public void Open(string fileName)
{
var indexFile = IsobaricResultXmlIndexBuilder.GetTargetFile(fileName);
if (!File.Exists(indexFile))
{
new IsobaricResultXmlIndexBuilder()
{
Progress = this.Progress
}.Process(fileName);
}
Progress.SetMessage("Reading index from " + indexFile + " ...");
this._indexItems = new FileIndexFormat().ReadFromFile(indexFile).ToDictionary(m => m.Key);
Progress.SetMessage("Reading index from " + indexFile + " finished.");
this._stream = FileUtils.OpenReadFile(fileName);
}
public override void WriteToFile(string fileName, IsobaricResult t)
{
using (XmlTextWriter w = XmlUtils.CreateWriter(fileName, Encoding.ASCII))
{
StartWriteDocument(w, t);
foreach (var item in t)
{
WriteIsobaricItem(w, t, item);
}
EndWriteDocument(w);
}
var indexBuilder = new IsobaricResultXmlIndexBuilder(true)
{
Progress = this.Progress
};
indexBuilder.Process(fileName);
}
public override IEnumerable <string> Process(string targetFileName)
{
this.options.Reader.Progress = this.Progress;
List <string> resultFile = new List <string>();
List <IsobaricScan> result = new List <IsobaricScan>();
var format = new IsobaricResultXmlFormat();
XmlTextWriter sw = null;
try
{
for (int i = 0; i < options.RawFiles.Count(); i++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.SetMessage(1, MyConvert.Format("Processing {0}/{1} ...", i + 1, options.RawFiles.Count()));
var fileoptions = new IsobaricResultFileDistillerOptions()
{
Reader = options.Reader,
InputFile = options.RawFiles[i],
PerformMassCalibration = options.PerformMassCalibration,
PerformPurityCorrection = options.PerformPurityCorrection,
MinPeakCount = options.MinPeakCount,
PrecursorPPMTolerance = options.PrecursorPPMTolerance,
ProductPPMTolerance = options.ProductPPMTolerance,
RequiredChannels = options.RequiredChannels,
UsedChannels = options.UsedChannels
};
var distiller = new IsobaricResultFileDistiller(fileoptions)
{
Progress = this.Progress,
};
if (options.Individual)
{
string itraqFile = distiller.Process().First();
resultFile.Add(itraqFile);
}
else
{
var curResult = distiller.BuildIsobaricResult();
if (!options.Individual)
{
if (sw == null)
{
sw = XmlUtils.CreateWriter(targetFileName, Encoding.ASCII);
format.StartWriteDocument(sw, curResult);
}
}
foreach (var item in curResult)
{
format.WriteIsobaricItem(sw, curResult, item);
}
curResult = null;
}
GC.Collect();
GC.WaitForFullGCComplete();
}
Progress.SetMessage(0, "");
}
finally
{
if (!options.Individual && sw != null)
{
sw.Close();
}
}
if (!options.Individual)
{
var indexBuilder = new IsobaricResultXmlIndexBuilder(true)
{
Progress = this.Progress
};
indexBuilder.Process(targetFileName);
resultFile.Add(targetFileName);
}
Progress.SetMessage(1, "Finished!");
return(resultFile);
}
