public void MSAlignTargetDataTest()
{
var testFile = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\SBEP_STM_001_02222012_Aragon.raw";
var targetsFile = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\salmonella_top_target.txt";
var resultsFolder = @"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\Results";
//Backend.Utilities.SipperDataDump.DataDumpSetup(@"\\protoapps\UserData\Fujimoto\TopDownTesting\Charles_Data\Results\detailed_results.txt");
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
executorBaseParameters.ChromGenSourceDataPeakBR = 3;
executorBaseParameters.ChromGenSourceDataSigNoise = 2;
executorBaseParameters.TargetsFilePath = targetsFile;
executorBaseParameters.OutputFolderBase = resultsFolder;
var run = new RunFactory().CreateRun(testFile);
var executor = new TopDownMSAlignExecutor(executorBaseParameters, run);
var s = Stopwatch.StartNew();
executor.LoadAndInitializeTargets(targetsFile);
s.Stop();
var rt = s.Elapsed;
Console.WriteLine("import: " + rt);
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.ChromNETTolerance = 0.05;
targetedWorkflowParameters.ChromatogramCorrelationIsPerformed = true;
targetedWorkflowParameters.ChromSmootherNumPointsInSmooth = 15;
targetedWorkflowParameters.MSToleranceInPPM = 15;
targetedWorkflowParameters.NumMSScansToSum = 5;
//define workflows for parentTarget and childTargets
var parentWorkflow = new ChromPeakDeciderTopDownIqWorkflow(run, targetedWorkflowParameters);
var childWorkflow = new ChargeStateChildTopDownIqWorkflow(run, targetedWorkflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);
var stopwatch = Stopwatch.StartNew();
//Main line for executing IQ:
executor.Execute();
stopwatch.Stop();
var runtime = stopwatch.Elapsed;
Console.WriteLine("Runtime: " + runtime);
}
public void ChromPeakAnalyzerWorkflowTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var testTarget = new ChromPeakIqTarget();
ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var testPeak = new ChromPeak(5184, 840963, 50, 0);
var executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new TopDownMSAlignExecutor(executorBaseParameters, run);
executor.ChromSourceDataFilePath = peaksTestFile;
var workflow = new ChromPeakAnalyzerIqWorkflow(run, parameters);
testTarget.SetWorkflow(workflow);
testTarget.ID = 1;
testTarget.Code = "NGIIMMENR";
testTarget.EmpiricalFormula = "C43H76N14O14S2";
testTarget.MonoMassTheor = 1076.510631;
testTarget.ChromPeak = testPeak;
testTarget.ChargeState = 1;
testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);
var testTargetList = new List <IqTarget>();
IqTarget testParent = new IqChargeStateTarget();
testParent.AddTarget(testTarget);
testTargetList.Add(testTarget);
executor.Execute(testTargetList);
var result = testTarget.GetResult();
Assert.NotNull(result.LCScanSetSelected);
Assert.AreNotEqual(1, result.FitScore);
Assert.AreEqual(true, result.IsotopicProfileFound);
}
