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);
}
/// <summary>
/// Performs charge correlation on a pair of ChromPeakIqTarget peaks
/// </summary>
/// <param name="referenceTarget"></param>
/// <param name="compTarget"></param>
/// <returns></returns>
public double PairWiseChargeCorrelation(ChromPeakIqTarget referenceTarget, ChromPeakIqTarget compTarget, Run run, int peaksToCorrelate)
{
//Gets the ChromPeaks base width in scans for correlation
int startScan, stopScan;
GetBaseScanRange(referenceTarget.ChromPeak, out startScan, out stopScan);
//Generates an array of XICs for the reference peak
var referenceMZList = DeconTools.Backend.Utilities.IsotopicProfileUtilities.GetTopNMZValues(referenceTarget.TheorIsotopicProfile.Peaklist, peaksToCorrelate);
var referenceXIC = GetCorrelationXICs(peaksToCorrelate, referenceMZList, run, startScan, stopScan);
if (compTarget.ChromPeak.XValue > startScan && compTarget.ChromPeak.XValue < stopScan)
{
//Generates an XIC array for the peak being correlated.
var correlationMZList = DeconTools.Backend.Utilities.IsotopicProfileUtilities.GetTopNMZValues(compTarget.TheorIsotopicProfile.Peaklist, peaksToCorrelate);
var correlationXIC = GetCorrelationXICs(peaksToCorrelate, correlationMZList, run, startScan, stopScan);
//Generates new correlation data item for current correlation
var rsquaredVals = new double[peaksToCorrelate];
for (var i = 0; i < peaksToCorrelate; i++)
{
//Checks if either of the XICs are null
if (referenceXIC[i] != null && correlationXIC[i] != null)
{
double slope, intercept, rsquaredval;
GetElutionCorrelationData(referenceXIC[i], FillInAnyMissingValuesInChromatogram(referenceXIC[i].Xvalues, correlationXIC[i]), out slope, out intercept, out rsquaredval);
rsquaredVals[i] = rsquaredval;
}
else
{
//A placeholder to show that the data was poor
rsquaredVals[i] = 0;
}
}
return(MathUtils.GetMedian(rsquaredVals));
}
return(0);
}
public ChargeCorrelationItem(ChromPeakIqTarget referenceTarget)
{
SelectedTargetGrouping = false;
ReferenceTarget = referenceTarget;
PeakCorrelationData = new Dictionary <ChromPeakIqTarget, ChromCorrelationData>();
}
