public void executeWorkflowTest1()
{
var testFile = FileRefs.SipperRawDataFile;
var exportedResultFile = Path.Combine(FileRefs.OutputFolderPath, "ExportedSipperResults1.txt");
var peaksFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_peaks.txt";
var run = RunUtilities.CreateAndLoadPeaks(testFile, peaksFile);
var lcmsfeaturesFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_LCMSFeatures.txt";
// load LCMSFeatures as targets
var importer =
new LcmsTargetFromFeaturesFileImporter(lcmsfeaturesFile);
var lcmsTargetCollection = importer.Import();
// load MassTags
var massTagFile1 =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28_MassTags.txt";
var massTagImporter = new MassTagFromTextFileImporter(massTagFile1);
var massTagCollection = massTagImporter.Import();
//enriched
var testMassTags = new int[] { 355116553, 355129038, 355160150, 355162540, 355163371 };
var filteredLcmsFeatureTargets = (from n in lcmsTargetCollection.TargetList
where testMassTags.Contains(((LcmsFeatureTarget)n).FeatureToMassTagID)
select n).ToList();
TargetCollection.UpdateTargetsWithMassTagInfo(filteredLcmsFeatureTargets, massTagCollection.TargetList);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget;
var workflow = new SipperTargetedWorkflow(run, parameters);
foreach (var target in filteredLcmsFeatureTargets)
{
run.CurrentMassTag = target;
workflow.Execute();
}
var results = run.ResultCollection.GetMassTagResults();
var repo = new TargetedResultRepository();
repo.AddResults(run.ResultCollection.GetMassTagResults());
var exporter = new SipperResultToLcmsFeatureExporter(exportedResultFile);
exporter.ExportResults(repo.Results);
}
public void SaveResults()
{
try
{
var exporter = new SipperResultToLcmsFeatureExporter(FileInputs.ResultsSaveFilePath);
exporter.ExportResults(Results);
}
catch (Exception ex)
{
GeneralStatusMessage = "Error saving results. Error message: " + ex.Message;
throw;
}
GeneralStatusMessage = "Results saved to: " + Path.GetFileName(FileInputs.ResultsSaveFilePath);
}
public void SaveResults()
{
if (FileInputs.ResultsSaveFilePath == null) return;
try
{
var exporter = new SipperResultToLcmsFeatureExporter(FileInputs.ResultsSaveFilePath);
exporter.ExportResults(_resultRepositorySource.Results);
}
catch (Exception ex)
{
GeneralStatusMessage = "Error saving results. Error message: " + ex.Message;
return;
}
GeneralStatusMessage = "Results saved to: " + Path.GetFileName(FileInputs.ResultsSaveFilePath);
}
