public override IEnumerable <string> Process()
{
IsobaricResult result = BuildIsobaricResult();
Progress.SetMessage("Saving data to {0} ...", options.OutputFile);
IsobaricResultFileFormatFactory.GetXmlFormat().WriteToFile(options.OutputFile, result);
Progress.SetMessage("Done.");
return(new[] { options.OutputFile });
}
/// <summary>
/// 从isobaricFile中读取spectra对应的isobaric labelling信息。
/// </summary>
/// <param name="spectra"></param>
/// <param name="isobaricFile"></param>
/// <param name="progress"></param>
public static void Load(List <IIdentifiedSpectrum> spectra, string isobaricFile, bool readPeaks = false, IProgressCallback progress = null)
{
if (progress == null)
{
progress = new EmptyProgressCallback();
}
var fileNames = new HashSet <string>(from s in spectra
let fs = s.Query.FileScan
select fs.Experimental + "," + fs.FirstScan.ToString());
using (var reader = IsobaricResultFileFormatFactory.GetXmlReader(true, readPeaks))
{
var usedChannels = IsobaricScanXmlUtils.GetUsedChannels(isobaricFile);
reader.Open(isobaricFile);
progress.SetMessage("Reading Isobaric from {0} ...", isobaricFile);
progress.SetRange(1, spectra.Count);
foreach (var spectrum in spectra)
{
if (progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
progress.Increment(1);
var fs = spectrum.Query.FileScan;
if (reader.Has(fs.Experimental, fs.FirstScan))
{
spectrum.SetIsobaricItem(reader.Read(fs.Experimental, fs.FirstScan, usedChannels));
}
else
{
spectrum.SetIsobaricItem(null);
}
}
}
}
public virtual IsobaricResult BuildIsobaricResult()
{
Progress.SetMessage("Processing " + options.InputFile + " ...");
string experimental = Path.GetFileNameWithoutExtension(options.InputFile);
var format = IsobaricResultFileFormatFactory.GetXmlFormat();
format.Progress = this.Progress;
format.HasReporters = false;
IsobaricResult result = null;
var reader = options.Reader;
if (!File.Exists(options.OriginalXmlFileName))
{
reader.Progress = this.Progress;
Progress.SetMessage("Reading isobaric tag channels from " + new FileInfo(options.InputFile).Name + "...");
var pkls = reader.ReadFromFile(options.InputFile);
Progress.SetMessage("Reading isobaric tag channels finished.");
if (pkls.Count == 0)
{
throw new Exception(MyConvert.Format("No isobaric tag information readed from file {0}, contact with author.", options.InputFile));
}
result = new IsobaricResult(pkls);
result.Comments["Mode"] = reader.ToString();
result.PlexType = options.PlexType;
result.ForEach(m => m.Experimental = experimental);
format.WriteToFile(options.OriginalXmlFileName, result);
}
else
{
Progress.SetMessage("Reading xml information from " + options.OriginalXmlFileName + " ...");
result = format.ReadFromFile(options.OriginalXmlFileName);
}
result.UsedChannels = (from ucha in options.UsedChannels
let cha = options.PlexType.Channels[ucha.Index]
select new UsedChannel()
{
Index = ucha.Index, Name = cha.Name, Mz = cha.Mz, MinMz = cha.Mz - IsobaricConsts.MAX_SHIFT, MaxMz = cha.Mz + IsobaricConsts.MAX_SHIFT
}).ToList();
if (options.PerformMassCalibration)
{
Progress.SetMessage("Performing mass calibration ...");
var calPeaks = result.GetMassCalibrationPeaks();
result.UsedChannels.CalibrateMass(calPeaks, options.OutputFile + ".calibration");
result.Comments["PerformMassCalibration"] = true.ToString();
}
foreach (var channel in result.UsedChannels)
{
var mztolerance = PrecursorUtils.ppm2mz(channel.Mz, options.ProductPPMTolerance);
channel.MinMz = channel.Mz - mztolerance;
channel.MaxMz = channel.Mz + mztolerance;
}
Progress.SetMessage("Building isobaric result ...");
result.ForEach(m => m.DetectReporter(result.UsedChannels));
result.RemoveAll(m => m.PeakCount() < options.MinPeakCount);
result.Comments["RequiredChannels"] = (from c in options.RequiredChannels select c.Name).Merge(",");
if (options.RequiredChannels.Count > 0)
{
options.RequiredChannels.ForEach(m => m.Index = result.UsedChannels.FindIndex(l => l.Name.Equals(m.Name)));
result.RemoveAll(m =>
{
foreach (var channel in options.RequiredChannels)
{
if (channel.GetValue(m) <= IsobaricConsts.NULL_INTENSITY)
{
return(true);
}
}
return(false);
});
}
if (options.PerformPurityCorrection)
{
Progress.SetMessage("Performing purity correction ...");
var tempFilename = options.OutputFile + ".csv";
new IsobaricPurityCorrectionRCalculator(options.PlexType, result.UsedChannels, options.RExecute, options.PerformPurityCorrection, true).Calculate(result, tempFilename);
result.ForEach(m => m.Reporters.ForEach(p =>
{
if (p.Intensity < IsobaricConsts.NULL_INTENSITY)
{
p.Intensity = IsobaricConsts.NULL_INTENSITY;
}
}));
result.Comments["PerformPurityCorrection"] = true.ToString();
}
result.RemoveAll(m => m.PeakCount() < options.MinPeakCount);
Progress.SetMessage("Calculating precursor percentage ...");
result.ForEach(m => m.PrecursorPercentage = m.PeakInIsolationWindow.GetPrecursorPercentage(options.PrecursorPPMTolerance));
return(result);
}
