public override IEnumerable <string> Process(string targetDir)
{
foreach (var raw in rawFiles)
{
List <SimplePeakChro> waitingPeaks = new List <SimplePeakChro>();
foreach (var peak in targetPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
if (force || !File.Exists(file))
{
waitingPeaks.Add(peak);
}
else
{
var p = new SimplePeakChroXmlFormat().ReadFromFile(file);
peak.MaxRetentionTime = p.MaxRetentionTime;
peak.Peaks = p.Peaks;
}
}
if (waitingPeaks.Count == 0)
{
continue;
}
rawReader.Open(raw);
try
{
int firstScan = rawReader.GetFirstSpectrumNumber();
int lastScan = rawReader.GetLastSpectrumNumber();
var lastRt = rawReader.ScanToRetentionTime(lastScan);
waitingPeaks.ForEach(m =>
{
m.Peaks.Clear();
m.MaxRetentionTime = lastRt;
});
Progress.SetMessage("Processing chromotograph extracting...");
Progress.SetRange(firstScan, lastScan);
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (rawReader.GetMsLevel(scan) != 1)
{
continue;
}
Progress.SetPosition(scan);
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
PeakList <Peak> pkl = rawReader.GetPeakList(scan);
double rt = rawReader.ScanToRetentionTime(scan);
foreach (var peak in waitingPeaks)
{
var env = pkl.FindPeak(peak.Mz, peak.MzTolerance);
Peak findPeak = new Peak(peak.Mz, 0.0, 0);
if (env.Count > 0)
{
if (env.Count == 1)
{
findPeak = env[0];
}
else
{
var charge = env.FindCharge(peak.Charge);
if (charge.Count > 0)
{
if (charge.Count == 1)
{
findPeak = charge[0];
}
else
{
findPeak = charge.FindMaxIntensityPeak();
}
}
else
{
findPeak = env.FindMaxIntensityPeak();
}
}
}
peak.Peaks.Add(new ScanPeak()
{
Mz = findPeak.Mz,
Intensity = findPeak.Intensity,
Scan = scan,
RetentionTime = rt,
Charge = findPeak.Charge,
PPMDistance = PrecursorUtils.mz2ppm(peak.Mz, findPeak.Mz - peak.Mz)
});
}
}
waitingPeaks.ForEach(m => m.TrimPeaks(minRetentionTime));
}
finally
{
rawReader.Close();
}
Progress.SetMessage("Saving ... ");
foreach (var peak in waitingPeaks)
{
string file = GetTargetFile(targetDir, raw, peak);
new SimplePeakChroXmlFormat().WriteToFile(file, peak);
}
Progress.SetMessage("Finished.");
Progress.End();
}
return(new string[] { targetDir });
}
private void lvPeptides_SelectedIndexChanged(object sender, EventArgs e)
{
if (lvPeptides.SelectedItems.Count > 0)
{
var spectrum = lvPeptides.SelectedItems[0].Tag as IIdentifiedSpectrum;
var file = ProteinChromatographProcessor.GetTargetFile(GetOriginFile(), rawFile.FullName, SpectrumToChro(spectrum));
var chro = new SimplePeakChroXmlFormat().ReadFromFile(file);
try
{
zgcScans.ClearData(false);
var mainPane = ZedGraphicExtension.InitMasterPanel(zgcScans, CreateGraphics(), 2, "Chromotograph");
if (chro.Peaks.Count > 0)
{
var pplSample = new PointPairList();
var pplppm = new PointPairList();
var bFirst = true;
foreach (ScanPeak p in chro.Peaks)
{
pplSample.Add(p.RetentionTime, p.Intensity);
pplppm.Add(p.RetentionTime, p.PPMDistance);
//if (p.Intensity > 0)
//{
// pplSample.Add(p.RetentionTime, p.Intensity);
// pplppm.Add(p.RetentionTime, p.PPMDistance);
//}
//else if (pplSample.Count > 0)
//{
// if (bFirst)
// {
// mainPane.PaneList[0].AddCurve(MyConvert.Format("{0:0.0000},{1}", chro.Mz, chro.Charge), pplSample, Color.Red, SymbolType.None);
// mainPane.PaneList[1].AddCurve(MyConvert.Format("{0:0.0000},{1}", chro.Mz, chro.Charge), pplppm, Color.Red, SymbolType.None);
// }
// else
// {
// mainPane.PaneList[0].AddCurve("a", pplSample, Color.Red, SymbolType.None);
// mainPane.PaneList[1].AddCurve("a", pplppm, Color.Red, SymbolType.None);
// }
// pplSample.Clear();
// pplppm.Clear();
// bFirst = false;
//}
}
if (pplSample.Count > 0)
{
if (bFirst)
{
mainPane.PaneList[0].AddCurve(MyConvert.Format("{0:0.0000},{1}", chro.Mz, chro.Charge), pplSample, Color.Red, SymbolType.None);
mainPane.PaneList[1].AddCurve(MyConvert.Format("{0:0.0000},{1}", chro.Mz, chro.Charge), pplppm, Color.Red, SymbolType.None);
}
else
{
mainPane.PaneList[0].AddCurve("a", pplSample, Color.Red, SymbolType.None);
mainPane.PaneList[1].AddCurve("a", pplppm, Color.Red, SymbolType.None);
}
}
}
}
finally
{
ZedGraphicExtension.UpdateGraph(zgcScans);
}
}
}
