public void TestBuild()
{
var indexFile = new ITraqResultXmlIndexBuilder(true).Process(dataFile).First();
FileAssert.AreEqual(expectFile, indexFile);
File.Delete(indexFile);
}
public void Open(string fileName)
{
var indexFile = ITraqResultXmlIndexBuilder.GetTargetFile(fileName);
if (!File.Exists(indexFile))
{
new ITraqResultXmlIndexBuilder()
{
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.Mode);
foreach (var item in t)
{
WriteIsobaricItem(w, item);
}
EndWriteDocument(w);
}
var indexBuilder = new ITraqResultXmlIndexBuilder(true)
{
Progress = this.Progress
};
indexBuilder.Process(fileName);
}
public override IEnumerable <string> Process(string targetFileName)
{
this.reader.Progress = this.Progress;
List <string> resultFile = new List <string>();
List <IsobaricItem> result = new List <IsobaricItem>();
ITraqResultXmlFormatFast format = new ITraqResultXmlFormatFast();
XmlTextWriter sw = null;
if (!individual)
{
sw = XmlUtils.CreateWriter(targetFileName, Encoding.ASCII);
ITraqResultXmlFormatFast.StartWriteDocument(sw, reader.ToString());
}
try
{
for (int i = 0; i < rawFiles.Count(); i++)
{
if (Progress.IsCancellationPending())
{
throw new UserTerminatedException();
}
Progress.SetMessage(1, MyConvert.Format("Processing {0}/{1} ...", i + 1, rawFiles.Count()));
using (var rawreader = RawFileFactory.GetRawFileReader(rawFiles[i]))
{
reader.RawReader = rawreader;
ITraqResultFileDistiller distiller = new ITraqResultFileDistiller(reader, minPeakCount, plexType, isotopeImpurityCorrectionTableFileName, precursorPPMTolearnce)
{
Progress = this.Progress,
NormalizationBuilder = this.builder
};
if (individual)
{
string itraqFile = distiller.Process(rawFiles[i]).First();
resultFile.Add(itraqFile);
}
else
{
var curResult = distiller.GetTraqResult(rawFiles[i]);
foreach (var item in curResult)
{
ITraqResultXmlFormatFast.WriteIsobaricItem(sw, item);
}
curResult = null;
}
GC.Collect();
GC.WaitForFullGCComplete();
}
}
Progress.SetMessage(0, "");
}
finally
{
if (!individual)
{
sw.Close();
}
}
if (!individual)
{
var indexBuilder = new ITraqResultXmlIndexBuilder(true)
{
Progress = this.Progress
};
indexBuilder.Process(targetFileName);
resultFile.Add(targetFileName);
}
Progress.SetMessage(1, "Finished!");
return(resultFile);
}
