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);
}