public void Normalize(IsobaricResult result)
{
if (result.Count == 0)
{
return;
}
if (ByIonInjectionTime && result.HasIonInjectionTime())
{
result.ForEach(m => m.MultiplyIntensityByInjectionTime());
}
var defs = result.First().Definition.Items;
var sums = (from def in defs
select GetIonBase(result, m => m[def.Index])).ToArray();
for (int i = 1; i < sums.Length; i++)
{
sums[i] = sums[0] / sums[i];
}
result.ForEach(m =>
{
for (int i = 1; i < defs.Length; i++)
{
m[defs[i].Index] *= sums[i];
}
});
if (ByIonInjectionTime && result.HasIonInjectionTime())
{
result.ForEach(m => m.DevideIntensityByInjectionTime());
}
}
public IsobaricResult GetTraqResult(string rawFileName)
{
Progress.SetMessage("Processing " + rawFileName + " ...");
string experimental = FileUtils.ChangeExtension(new FileInfo(rawFileName).Name, "");
string originalFileName = GetOriginalITraqFileName(rawFileName);
string paramFileName = originalFileName + ".param";
IsobaricResult result = null;
ITraqFileBuilder builder = new ITraqFileBuilder(itraqReader.PlexType.GetDefinition());
if (!CheckOriginalFile(originalFileName) || !File.Exists(paramFileName))
{
itraqReader.Progress = this.Progress;
Progress.SetMessage("Reading isobaric tag channels from " + new FileInfo(rawFileName).Name + "...");
List <IsobaricItem> pkls = itraqReader.ReadFromFile(rawFileName);
Progress.SetMessage("Reading isobaric tag channels finished.");
if (pkls.Count == 0)
{
throw new Exception(MyConvert.Format("No isobaric tag information readed from file {0}, contact with author.", rawFileName));
}
var accs = builder.GetDistances(from pkl in pkls select pkl.RawPeaks);
if (accs.Count == 0)
{
throw new Exception(MyConvert.Format("No isobaric tag information readed from file {0}, contact with author.", rawFileName));
}
result = builder.GetITraqResult(pkls, accs, SigmaFoldTolerance, 1);
result.Mode = itraqReader.ToString();
result.ForEach(m => m.Experimental = experimental);
ITraqResultFileFormatFactory.GetXmlFormat().WriteToFile(originalFileName, result);
using (StreamWriter sw = new StreamWriter(paramFileName))
{
sw.WriteLine("Ion\tDetectedIon\tDeltaMass\tDeltaPPM\tDetectedSigma");
var ions = builder.Definition.Items;
for (int i = 0; i < ions.Length; i++)
{
sw.WriteLine("{0:0.00000}\t{1:0.00000}\t{2:0.00000}\t{3:0.00}\t{4:0.00000}", ions[i].Mass, ions[i].Mass + accs[i].Mean, accs[i].Mean, PrecursorUtils.mz2ppm(ions[i].Mass, accs[i].Mean), accs[i].StdDev);
}
}
}
else
{
Progress.SetMessage("Read xml information from " + originalFileName + " ...");
var format = ITraqResultFileFormatFactory.GetXmlFormat();
format.Progress = this.Progress;
result = format.ReadFromFile(originalFileName);
}
result.RemoveAll(m => m.PeakCount() < minPeakCount);
result.ForEach(m => calc.Correct(m));
result.RemoveAll(m => m.PeakCount() < minPeakCount);
result.ForEach(m => m.PrecursorPercentage = m.PeakInIsolationWindow.GetPrecursorPercentage(this.precursorPPM));
if (NormalizationBuilder != null)
{
NormalizationBuilder.Normalize(result);
}
return(result);
}