public void Test1()
{
TargetedWorkflowParameters o16o18workflowParameters = new O16O18WorkflowParameters();
var parentWorkflow = new O16O18IqWorkflow(o16o18workflowParameters);
TargetedWorkflowParameters workflowParameters = new BasicTargetedWorkflowParameters();
var childWorkflow = new BasicIqWorkflow(workflowParameters);
IqTarget parentTarget = new IqChargeStateTarget();
IqTarget childTarget1 = new IqChargeStateTarget();
IqTarget childTarget2 = new IqChargeStateTarget();
IqTarget childTarget3 = new IqChargeStateTarget();
parentTarget.AddTarget(childTarget1);
parentTarget.AddTarget(childTarget2);
parentTarget.AddTarget(childTarget3);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, parentTarget);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, parentTarget);
Assert.IsNotNull(parentTarget.ChildTargets().First().Workflow);
var childTargets = parentTarget.ChildTargets();
foreach (var childTarget in childTargets)
{
Assert.IsTrue(childTarget.Workflow is BasicIqWorkflow);
}
Assert.IsTrue(parentTarget.Workflow is O16O18IqWorkflow);
}
public void NodeLevelTest1()
{
var util = new IqTargetUtilities();
IqTarget iqTarget1 = new IqChargeStateTarget();
IqTarget iqTarget2 = new IqChargeStateTarget();
IqTarget iqTarget3_1 = new IqChargeStateTarget();
iqTarget3_1.ID = 3001;
IqTarget iqTarget3_2 = new IqChargeStateTarget();
iqTarget3_2.ID = 3002;
IqTarget iqTarget4 = new IqChargeStateTarget();
IqTarget iqTarget5 = new IqChargeStateTarget();
iqTarget4.AddTarget(iqTarget5);
iqTarget3_1.AddTarget(iqTarget4);
iqTarget2.AddTarget(iqTarget3_1);
iqTarget2.AddTarget(iqTarget3_2);
iqTarget1.AddTarget(iqTarget2);
var rootNode = iqTarget5.RootTarget;
Assert.AreEqual(rootNode, iqTarget1);
var nodeLevelCount = util.GetTotalNodelLevels(iqTarget1);
Assert.AreEqual(5, nodeLevelCount);
nodeLevelCount = util.GetTotalNodelLevels(iqTarget5);
Assert.AreEqual(5, nodeLevelCount);
var targetList = new List <IqTarget>();
targetList.Add(iqTarget1);
var level2Targets = util.GetTargetsFromNodelLevel(targetList, 2);
foreach (var level2Target in level2Targets)
{
Console.WriteLine(level2Target);
}
}
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);
}