public PeakList()
{
ScanMode = string.Empty;
PrecursorPercentage = 0.0;
Precursor = new PrecursorPeak();
CombinedCount = 1;
}
protected virtual IEnumerable <string> DoProcess(string fileName, List <int> ignoreScans, int lastScan, bool bContinue)
{
var result = new List <string>();
bool bReadAgain = false;
using (var rawReader = RawFileFactory.GetRawFileReader(fileName))
{
try
{
if (!bContinue)
{
DoInitialize(rawReader, fileName);
}
string experimental = rawReader.GetFileNameWithoutExtension(fileName);
SetMessage("Processing " + fileName + " ...");
int firstSpectrumNumber = rawReader.GetFirstSpectrumNumber();
int lastSpectrumNumber = rawReader.GetLastSpectrumNumber();
//int firstSpectrumNumber = 79800;
SetRange(firstSpectrumNumber, lastSpectrumNumber);
lastScan = Math.Max(lastScan, firstSpectrumNumber);
for (int scan = lastScan; scan <= lastSpectrumNumber; scan++)
{
lastScan = scan;
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
if (IsLoopStopped)
{
return(result);
}
if (ignoreScans.Contains(scan))
{
continue;
}
SetPosition(scan);
int msLevel = rawReader.GetMsLevel(scan);
if (!DoAcceptMsLevel(msLevel))
{
continue;
}
//Console.WriteLine("Reading scan {0}", scan);
PeakList <Peak> pkl;
try
{
PrecursorPeak precursor = null;
if (msLevel > 1)
{
precursor = new PrecursorPeak(rawReader.GetPrecursorPeak(scan));
}
pkl = rawReader.GetPeakList(scan);
pkl.MsLevel = msLevel;
pkl.Experimental = experimental;
pkl.ScanMode = rawReader.GetScanMode(scan);
pkl.Precursor = precursor;
if (msLevel > 1 && precursor.Charge == 0)
{
precursor.Charge = PrecursorUtils.GuessPrecursorCharge(pkl, pkl.PrecursorMZ);
}
}
catch
{
Console.WriteLine("Scan {0} ignored.", scan);
ignoreScans.Add(scan);
File.WriteAllLines(GetIgnoreScanFile(fileName), (from i in ignoreScans
let s = i.ToString()
select s).ToArray());
bReadAgain = true;
break;
}
PeakList <Peak> pklProcessed;
if (msLevel > 1)
{
if (null == this.PeakListProcessor || (options.ExtractRawMS3 && pkl.MsLevel >= 3))
{
pklProcessed = pkl;
}
else
{
pklProcessed = this.PeakListProcessor.Process(pkl);
}
}
else
{
pklProcessed = pkl;
}
if (null != pklProcessed && pklProcessed.Count > 0)
{
DoWritePeakList(rawReader, pklProcessed, fileName, result);
}
}
}
finally
{
if (!bReadAgain)
{
DoFinalize(bReadAgain, rawReader, fileName, result);
}
}
}
if (bReadAgain)
{
return(DoProcess(fileName, ignoreScans, lastScan, true));
}
else
{
return(result);
}
}
