private int DoWritePeakList(IRawFile2 rawReader, int scan, string fileName, List <string> returnFiles, string experimental, int lastSpectrumNumber, List <int> ignoreScans, ref bool bReadAgain)
{
var result = scan + 1;
if (ignoreScans.Contains(scan))
{
return(result);
}
SetPosition(scan);
int msLevel = rawReader.GetMsLevel(scan);
if (!DoAcceptMsLevel(msLevel))
{
return(result);
}
//Console.WriteLine("Reading scan {0}", scan);
PeakList <Peak> pkl;
try
{
pkl = rawReader.GetPeakList(scan);
}
catch (RawReadException ex)
{
ignoreScans.Add(ex.Scan);
File.WriteAllLines(GetIgnoreScanFile(fileName), (from i in ignoreScans
let s = i.ToString()
select s).ToArray());
bReadAgain = true;
return(result);
}
pkl.MsLevel = msLevel;
pkl.Experimental = experimental;
pkl.ScanTimes.Add(new ScanTime(scan, rawReader.ScanToRetentionTime(scan)));
pkl.ScanMode = rawReader.GetScanMode(scan);
PeakList <Peak> pklProcessed;
if (msLevel > 1)
{
pkl.Precursor = new PrecursorPeak(rawReader.GetPrecursorPeak(scan));
if (pkl.PrecursorCharge == 0)
{
pkl.PrecursorCharge = PrecursorUtils.GuessPrecursorCharge(pkl, pkl.PrecursorMZ);
}
if (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, returnFiles);
if (!options.MzXmlNestedScan)
{
var intent = GetScanIntent(pkl.MsLevel);
sw.WriteLine(intent + "</scan>");
}
while (result < lastSpectrumNumber && rawReader.GetMsLevel(result) > msLevel)
{
result = DoWritePeakList(rawReader, result, fileName, returnFiles, experimental, lastSpectrumNumber, ignoreScans, ref bReadAgain);
if (bReadAgain)
{
return(result);
}
}
if (options.MzXmlNestedScan)
{
var intent = GetScanIntent(pkl.MsLevel);
sw.WriteLine(intent + "</scan>");
}
}
return(result);
}
public RCPA.Proteomics.Spectrum.Peak GetPrecursorPeak(int scan)
{
return(rawFile.GetPrecursorPeak(scan));
}