private void CreatSpectralCountTablesSEQSYN(ICollection <string> datasetNames, DoWorkEventArgs e)
{
var dir = new DirectoryInfo(mstrAnalysisFolder);
foreach (var f in dir.GetFiles())
{
if (!f.Name.EndsWith("_syn.txt", StringComparison.CurrentCultureIgnoreCase))
{
continue;
}
var dName = f.Name.Substring(0, f.Name.IndexOf("_syn.txt", StringComparison.CurrentCultureIgnoreCase));
if (datasetNames.Contains(dName))
{
successfulDataSets.Add(dName);
}
}
if (successfulDataSets.Count > 1)
{
var fileList = @"c(""" + successfulDataSets[0];
var rcmd = "X <- createMSMSdt.SpectralCount(";
var dataFolder = mstrAnalysisFolder.Replace("\\", "/");
for (var i = 1; i < successfulDataSets.Count; i++)
{
fileList = fileList + @""",""" + successfulDataSets[i];
}
fileList += @""")";
rcmd += fileList + @",""" + dataFolder + @""",XcRank=" + XcRank +
"," + XCorrTh + "," + DelCn2Th + "," + TrypState + ")";
try
{
backgroundWorker1.ReportProgress(70,
"Creating peptide count table ... may take a while for large datasets ...");
rConnector.EvaluateNoReturn(rcmd);
rConnector.EvaluateNoReturn("Eset <- X$eset");
rConnector.EvaluateNoReturn("EsetRows <- X$rows");
var rows = rConnector.GetSymbolAsNumbers("EsetRows");
if ((int)rows[0] > 0)
{
if (rConnector.GetTableFromRmatrix("Eset"))
{
mDTEset = rConnector.DataTable.Copy();
mDTEset.TableName = "Eset";
rConnector.EvaluateNoReturn("cat(\"Spectral count data obtained.\n\")");
e.Result = enmDataType.ESET;
}
else
{
e.Result = null;
}
}
else
{
e.Result = null;
}
}
catch (Exception ex)
{
MessageBox.Show("R.Net failed: " + ex.Message, "Error!");
e.Result = null;
e.Cancel = true;
}
backgroundWorker1.ReportProgress(100, "Done.");
}
else
{
backgroundWorker1.ReportProgress(100, "You need at leaset two unique datasets... Giving up.");
}
}
