public void parameterFileTest1()
{
var parameters = new BasicTargetedWorkflowParameters();
parameters.ChromGenSourceDataPeakBR = 2;
parameters.ChromGenSourceDataSigNoise = 3;
parameters.ChromGeneratorMode = Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK;
parameters.ChromNETTolerance = 0.025;
parameters.ChromPeakDetectorPeakBR = 1;
parameters.ChromPeakDetectorSigNoise = 1;
parameters.ChromPeakSelectorMode = Globals.PeakSelectorMode.Smart;
parameters.ChromSmootherNumPointsInSmooth = 9;
parameters.ChromGenTolerance = 10;
parameters.ChromatogramCorrelationIsPerformed = true;
parameters.MSPeakDetectorPeakBR = 1.3;
parameters.MSPeakDetectorSigNoise = 3;
parameters.MSToleranceInPPM = 10;
parameters.NumMSScansToSum = 5;
parameters.SmartChromPeakSelectorNumMSSummed = 3;
var exportedParameterFilename =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Parameters\BasicTargetedWorkflowParameters1_autoexported.xml";
parameters.SaveParametersToXML(exportedParameterFilename);
}
public void exportParametersTest1()
{
var exportedParametersFile = Path.Combine(FileRefs.OutputFolderPath, "exportedBasicTargetedWorkflowParameters.xml");
if (File.Exists(exportedParametersFile))
{
File.Delete(exportedParametersFile);
}
var parameters = new BasicTargetedWorkflowParameters();
parameters.SaveParametersToXML(exportedParametersFile);
Assert.That(File.Exists(exportedParametersFile), "Parameter file doesn't exist: " + exportedParametersFile);
}
public void TargetedWorkflowUsingMsgfInputsTest1()
{
var executorParameters = new BasicTargetedWorkflowExecutorParameters();
executorParameters.TargetsFilePath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\Yellow_C13_070_23Mar10_Griffin_10-01-28_msgfplus.tsv";
executorParameters.TargetedAlignmentIsPerformed = false;
executorParameters.SaveParametersToXML(
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\IQConsoleDemo\IqExecutorParameters.xml");
var workflowParameters = new BasicTargetedWorkflowParameters();
workflowParameters.ChromSmootherNumPointsInSmooth = 9;
workflowParameters.ChromPeakDetectorPeakBR = 1;
workflowParameters.ChromPeakDetectorSigNoise = 3;
workflowParameters.ChromGenTolerance = 20;
workflowParameters.ChromNETTolerance = 0.025;
workflowParameters.MSToleranceInPPM = 20;
workflowParameters.SaveParametersToXML(
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\IQConsoleDemo\IqWorkflowParameters.xml");
var workflow = new BasicTargetedWorkflow(workflowParameters);
var testDatasetPath =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\SIPPER_standard_testing\Yellow_C13_070_23Mar10_Griffin_10-01-28.raw";
TargetedWorkflowExecutor executor = new BasicTargetedWorkflowExecutor(executorParameters, workflow, testDatasetPath);
executor.Targets.TargetList = executor.Targets.TargetList.Take(10).ToList();
executor.Execute();
}