat.ElementToScan(a)).ToList();
if (result.Intensities.Count > 0)
{
result.PrecursorMZ = result.Intensities[0].PrecursorMz;
result.ProductIon = result.Intensities[0].ProductMz;
}
return(result);
}
private XElement TransactionToElement(SrmTransition trans, string name)
{
if (trans == null)
{
return(null);
}
return(new XElement(name,
new XElement("Noise", trans.Noise),
new XElement("SignalToNoise", trans.SignalToNoise),
from s in trans.Intensities
select SrmScanFileFormat.ScanToElement(s, "Scan")));
}
private SrmPairedPeptideItem ItemToPeptide(XElement item)
{
if (item == null)
{
return(null);
}
SrmPairedPeptideItem result = new SrmPairedPeptideItem();
result.Enabled = Convert.ToBoolean(item.Element("Enabled").Value);
result.ProductIonPairs = new List <SrmPairedProductIon>();
foreach (var p in item.Descendants("ProductIonPair"))
{
SrmPairedProductIon ion = new SrmPairedProductIon();
ion.Enabled = Convert.ToBoolean(p.Element("Enabled").Value);
ion.Ratio = MyConvert.ToDouble(p.Element("Ratio").Value);
ion.Distance = MyConvert.ToDouble(p.Element("Distance").Value);
ion.RegressionCorrelation = MyConvert.ToDouble(p.Element("RegressionCorrelation").Value);
var scanEle = p.Elements("Scan");
if (scanEle.Count() > 0)
{
var scans = (from a in scanEle
select new SrmPairedScan()
{
Light = SrmScanFileFormat.ElementToScan(a.Element("Light")),
Heavy = SrmScanFileFormat.ElementToScan(a.Element("Heavy"))
}).ToList();
if (scans.Count > 0)
{
if (scans[0].Light != null)
{
var light = new SrmTransition(scans[0].Light.PrecursorMz, scans[0].Light.ProductMz);
light.Intensities = (from s in scans
select s.Light).ToList();
ion.Light = light;
}
if (scans[0].Heavy != null)
{
var heavy = new SrmTransition(scans[0].Heavy.PrecursorMz, scans[0].Heavy.ProductMz);
heavy.Intensities = (from s in scans
select s.Heavy).ToList();
ion.Heavy = heavy;
}
}
}
else
{
ion.Light = ElementToTransaction(p.Element("LightTransaction"));
ion.Heavy = ElementToTransaction(p.Element("HeavyTransaction"));
}
if (p.Element("LightArea") != null)
{
ion.LightArea = MyConvert.ToDouble(p.Element("LightArea").Value);
ion.HeavyArea = MyConvert.ToDouble(p.Element("HeavyArea").Value);
}
result.ProductIonPairs.Add(ion);
}
if (item.Element("Ratio") != null)
{
result.Ratio = MyConvert.ToDouble(item.Element("Ratio").Value);
if (item.Element("SD").Value.Equals("-"))
{
result.SD = double.NaN;
}
else
{
result.SD = MyConvert.ToDouble(item.Element("SD").Value);
}
}
else
{
result.CalculatePeptideRatio();
}
var objname = string.Empty;
var pepname = string.Empty;
var pepcharge = 0;
if (item.Element("ObjectName") != null)
{
objname = item.Element("ObjectName").Value;
}
if (item.Element("PrecursorFormula") != null)
{
pepname = item.Element("PrecursorFormula").Value;
}
if (item.Element("PrecursorCharge") != null)
{
pepcharge = int.Parse(item.Element("PrecursorCharge").Value);
}
result.ProductIonPairs.ForEach(m =>
{
if (m.Light != null)
{
m.Light.ObjectName = objname;
m.Light.PrecursorFormula = pepname;
m.Light.PrecursorCharge = pepcharge;
}
if (m.Heavy != null)
{
m.Heavy.ObjectName = objname;
m.Heavy.PrecursorFormula = pepname;
m.Heavy.PrecursorCharge = pepcharge;
}
});
return(result);
}
