/// <summary>
/// Factory method for creating the Workflow object using the WorkflowType information in the parameter object
/// </summary>
/// <param name="workflowParameters"></param>
/// <returns></returns>
public static TargetedWorkflow CreateWorkflow(WorkflowParameters workflowParameters)
{
TargetedWorkflow wf;
switch (workflowParameters.WorkflowType)
{
case Globals.TargetedWorkflowTypes.Undefined:
wf = new BasicTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.UnlabelledTargeted1:
wf = new BasicTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.O16O18Targeted1:
wf = new O16O18Workflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.N14N15Targeted1:
wf = new N14N15Workflow2(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.SipperTargeted1:
wf = new SipperTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.TargetedAlignerWorkflow1:
wf = new TargetedAlignerWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.TopDownTargeted1:
wf = new TopDownTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
case Globals.TargetedWorkflowTypes.PeakDetectAndExportWorkflow1:
throw new System.NotImplementedException("Cannot create this workflow type here.");
case Globals.TargetedWorkflowTypes.BasicTargetedWorkflowExecutor1:
throw new System.NotImplementedException("Cannot create this workflow type here.");
case Globals.TargetedWorkflowTypes.UIMFTargetedMSMSWorkflowCollapseIMS:
wf = new UIMFTargetedMSMSWorkflowCollapseIMS(workflowParameters as TargetedWorkflowParameters);
break;
default:
wf = new BasicTargetedWorkflow(workflowParameters as TargetedWorkflowParameters);
break;
}
return(wf);
}
public override void Execute()
{
List <TargetedResultBase> resultsPassingCriteria;
_targetedResultRepository = new TargetedResultRepository();
var featuresAreImportedFromFile = !string.IsNullOrEmpty(AlignerParameters.ImportedFeaturesFilename);
if (featuresAreImportedFromFile)
{
//load them from the Features file
var importer = new UnlabelledTargetedResultFromTextImporter(AlignerParameters.ImportedFeaturesFilename);
var repo = importer.Import();
_targetedResultRepository.Results = repo.Results;
}
else
{
Check.Require(Run.ResultCollection.MSPeakResultList != null && Run.ResultCollection.MSPeakResultList.Count > 0, "Dataset's Peak-level data is empty. This is needed for chromatogram generation.");
//execute targeted feature finding to find the massTags in the raw data
_workflow = new BasicTargetedWorkflow(Run, AlignerParameters);
var netGrouping = 0.2;
double chromTolerance = 5; //in ppm
var progressString = "First trying to find alignment targets using narrow mass tolerances.... ";
ReportProgress(0, progressString);
var firstPassResults = FindTargetsThatPassSpecifiedMassTolerance(netGrouping, chromTolerance);
if (firstPassResults.Count < 10)
{
//try another netGrouping
netGrouping = 0.3;
chromTolerance = 20;
progressString = "Couldn't find enough. Now trying wider mass tolerance = " + chromTolerance;
ReportProgress(0, progressString);
var secondPassResults = FindTargetsThatPassSpecifiedMassTolerance(netGrouping, chromTolerance);
firstPassResults.AddRange(secondPassResults);
}
if (firstPassResults.Count < 10)
{
netGrouping = 0.4;
chromTolerance = 50;
progressString = "Ok this is a tough one. Now going even wider. Mass tolerance = " + chromTolerance;
ReportProgress(0, progressString);
var thirdPassResults = FindTargetsThatPassSpecifiedMassTolerance(netGrouping, chromTolerance);
firstPassResults.AddRange(thirdPassResults);
}
var ppmErrors = getMassErrors(firstPassResults);
var filteredUsingGrubbsPPMErrors = MathUtilities.filterWithGrubbsApplied(ppmErrors);
var canUseNarrowTolerances = executeDecisionOnUsingTightTolerances(filteredUsingGrubbsPPMErrors);
if (canUseNarrowTolerances)
{
var avgPPMError = filteredUsingGrubbsPPMErrors.Average();
var stdev = MathUtilities.GetStDev(filteredUsingGrubbsPPMErrors);
var tolerance = Math.Abs(avgPPMError) + 2 * stdev;
this.AlignerParameters.ChromGenTolerance = (int)Math.Ceiling(tolerance);
this.AlignerParameters.MSToleranceInPPM = (int)Math.Ceiling(tolerance);
progressString = "STRICT_Matches_AveragePPMError = \t" + avgPPMError.ToString("0.00") + "; Stdev = \t" + stdev.ToString("0.00000");
ReportProgress(0, progressString);
progressString = "NOTE: using the new PPMTolerance= " + this.AlignerParameters.ChromGenTolerance;
ReportProgress(0, progressString);
_workflow = new BasicTargetedWorkflow(Run, AlignerParameters);
}
else
{
double avgPPMError = 0;
double stdev = 0;
if (filteredUsingGrubbsPPMErrors.Count != 0)
{
avgPPMError = filteredUsingGrubbsPPMErrors.Average();
stdev = MathUtilities.GetStDev(filteredUsingGrubbsPPMErrors);
}
progressString = "STRICT_Matches_AveragePPMError = \t" + avgPPMError.ToString("0.00") + "; Stdev = \t" + stdev.ToString("0.00000");
ReportProgress(0, progressString);
progressString = "Cannot use narrow ppm tolerances during NET/Mass alignment. Either the massError was too high or couldn't find enough strict matches.";
ReportProgress(0, progressString);
// find a way to work with datasets with masses way off but low stdev
}
resultsPassingCriteria = FindTargetsThatPassCriteria();
_targetedResultRepository.AddResults(resultsPassingCriteria);
}
var canDoAlignment = _targetedResultRepository.Results.Count > 0;
if (canDoAlignment)
{
doAlignment();
}
}
protected override void DoPostInitialization()
{
base.DoPostInitialization();
_workflow = new BasicTargetedWorkflow(Run, WorkflowParameters as TargetedWorkflowParameters);
}