public void ChromPeakAnalyzerWorkflowTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
string testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
string peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
Run run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
ChromPeakIqTarget testTarget = new ChromPeakIqTarget();
ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
ChromPeak testPeak = new ChromPeak(5184, 840963, 50, 0);
testTarget.SetWorkflow(new ChromPeakAnalyzerIqWorkflow(run, parameters));
testTarget.Code = "NGIIMMENR";
testTarget.EmpiricalFormula = "C43H76N14O14S2";
testTarget.MonoMassTheor = 1076.510631;
testTarget.ChromPeak = testPeak;
testTarget.ChargeState = 1;
testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);
testTarget.DoWorkflow();
IqResult result = testTarget.GetResult();
Console.WriteLine("Fit Score: " + result.FitScore + " Flagged: " + result.IsIsotopicProfileFlagged);
}
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);
}
