public override IEnumerable <string> Process(string filename)
{
string msLevelFilename = filename + ".msLevel";
using (IRawFile rawFile = new RawFileImpl(filename))
{
using (var sw = new StreamWriter(msLevelFilename))
{
int firstScan = rawFile.GetFirstSpectrumNumber();
int lastScan = rawFile.GetLastSpectrumNumber();
Progress.SetRange(rawFile.GetFirstSpectrumNumber(), rawFile.GetLastSpectrumNumber());
Progress.SetMessage("Processing " + filename + "...");
sw.WriteLine("Scan\tMsLevel");
for (int scan = firstScan; scan <= lastScan; scan++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
sw.WriteLine(scan + "\t" + rawFile.GetMsLevel(scan));
Progress.SetPosition(scan);
}
Progress.SetPosition(lastScan);
Progress.SetMessage("Processing " + filename + " finished.");
}
}
return(new[] { msLevelFilename });
}
public override IEnumerable <string> Process(string fileName)
{
string resultFilename = fileName + ".tic";
if (ignoreWhenResultExist && File.Exists(resultFilename))
{
return(new string[] { resultFilename });
}
using (IRawFile reader = new RawFileImpl(fileName))
{
Progress.SetMessage(MyConvert.Format("Processing {0} ...", new FileInfo(fileName).Name));
using (StreamWriter sw = new StreamWriter(resultFilename))
{
sw.WriteLine("Scan\tMode\tPrecursor\tTIC");
int firstScan = reader.GetFirstSpectrumNumber();
int lastScan = reader.GetLastSpectrumNumber();
Progress.SetRange(firstScan, lastScan);
for (int i = firstScan; i <= lastScan; i++)
{
if (Progress.IsCancellationPending())
{
sw.Close();
File.Delete(resultFilename);
throw new UserTerminatedException();
}
if (1 == reader.GetMsLevel(i))
{
continue;
}
PeakList <Peak> pkl = reader.GetPeakList(i);
Peak precursor = reader.GetPrecursorPeak(i);
double tic = (from p in pkl
select p.Intensity).Sum();
string mode = reader.GetScanMode(i);
sw.WriteLine("{0}\t{1}\t{2:0.0000}\t{3:0.0}", i, mode.ToUpper(), precursor.Mz, tic);
Progress.SetPosition(i);
}
Progress.End();
}
Progress.SetMessage(MyConvert.Format("Processing {0} finished.", new FileInfo(fileName).Name));
}
return(new string[] { resultFilename });
}
