private O18QuanEnvelope GetCorrespondingEnvelope(IRawFile rawFile, double theoreticalMz, int charge, double mzTolerance, int scan)
{
PeakList <Peak> pkl = rawFile.GetPeakList(scan);
if (pkl.ScanTimes.Count == 0)
{
pkl.ScanTimes.Add(new ScanTime(scan, rawFile.ScanToRetentionTime(scan)));
}
PeakList <Peak> O16 = pkl.FindEnvelopeDirectly(theoreticalMz, charge, mzTolerance, 4, () => new Peak());
PeakList <Peak> O181 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap1[charge], charge, mzTolerance, 2, () => new Peak());
for (int i = 2; i < 4; i++)
{
if (O16[i].Intensity < O181[i - 2].Intensity)
{
O16[i].Mz = O181[i - 2].Mz;
O16[i].Intensity = O181[i - 2].Intensity;
}
}
PeakList <Peak> O182 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap2[charge], charge, mzTolerance, 2, () => new Peak());
O16.AddRange(O182);
return(new O18QuanEnvelope(O16));
}
public static QuantificationScan GetQuantificationScan(this PeakList <Peak> observed, List <Envelope> theoretical, double mzTolerance)
{
QuantificationScan result = new QuantificationScan();
result.Envelopes = new List <QuantificationEnvelope>();
foreach (var mz in theoretical)
{
var pkl = observed.FindEnvelopeDirectly(mz, mzTolerance, () => new Peak());
result.Envelopes.Add(new QuantificationEnvelope(mz.ToArray(), pkl.ToArray()));
}
return(result);
}
private SilacPeakListPair GetLightHeavyPeakList(IRawFile rawFile, SilacCompoundInfo sci, int maxIndex, double mzTolerance, int scan, bool force = false)
{
PeakList <Peak> pkl = rawFile.GetPeakList(scan);
if (pkl.Count == 0)
{
return(null);
}
var scantime = new ScanTime(scan, rawFile.ScanToRetentionTime(scan));
PeakList <Peak> light = pkl.FindEnvelopeDirectly(sci.Light.Profile, option.ProfileLength, mzTolerance, () => new Peak());
//如果电荷不对，则认为该scan无效。
if (!CheckPeakListCharge(light, maxIndex, sci.Light.Charge) && !force)
{
return(null);
}
PeakList <Peak> heavy = pkl.FindEnvelopeDirectly(sci.Heavy.Profile, option.ProfileLength, mzTolerance, () => new Peak());
//如果电荷不对，则认为该scan无效。
if (!CheckPeakListCharge(heavy, maxIndex, sci.Heavy.Charge) && !force)
{
return(null);
}
//如果轻或者重的总强度为0，则认为该scan无效。
if ((0 == light.Sum(m => m.Intensity) || 0 == heavy.Sum(m => m.Intensity)) && !force)
{
return(null);
}
light.ScanTimes.Add(scantime);
heavy.ScanTimes.Add(scantime);
return(new SilacPeakListPair(light, heavy));
}
public override IEnumerable <string> Process(string targetDir)
{
foreach (var raw in rawFiles)
{
List <RetentionTimePeak> waitingPeaks = new List <RetentionTimePeak>();
foreach (var peak in targetPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
if (force || !File.Exists(file))
{
waitingPeaks.Add(peak);
}
}
if (waitingPeaks.Count == 0)
{
continue;
}
rawReader.Open(raw);
try
{
int firstScan = rawReader.GetFirstSpectrumNumber();
int lastScan = rawReader.GetLastSpectrumNumber();
waitingPeaks.ForEach(m => m.Chromotographs.Clear());
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (rawReader.GetMsLevel(scan) != 1)
{
continue;
}
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
PeakList <Peak> pkl = rawReader.GetPeakList(scan);
double rt = rawReader.ScanToRetentionTime(scan);
var st = new ScanTime(scan, rt);
foreach (var peak in waitingPeaks)
{
var env = pkl.FindEnvelopeDirectly(peak.PeakEnvelope, peak.MzTolerance, () => new Peak());
env.ScanTimes.Add(st);
peak.Chromotographs.Add(env);
}
}
waitingPeaks.ForEach(m => m.TrimPeaks());
}
finally
{
rawReader.Close();
}
foreach (var peak in waitingPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
new RetentionTimePeakXmlFormat().WriteToFile(file, peak);
}
}
return(new string[] { targetDir });
}
