protected void AppendScan(List <IsobaricItem> result, int scan, string mode, double isolationWidth)
{
IsobaricItem item = new IsobaricItem();
PeakList <Peak> pkl = RawReader.GetPeakList(scan, MinMz, MaxMz);
if (pkl.Count < MinPeakCount)
{
return;
}
var recordScan = GetIdentificationScan(scan);
if (pkl.ScanTimes.Count == 0)
{
pkl.ScanTimes.Add(RawReader.GetScanTime(recordScan));
}
item.ScanMode = mode;
item.RawPeaks = pkl;
item.PeakInIsolationWindow = RawReader.GetPeakInIsolationWindow(scan, isolationWidth);
item.PlexType = this.PlexType;
result.Add(item);
}
public override List <IsobaricItem> ReadFromFile(string fileName)
{
var result = new List <IsobaricItem>();
RawReader.Open(fileName);
try
{
int startScan = RawReader.GetFirstSpectrumNumber();
int endScan = RawReader.GetLastSpectrumNumber();
Progress.SetRange(startScan, endScan);
for (int scan = startScan; scan <= endScan; scan++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.SetPosition(scan);
if (2 == RawReader.GetMsLevel(scan))
{
string scanMode = RawReader.GetScanMode(scan);
if (string.IsNullOrEmpty(scanMode))
{
AppendScan(result, scan, "UNKNOWN");
continue;
}
scanMode = scanMode.ToLower();
if (scanMode.Equals("pqd"))
{
AppendScan(result, scan, "PQD");
}
else if (scanMode.Equals("cid"))
{
//如果上一个scan是pqd，那么，现在这个cid的结果从该pqd读取。
if (result.Count > 0 && result[result.Count - 1].RawPeaks.ScanTimes[0].Scan == scan - 1 && result[result.Count - 1].RawPeaks.ScanMode == "PQD")
{
var lastItem = result[result.Count - 1];
var item = new IsobaricItem(lastItem);
item.Scan = RawReader.GetScanTime(scan);
item.ScanMode = "CID";
result.Add(item);
}
else//否则，从自己的peaklist中读取。
{
AppendScan(result, scan, "CID");
}
}
else
{
Console.WriteLine("Scan {0} is skipped with mode {1}", scan, scanMode);
}
}
}
}
finally
{
RawReader.Close();
}
return(result);
}