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 ProcessDataset()
{
//apply mass calibration and NET alignment from .txt files, if they exist
PerformAlignment();
var runIsNotAligned = (!Run.MassIsAligned && !Run.NETIsAligned); //if one of these two is aligned, the run is considered to be aligned
//Perform targeted alignment if 1) run is not aligned 2) parameters permit it
if (runIsNotAligned && this.ExecutorParameters.TargetedAlignmentIsPerformed)
{
Check.Ensure(this.MassTagsForTargetedAlignment != null && this.MassTagsForTargetedAlignment.TargetList.Count > 0, "MassTags for targeted alignment have not been defined. Check path within parameter file.");
ReportGeneralProgress("Performing TargetedAlignment using mass tags from file: " + GetTargetFilePathForIqAlignment());
ReportGeneralProgress("Total mass tags to be aligned = " + this.MassTagsForTargetedAlignment.TargetList.Count);
this.TargetedAlignmentWorkflow = new TargetedAlignerWorkflow(this.TargetedAlignmentWorkflowParameters);
this.TargetedAlignmentWorkflow.SetMassTags(this.MassTagsForTargetedAlignment.TargetList);
this.TargetedAlignmentWorkflow.Run = Run;
this.TargetedAlignmentWorkflow.Execute();
ReportGeneralProgress("Targeted Alignment COMPLETE.");
ReportGeneralProgress("Targeted Alignment Report: ");
ReportGeneralProgress(this.TargetedAlignmentWorkflow.GetAlignmentReport1());
PerformAlignment(); //now perform alignment, based on alignment .txt files that were outputted from the targetedAlignmentWorkflow
TargetedAlignmentWorkflow.SaveFeaturesToTextfile(_alignmentFolder);
if (Run.AlignmentInfo != null)
{
TargetedAlignmentWorkflow.SaveAlignmentData(_alignmentFolder);
}
ReportGeneralProgress("MassAverage = \t" + this.TargetedAlignmentWorkflow.Aligner.Result.MassAverage.ToString("0.00000"));
ReportGeneralProgress("MassStDev = \t" + this.TargetedAlignmentWorkflow.Aligner.Result.MassStDev.ToString("0.00000"));
ReportGeneralProgress("NETAverage = \t" + this.TargetedAlignmentWorkflow.Aligner.Result.NETAverage.ToString("0.00000"));
ReportGeneralProgress("NETStDev = \t" + this.TargetedAlignmentWorkflow.Aligner.Result.NETStDev.ToString("0.00000"));
ReportGeneralProgress("---------------- END OF Alignment info -------------");
}
this.TargetedWorkflow.Run = Run;
ResultRepository.Results.Clear();
var mtCounter = 0;
var totalTargets = Targets.TargetList.Count;
ReportGeneralProgress("Processing...", 0);
foreach (var massTag in this.Targets.TargetList)
{
mtCounter++;
#if DEBUG
var stopwatch = new System.Diagnostics.Stopwatch();
stopwatch.Start();
#endif
Run.CurrentMassTag = massTag;
try
{
this.TargetedWorkflow.Execute();
ResultRepository.AddResult(this.TargetedWorkflow.Result);
}
catch (Exception ex)
{
var errorString = "Error on MT\t" + massTag.ID + "\tchargeState\t" + massTag.ChargeState + "\t" + ex.Message + "\t" + ex.StackTrace;
ReportGeneralProgress(errorString, mtCounter);
throw;
}
#if DEBUG
stopwatch.Stop();
Console.WriteLine(massTag.ID + "\tprocessing time = " + stopwatch.ElapsedMilliseconds);
#endif
var progressString = "Percent complete = " + ((double)mtCounter / totalTargets * 100.0).ToString("0.0") + "\tTarget " + mtCounter + " of " + totalTargets;
if (_backgroundWorker != null)
{
if (_backgroundWorker.CancellationPending)
{
return;
}
}
ReportProcessingProgress(progressString, mtCounter);
}
ReportGeneralProgress("---- PROCESSING COMPLETE ---------------", 100);
}