public void exportParametersTest1()
{
var exportedParametersFile = Path.Combine(FileRefs.OutputFolderPath, "exportedN14N15WorkflowParameters.xml");
var parameters = new N14N15Workflow2Parameters();
parameters.SaveParametersToXML(exportedParametersFile);
}
public void exportParametersTest1()
{
var exportedParametersFile = Path.Combine(FileRefs.OutputFolderPath, "exportedN14N15WorkflowParameters.xml");
exportedParametersFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Parameters\N14N15WorkflowParameters1.xml";
var parameters = new N14N15Workflow2Parameters();
parameters.SaveParametersToXML(exportedParametersFile);
}
public void WorkflowTest1()
{
//GORD: 3/18/2013 - this test is broken. We need to fix the N14N15 workflow and get this to pass
// See: https://jira.pnnl.gov/jira/browse/OMCS-409
var run = RunUtilities.CreateAndAlignRun(bruker9t_samplefile1, bruker9t_peaksfile1);
var targetsFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Targets\POnly_MassTagsMatchingInHalfOfDatasets_Filtered0.45-0.47NET_first18.txt";
var importer = new MassTagFromTextFileImporter(targetsFile);
var targetCollection = importer.Import();
run.CurrentMassTag = targetCollection.TargetList.FirstOrDefault(p => p.ChargeState == 1);
var parameters = new N14N15Workflow2Parameters();
parameters.LoadParameters(Path.Combine(FileRefs.ImportedData, "importedN14N15WorkflowParameters.xml"));
parameters.ChromGenTolerance = 25;
parameters.MSToleranceInPPM = 25;
parameters.TargetedFeatureFinderToleranceInPPM = 25;
parameters.MultipleHighQualityMatchesAreAllowed = true;
parameters.NumMSScansToSum = 5;
parameters.SaveParametersToXML(
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\N14N15_standard_testing\Parameters\N14N15WorkflowParameters1_test.xml");
Console.WriteLine(parameters.ToStringWithDetails());
var workflow = new N14N15Workflow2(run, parameters);
workflow.Execute();
Assert.IsTrue(run.ResultCollection.ResultType == Globals.ResultType.N14N15_TARGETED_RESULT);
//TestUtilities.DisplayXYValues(workflow.ChromatogramXYData);
var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as N14N15_TResult;
result.DisplayToConsole();
Assert.AreEqual(23085448, result.Target.ID);
Assert.AreEqual(1, result.IsotopicProfile.ChargeState);
Assert.IsNotNull(result.ScanSet);
Assert.IsNotNull(result.ChromPeakSelected);
Assert.IsNotNull(result.ChromPeakSelectedN15);
return;
Assert.AreEqual(1639.3m, (decimal)Math.Round(result.ChromPeakSelected.XValue, 1));
Assert.AreEqual(1638.5m, (decimal)Math.Round(result.ChromPeakSelectedN15.XValue, 1));
Assert.IsNotNull(result.IsotopicProfile);
Assert.IsNotNull(result.IsotopicProfileLabeled);
Console.WriteLine("theor monomass= \t" + result.Target.MonoIsotopicMass);
Console.WriteLine("monomass= \t" + result.IsotopicProfile.MonoIsotopicMass);
Console.WriteLine("monomassN15= \t" + result.IsotopicProfileLabeled.MonoIsotopicMass);
Console.WriteLine("monoMZ= \t" + result.IsotopicProfile.MonoPeakMZ);
Console.WriteLine("monoMZN15= \t" + result.IsotopicProfileLabeled.MonoPeakMZ);
Console.WriteLine("ppmError= \t" + result.MassErrorAfterAlignment);
Console.WriteLine("Database NET= " + result.Target.NormalizedElutionTime);
Console.WriteLine("Result NET= " + result.GetNET());
Console.WriteLine("Result NET Error= " + result.GetNETAlignmentError());
Console.WriteLine("NumChromPeaksWithinTol= " + result.NumChromPeaksWithinTolerance);
Console.WriteLine("NumChromPeaksWithinTolN15= " + result.NumChromPeaksWithinToleranceForN15Profile);
}
