protected void PerformAlignment() { if (!string.IsNullOrEmpty(_alignmentFolder)) { RunUtilities.AlignRunUsingAlignmentInfoInFiles(Run, _alignmentFolder); } if (Run.MassIsAligned) { ReportGeneralProgress("Run has been mass aligned"); } else { ReportGeneralProgress("FYI - Run has NOT been mass aligned."); } if (Run.NETIsAligned) { ReportGeneralProgress("Run has been NET aligned using info in either the _NETAlignment.txt file or the _UMCs.txt file"); } else { ReportGeneralProgress("Warning - Run has NOT been NET aligned."); } }
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 findSingleMassTag_checkAlignmentData_test1() { var testFile = DeconTools.UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1; var peaksTestFile = DeconTools.UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500; var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt"; var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksTestFile); var mtc = new TargetCollection(); var mtimporter = new MassTagFromTextFileImporter(massTagFile); mtc = mtimporter.Import(); var testMassTagID = 24800; run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == 2 select n).First(); TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters(); var workflow = new BasicTargetedWorkflow(run, parameters); workflow.Execute(); var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag) as MassTagResult; Assert.AreEqual(false, result.FailedResult); result.DisplayToConsole(); Assert.IsNotNull(result.IsotopicProfile); Assert.IsNotNull(result.ScanSet); Assert.IsNotNull(result.ChromPeakSelected); Assert.AreEqual(2, result.IsotopicProfile.ChargeState); Assert.AreEqual(718.41m, (decimal)Math.Round(result.IsotopicProfile.GetMZ(), 2)); Assert.AreEqual(5947m, (decimal)Math.Round(result.ChromPeakSelected.XValue)); Assert.AreEqual(5.91, (decimal)(Math.Round(result.GetMassErrorAfterAlignmentInPPM(), 2))); Assert.AreEqual(0.0001585m, (decimal)(Math.Round(result.GetNETAlignmentError(), 7))); RunUtilities.AlignRunUsingAlignmentInfoInFiles(run); //these might change due to unit tests elsewhere. Need a better way of doing this //Assert.AreEqual(1.99290383722318m, (decimal)result.GetMassErrorAfterAlignmentInPPM()); //Assert.AreEqual(0.00076708197593689m, (decimal)result.GetNETAlignmentError()); }
public void Test1() { var rawdataFile = @"D:\Data\Orbitrap\QC_Shew_09_05-pt5-6_4Jan10_Doc_09-11-08.RAW"; var massTagFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt"; var parameterFile = @"\\protoapps\UserData\Slysz\Data\QCShew_MassiveTargeted\WorkflowParameterFiles\UnlabelledTargeted_WorkflowParameters_noSum.xml"; var mtimporter = new MassTagFromTextFileImporter(massTagFile); var mtc = new TargetCollection(); mtc = mtimporter.Import(); var run = new RunFactory().CreateRun(rawdataFile); //RunUtilities.AlignRunUsingAlignmentInfoInFiles(run); var expectedPeaksFilename = Path.Combine(run.DataSetPath, run.DatasetName + "_peaks.txt"); var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(expectedPeaksFilename, null); peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList); var testMassTagID = 3513677; var massTagChargeState = 2; run.CurrentMassTag = (from n in mtc.TargetList where n.ID == testMassTagID && n.ChargeState == massTagChargeState select n).First(); var parameters = WorkflowParameters.CreateParameters(parameterFile); var workflow = TargetedWorkflow.CreateWorkflow(parameters); workflow.Run = run; workflow.Execute(); workflow.Result.DisplayToConsole(); RunUtilities.AlignRunUsingAlignmentInfoInFiles(run); workflow.Execute(); workflow.Result.DisplayToConsole(); }