/// <summary>
/// Get corresponding isolation scan
/// </summary>
/// <param name="scan"></param>
/// <returns></returns>
protected virtual int GetIsolationScan(int scan)
{
var mslevel = RawReader.GetMsLevel(scan);
var targetlevel = mslevel - 1;
scan--;
while (scan >= FirstScan)
{
if (targetlevel == RawReader.GetMsLevel(scan))
{
return(scan);
}
}
return(scan);
}
protected override int GetMS2Scan(int scan)
{
var result = scan;
while (true)
{
var msLevel = RawReader.GetMsLevel(result);
if (msLevel == 2)
{
break;
}
result--;
if (result < FirstScan)
{
result = scan;
break;
}
}
return(result);
}
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);
}
public virtual List <IsobaricItem> ReadFromFile(string fileName)
{
var result = new List <IsobaricItem>();
var askedScanMode = GetScanMode();
var lowerScanMode = new HashSet <string>(from a in askedScanMode
select a.ToLower());
RawReader.Open(fileName);
try
{
FirstScan = RawReader.GetFirstSpectrumNumber();
EndScan = RawReader.GetLastSpectrumNumber();
DoAfterFileOpen();
var firstIsolationWidth = 0.0;
var icount = 0;
for (int scan = FirstScan; scan <= EndScan; scan++)
{
if (!RawReader.IsScanValid(scan))
{
continue;
}
if (this.MsLevel == RawReader.GetMsLevel(scan))
{
firstIsolationWidth = RawReader.GetIsolationWidth(scan);
if (firstIsolationWidth > 0 && firstIsolationWidth < 5)
{
break;
}
icount++;
if (icount > 10)
{
break;
}
}
}
if (firstIsolationWidth == 0.0)
{
firstIsolationWidth = defaultIsolationWidth;
}
Progress.SetMessage("Reading channel information ...");
Progress.SetRange(FirstScan, EndScan);
for (int scan = FirstScan; scan <= EndScan; scan++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
if (!RawReader.IsScanValid(scan))
{
continue;
}
Progress.SetPosition(scan);
if (this.MsLevel == RawReader.GetMsLevel(scan))
{
string scanMode = RawReader.GetScanMode(scan).ToLower();
if (string.IsNullOrEmpty(scanMode))
{
AppendScan(result, scan, "UNKNOWN", firstIsolationWidth);
}
else if (lowerScanMode.Count == 0 || lowerScanMode.Contains(scanMode))
{
AppendScan(result, scan, scanMode.ToUpper(), firstIsolationWidth);
}
else
{
Console.WriteLine("Scan {0} is skipped with mode {1}", scan, scanMode);
}
}
}
}
finally
{
RawReader.Close();
}
return(result);
}