private bool AddPeaks(IRawFile rawReader, int scan, SimplePeakChro chro, bool bIdentified)
{
var pkl = rawReader.GetPeakList(scan, chro.Mz - chro.MzTolerance, chro.Mz + chro.MzTolerance);
if (pkl.Count == 0)
{
return(false);
}
var p = (from o in pkl
where (o.Charge == chro.Charge) || (o.Charge == 0)
orderby o.Intensity descending
select o).FirstOrDefault();
if (null == p)
{
return(false);
}
var iit = rawReader.GetIonInjectionTime(scan);
if (iit <= 0)
{
iit = 1.0;
}
chro.Peaks.Add(new ScanPeak()
{
Mz = p.Mz,
Intensity = p.Intensity,
Charge = p.Charge,
Scan = scan,
RetentionTime = rawReader.ScanToRetentionTime(scan),
IonInjectionTime = iit,
Identified = bIdentified
});
return(true);
}
public override IEnumerable <string> Process(string targetDir)
{
if (!Directory.Exists(targetDir))
{
Directory.CreateDirectory(targetDir);
}
var option = new ParallelOptions()
{
MaxDegreeOfParallelism = Environment.ProcessorCount,
CancellationToken = token
};
foreach (var entry in this.spectra)
{
if (!this.rawFiles.ContainsKey(entry.Key))
{
throw new Exception(string.Format("Cannot find raw file for {0}", entry.Key));
}
}
SimplePeakChroPngWriter writer = new SimplePeakChroPngWriter();
Parallel.ForEach(spectra, option, raw =>
{
var peptides = raw.ToList();
var waitingPeaks = new List <IIdentifiedSpectrum>();
foreach (var peak in peptides)
{
string file = GetTargetFile(targetDir, peak);
if (force || !File.Exists(file))
{
waitingPeaks.Add(peak);
}
}
if (waitingPeaks.Count == 0)
{
return;
}
using (var rawReader = new CacheRawFile(RawFileFactory.GetRawFileReader(this.rawFiles[raw.Key.ToLower()])))
{
int firstScan = rawReader.GetFirstSpectrumNumber();
int lastScan = rawReader.GetLastSpectrumNumber();
foreach (var peak in waitingPeaks)
{
//if (peak.Query.FileScan.FirstScan != 7628)
//{
// continue;
//}
var chro = new SimplePeakChro();
chro.Mz = peak.ObservedMz;
chro.Charge = peak.Query.Charge;
chro.MzTolerance = PrecursorUtils.ppm2mz(chro.Mz, this.ppmTolerance);
chro.Sequence = peak.Sequence;
bool bFirst = true;
for (int scan = peak.Query.FileScan.FirstScan - 1; scan >= firstScan; scan--)
{
if (Progress.IsCancellationPending())
{
return;
}
if (rawReader.GetMsLevel(scan) == 1)
{
if (!AddPeaks(rawReader, scan, chro, bFirst))
{
break;
}
bFirst = false;
}
}
chro.Peaks.Reverse();
for (int scan = peak.Query.FileScan.FirstScan + 1; scan <= lastScan; scan++)
{
if (Progress.IsCancellationPending())
{
return;
}
if (rawReader.GetMsLevel(scan) == 1)
{
if (!AddPeaks(rawReader, scan, chro, false))
{
break;
}
}
}
string file = GetTargetFile(targetDir, peak);
new SimplePeakChroXmlFormat().WriteToFile(file, chro);
var pngFile = GetTargetImageFile(targetDir, peak);
writer.WriteToFile(pngFile, chro);
}
}
});
return(new string[] { targetDir });
}
public static string GetTargetFile(string targetDir, string raw, SimplePeakChro peak)
{
var result = MyConvert.Format(@"{0}\{1}_{2}_{3:0.0000}_{4}.chro", targetDir, FileUtils.ChangeExtension(new FileInfo(raw).Name, ""), peak.Sequence, peak.Mz, peak.Charge);
return(new FileInfo(result).FullName);
}
