public void Deconvolute()
{
try
{
bool areRequirementsMet = validateDeconRequirements();
if (areRequirementsMet)
{
state = DeconState.RUNNING_DECON;
this.oldschoolprocRunner = new OldSchoolProcRunner(this.dataFile, FileTypeConverter.ConvertDeconEngineFileType(fileType), this.paramFile, null);
this.oldschoolprocRunner.IsosResultThreshold = 50000;
this.oldschoolprocRunner.Execute();
state = DeconState.DONE;
}
else
{
return;
}
}
catch (Exception ex)
{
EventLog elog = new EventLog();
elog.Log = "Application";
elog.Source = "Decon2LS";
elog.WriteEntry(ex.Message + ex.StackTrace);
elog.Close();
state = DeconState.ERROR;
throw ex;
}
}
public void ExecuteRunnerAndSerializeResultsOnUIMF()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(uimfFilepath2, Globals.MSFileType.PNNL_UIMF, uimfParameterFile3);
runner.IsosResultThreshold = 100;
runner.Execute();
}
public void oldSchoolProcRunnerTest1()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(lowmwRawfile, Globals.MSFileType.Finnigan, xcaliburParameterFile1);
Assert.AreEqual(false, runner.Project.Parameters.OldDecon2LSParameters.HornTransformParameters.UseScanRange);
runner.Execute();
}
public void loadParametersTest1()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(uimfFilepath, Globals.MSFileType.PNNL_UIMF, uimfParameterFile1);
Assert.AreEqual(3, runner.Project.Parameters.NumFramesSummed);
Assert.AreEqual(1, runner.Project.Parameters.NumScansSummed);
Assert.AreEqual(true, runner.Project.Parameters.OldDecon2LSParameters.HornTransformParameters.UseRAPIDDeconvolution);
}
public void ExecuteRunnerOnXCaliburDataTest1()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(xcaliburTestfile, Globals.MSFileType.Finnigan, xcaliburParameterFile1);
runner.Execute();
//Assert.AreEqual(12607, runner.Project.RunCollection[0].ResultCollection.ResultList.Count);
}
public void checkRunsAndTasksTest1()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(uimfFilepath, Globals.MSFileType.PNNL_UIMF, uimfParameterFile1);
Assert.AreEqual(6, runner.Project.TaskCollection.TaskList.Count);
Assert.IsInstanceOfType(typeof(UIMFRun), runner.Project.RunCollection[0]);
Assert.IsInstanceOfType(typeof(RapidDeconvolutor), runner.Project.TaskCollection.TaskList[2]);
Assert.IsInstanceOfType(typeof(UIMF_MSGenerator), runner.Project.TaskCollection.TaskList[0]);
}
public void ExecuteRunnerOnIMFFileTest2()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(imfFilepath, Globals.MSFileType.PNNL_IMS, imfParameterFile2);
Assert.AreEqual(5, runner.Project.Parameters.NumScansSummed);
Assert.AreEqual(true, runner.Project.Parameters.OldDecon2LSParameters.HornTransformParameters.UseScanRange);
runner.Execute();
Assert.AreEqual(5, runner.Project.RunCollection[0].ResultCollection.ResultList.Count);
}
public void ExecuteRunner_mzXML_horn_Test1()
{
BackgroundWorker bw = new BackgroundWorker();
bw.WorkerReportsProgress = true;
bw.WorkerSupportsCancellation = true;
OldSchoolProcRunner runner = new OldSchoolProcRunner(mzxmlFilepath, Globals.MSFileType.MZXML_Rawdata, mzxmlParameterFile1, bw);
runner.Execute();
}
public void ExecuteRunnerAndWithPeakExporter_ExportMSMSTest1()
{
BackgroundWorker bw = new BackgroundWorker();
bw.WorkerReportsProgress = true;
bw.WorkerSupportsCancellation = true;
OldSchoolProcRunner runner = new OldSchoolProcRunner(xcaliburTestfile, Globals.MSFileType.Finnigan, parameterFile5);
runner.IsosResultThreshold = 1000;
runner.Execute();
}
public void ExecuteRunnerAndWithPeakExporterTest2()
{
BackgroundWorker bw = new BackgroundWorker();
bw.WorkerReportsProgress = true;
bw.WorkerSupportsCancellation = true;
OldSchoolProcRunner runner = new OldSchoolProcRunner(imfFilepath, Globals.MSFileType.PNNL_IMS, imfParameterFile3, bw);
runner.IsosResultThreshold = 100000;
runner.Execute();
}
public void ExecuteRunnerAndSerializeResultsOnUIMF2()
{
BackgroundWorker bw = new BackgroundWorker();
bw.WorkerReportsProgress = true;
bw.WorkerSupportsCancellation = true;
OldSchoolProcRunner runner = new OldSchoolProcRunner(uimfFilepath2, Globals.MSFileType.PNNL_UIMF, uimfParameterFile3, bw);
runner.IsosResultThreshold = 1000000;
runner.Execute();
}
public void ExecuteRunnerOnUIMFDataWithHornDeconTest1()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(uimfFile3, Globals.MSFileType.PNNL_UIMF, uimfParameterHorn1);
runner.IsosResultThreshold = 100;
runner.Execute();
//Assert.AreEqual(265, runner.Project.RunCollection[0].ResultCollection.ResultList.Count);
//Assert.AreEqual(1, runner.Project.RunCollection[0].ResultCollection.ScanResultList.Count);
//Assert.AreEqual(4916859, runner.Project.RunCollection[0].ResultCollection.ScanResultList[0].TICValue);
}
public void ExecuteRunner_withReplaceRapidScoresTest1()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(xcaliburTestfile, Globals.MSFileType.Finnigan, replaceRapidScoreParamFile1);
runner.Execute();
}
public void ExecuteRunnerOnUIMFDataTest2()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(uimfFile3, Globals.MSFileType.PNNL_UIMF, uimfParameterFile2);
runner.Execute();
}
public void ExecuteRunnerOnUIMFData_NoDeconvolutionTest1()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(uimfFile3, Globals.MSFileType.PNNL_UIMF, uimf_noDeconvolution_peaksOnly);
runner.Execute();
}
public void ExecuteRunner_horn_exportToSqlite()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(xcaliburTestfile, Globals.MSFileType.Finnigan, xcaliburParameterFile4_exporttoSqlite);
runner.Execute();
}
public void agilent_horn_Test1()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(agilentFile1, Globals.MSFileType.Agilent_D, agilentParams1);
runner.Execute();
}
public void xcaliburSum5_adv1_horn_test1()
{
OldSchoolProcRunner runner = new OldSchoolProcRunner(xcaliburTestfile, Globals.MSFileType.Finnigan, xcal_sum5_adv1_scans6000_6050);
runner.Execute();
}
