public PeakList <Peak> GetPeakList(int scan)
{
if (cachePeaks.ContainsKey(scan))
{
return(cachePeaks[scan]);
}
return(rawFile.GetPeakList(scan));
}
public static PeakList <Peak> GetPeakInIsolationWindow(this IRawFile2 RawReader, int scan, double defaultIsolationWidth)
{
PeakList <Peak> result = new PeakList <Peak>();
var precursor = RawReader.GetPrecursorPeakWithMasterScan(scan);
if (precursor.MasterScan == 0)
{
return(result);
}
if (0 == precursor.IsolationWidth || precursor.IsolationWidth > 5.0)
{
precursor.IsolationWidth = defaultIsolationWidth;
}
var isolationWidth = precursor.IsolationWidth /= 2;
var minMz = precursor.IsolationMass - isolationWidth;
var maxMz = precursor.IsolationMass + isolationWidth;
result = RawReader.GetPeakList(precursor.MasterScan, minMz, maxMz);
result.Precursor = precursor;
return(result);
}
protected void AppendScan(IRawFile2 rawReader, List <IsobaricScan> result, int scan, string mode, double isolationWidth)
{
IsobaricScan item = new IsobaricScan();
PeakList <Peak> pkl = rawReader.GetPeakList(scan, MinMz, MaxMz);
if (pkl.Count < MinPeakCount)
{
return;
}
var recordScan = GetIdentificationScan(scan);
item.ScanMode = mode;
item.RawPeaks = pkl;
item.PeakInIsolationWindow = rawReader.GetPeakInIsolationWindow(scan, isolationWidth);
item.Scan = rawReader.GetScanTime(recordScan);
result.Add(item);
}
protected List <PeakList <Peak> > ReadTandemMassFromRaw(FileInfo rawFilename, List <int> ignoreScans)
{
string experimental = FileUtils.ChangeExtension(rawFilename.Name, "");
var result = new List <PeakList <Peak> >();
bool bReadAgain = false;
rawReader.Open(rawFilename.FullName);
try
{
int firstSpectrumNumber = rawReader.GetFirstSpectrumNumber();
int lastSpectrumNumber = rawReader.GetLastSpectrumNumber();
Progress.SetRange(firstSpectrumNumber, lastSpectrumNumber);
Progress.Begin();
try
{
for (int scan = firstSpectrumNumber; scan <= lastSpectrumNumber; scan++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
if (ignoreScans.Contains(scan))
{
continue;
}
Progress.SetPosition(scan);
int msLevel = rawReader.GetMsLevel(scan);
if (msLevel > 1)
{
PeakList <Peak> pkl;
try
{
pkl = rawReader.GetPeakList(scan);
}
catch (RawReadException ex)
{
ignoreScans.Add(ex.Scan);
File.WriteAllLines(GetIgnoreScanFile(rawFilename), (from i in ignoreScans
let s = i.ToString()
select s).ToArray());
bReadAgain = true;
break;
}
pkl.Precursor = rawReader.GetPrecursorPeakWithMasterScan(scan);
pkl.MsLevel = msLevel;
pkl.Experimental = experimental;
pkl.ScanTimes.Add(new ScanTime(scan, rawReader.ScanToRetentionTime(scan)));
pkl.ScanMode = rawReader.GetScanMode(scan);
if (pkl.PrecursorCharge == 0)
{
pkl.PrecursorCharge = PrecursorUtils.GuessPrecursorCharge(pkl, pkl.PrecursorMZ);
}
PeakList <Peak> pklProcessed = this.pklProcessor.Process(pkl);
if (null != pklProcessed && pklProcessed.Count > 0)
{
result.Add(pklProcessed);
}
}
}
}
finally
{
Progress.End();
}
}
finally
{
rawReader.Close();
}
if (bReadAgain)
{
return(ReadTandemMassFromRaw(rawFilename, ignoreScans));
}
else
{
return(result);
}
}
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);
}
