public void importParametersTest1()
{
var importedParametersFile = Path.Combine(FileRefs.ImportedData, "importedBasicTargetedWorkflowParameters.xml");
var parameters = new BasicTargetedWorkflowParameters();
parameters.LoadParameters(importedParametersFile);
Assert.AreEqual("O16O18_TARGETED_RESULT", parameters.ResultType.ToString());
}
public void findFeatureIn_dataset_with_bad_massCalibration_test1()
{
//mass error in this dataset is typically ~50ppm.
var datasetFile = @"D:\Data\Orbitrap\Subissue01\QC_Shew_10_01-pt5-1_8Feb10_Doc_09-12-24.RAW";
var massTagFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\MassTags\QCShew_Formic_MassTags_Bin10_first10.txt";
var workflowParameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml";
var run = RunUtilities.CreateAndLoadPeaks(datasetFile, datasetFile.Replace(".RAW", "_peaks.txt"));
RunUtilities.AlignRunUsingAlignmentInfoInFiles(run);
Assert.IsTrue(run.MassIsAligned);
Assert.IsTrue(run.NETIsAligned);
var parameters = new BasicTargetedWorkflowParameters();
parameters.LoadParameters(workflowParameterFile);
var workflow = new BasicTargetedWorkflow(parameters);
workflow.Run = run;
var mtc = new TargetCollection();
var mtimporter = new MassTagFromTextFileImporter(massTagFile);
mtc = mtimporter.Import();
var mt1 = (from n in mtc.TargetList where n.ID == 24702 && n.ChargeState == 4 select n).First();
run.CurrentMassTag = mt1;
workflow.Execute();
var repo = new TargetedResultRepository();
repo.AddResult(workflow.Result);
Console.WriteLine("theor mono mass = " + mt1.MonoIsotopicMass);
Console.WriteLine("theorMZ = " + mt1.MZ);
Console.WriteLine("theorNET = " + mt1.NormalizedElutionTime);
Console.WriteLine("obsScan = " + repo.Results[0].ScanLC);
Console.WriteLine("obsNET = " + repo.Results[0].NET);
Console.WriteLine("NETError = " + repo.Results[0].NETError);
Console.WriteLine("obsMZ = " + repo.Results[0].MonoMZ);
Console.WriteLine("monoMass = " + repo.Results[0].MonoMass);
Console.WriteLine("obsMonoMassCalibrated = " + repo.Results[0].MonoMassCalibrated);
Console.WriteLine("MassErrorBeforeAlignment = " + (mt1.MZ - repo.Results[0].MonoMZ) / mt1.MZ * 1e6);
Console.WriteLine("MassErrorAfterAlignment = " + repo.Results[0].MassErrorBeforeCalibration);
}
public void importParametersTest2()
{
var importedParametersFile = Path.Combine(FileRefs.ImportedData, "importedParameters_MostIntenseChromPeakSelection.xml");
var parameters = new BasicTargetedWorkflowParameters();
parameters.LoadParameters(importedParametersFile);
Assert.AreEqual("BASIC_TARGETED_RESULT", parameters.ResultType.ToString());
Assert.AreEqual("MostIntense", parameters.ChromPeakSelectorMode.ToString());
}
public void parameterFileImportTest1()
{
var parameters = new BasicTargetedWorkflowParameters();
var importTestFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Parameters\BasicTargetedWorkflowParameters1_forImportTesting.xml";
parameters.LoadParameters(importTestFile);
//TODO: complete testing of other values
Assert.AreEqual(parameters.ChromGenToleranceUnit, Globals.ToleranceUnit.MZ);
Assert.AreEqual(0.01, parameters.ChromGenTolerance);
}
public void InvestigateIQFailures()
{
var executorParamFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Parameters\ExecutorParameters1 - Copy.xml";
var executorParameters =
new BasicTargetedWorkflowExecutorParameters();
executorParameters.LoadParameters(executorParamFile);
var testFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\LNA_A_Expo_Sample_SC_9_LNA_ExpA_Expo_Stat_SeattleBioMed_15Feb13_Cougar_12-12-35.raw";
var run = new RunFactory().CreateRun(testFile);
var iqparameterFile =
@"\\protoapps\DataPkgs\Public\2013\743_Mycobacterium_tuberculosis_Cys_and_Ser_ABP\IQ_Analysis\Testing\IQWorkflowParameters1.xml";
var workflowParameters = new BasicTargetedWorkflowParameters();
workflowParameters.LoadParameters(iqparameterFile);
workflowParameters.MSToleranceInPPM = 10;
workflowParameters.ChromPeakDetectorPeakBR = 0.25;
workflowParameters.ChromPeakDetectorSigNoise = 2;
var targetedWorkflow = new BasicTargetedWorkflow(run, workflowParameters);
var executor = new BasicTargetedWorkflowExecutor(executorParameters, targetedWorkflow, testFile);
//int[] testTargets = {349959971, 349951038,349954483 };
//int[] testTargets = { 349951038 };
//int[] testTargets = { 349954483 };
//int[] testTargets = { 2911730 };
int[] testTargets = { 349946881 };
var chargeState = 3;
executor.Targets.TargetList = (from n in executor.Targets.TargetList where testTargets.Contains(n.ID) select n).ToList();
executor.Targets.TargetList = (from n in executor.Targets.TargetList where n.ChargeState == chargeState select n).ToList();
executor.Execute();
//Results of investiga tion! - 349959971 was being missed because the MSTolerance was too narrow. When changed from 5 to 6, it was found. I think we can safely set this at 10.
//Results of investigation! - 349951038 was being missed because it was being flagged (peak to the left) problem.
TestUtilities.DisplayXYValues(executor.TargetedWorkflow.ChromatogramXYData);
}
public void ProblemTesting_correlationProb1()
{
//see JIRA https://jira.pnnl.gov/jira/browse/OMCS-628
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
var testDatasetPath =
@"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1B_8Apr13_Cougar_13-03-25.raw";
executorParameters.IsMassAlignmentPerformed = true;
executorParameters.IsNetAlignmentPerformed = true;
executorParameters.ReferenceTargetsFilePath =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set3_P892_targets.txt";
var run = new RunFactory().CreateRun(testDatasetPath);
var executor = new IqExecutor(executorParameters, run);
var targetsFile =
@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Targets\MT_Mouse_MHP_O18_Set3_P892_targets.txt";
executor.LoadAndInitializeTargets(targetsFile);
executor.SetupMassAndNetAlignment();
var testTarget = 6955012;
executor.Targets = (from n in executor.Targets where n.ID == testTarget select n).ToList();
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.LoadParameters(@"\\protoapps\DataPkgs\Public\2013\795_Iq_analysis_of_mouse_O16O18\Parameters\O16O18WorkflowParameters_2011_08_23_sum5.xml");
//define workflows for parentTarget and childTargets
var parentWorkflow = new O16O18ParentIqWorkflow(run, targetedWorkflowParameters);
var childWorkflow = new O16O18IqWorkflow(run, targetedWorkflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);
executor.DoAlignment();
executor.Execute();
}