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();
}