//TODO: remove code duplication (see DeconToolsPeakDetector)
public override List <Peak> FindPeaks(XYData xyData, double xMin = 0, double xMax = 0)
{
var peakList = new List <Peak>();
if (xyData == null)
{
return(peakList);
}
if (UseNewPeakDetector)
{
_peakDetectorV2.FindPeaks(xyData, xMin, xMax);
}
else
{
var xVals = xyData.Xvalues.ToList();
var yVals = xyData.Yvalues.ToList();
if (_oldPeakProcessor == null)
{
_oldPeakProcessor = new PeakProcessor();
}
BackgroundIntensity = _oldPeakProcessor.GetBackgroundIntensity(yVals);
_oldPeakProcessor.SetOptions(SigNoise, BackgroundIntensity * PeakBackgroundRatio, false, PeakFitType.Quadratic);
//Find peaks using DeconEngine
var largestXValue = xyData.Xvalues[xyData.Xvalues.Length - 1];
try
{
_oldPeakProcessor.DiscoverPeaks(xVals, yVals, 0, largestXValue);
}
catch (Exception ex)
{
Logger.Instance.AddEntry("ChromPeakDetector failed: " + ex.Message, true);
throw;
}
_oldDeconEnginePeaklist = _oldPeakProcessor.PeakData.PeakTops;
foreach (var peak in _oldDeconEnginePeaklist)
{
var chromPeak = new ChromPeak
{
XValue = peak.Mz, // here, mz is actually the scan / or NET
Height = (float)peak.Intensity,
SignalToNoise = peak.SignalToNoise,
Width = (float)peak.FWHM
};
peakList.Add(chromPeak);
}
}
//resultList.Run.PeakList = new List<IPeak>();
return(peakList);
}
protected override void ExecuteWorkflow(IqResult result)
{
var children = result.Target.ChildTargets().ToList();
foreach (var child in children)
{
child.DoWorkflow();
var childResult = child.GetResult();
var chromPeakLevelResults = childResult.ChildResults();
var filteredChromPeakResults = chromPeakLevelResults.Where(r => r.IsotopicProfileFound).ToList();
childResult.FavoriteChild = SelectBestChromPeakIqResult(childResult, filteredChromPeakResults);
GetDataFromFavoriteChild(childResult);
}
result.FavoriteChild = SelectBestChargeStateChildResult(result);
GetDataFromFavoriteChild(result);
var favResult = result.FavoriteChild;
double?rsquaredVal, slope;
getRsquaredVal(result, out rsquaredVal, out slope);
var favChargeState = result.FavoriteChild == null ? 0 : result.FavoriteChild.Target.ChargeState;
var favMz = result.FavoriteChild == null ? 0 : result.FavoriteChild.Target.MZTheor;
if (!_headerLogged)
{
_headerLogged = true;
IqLogger.Log.Info("\t" + "TargetID" + "\t\t\t" + "M/Z" + "\t" + "Charge" + "\t" + "LCScan" + "\t" + "RSquared" + "\t" + "Slope");
}
IqLogger.Log.Info("\t" + result.Target.ID + "\t\t\t" + favMz.ToString("0.000") + "\t" + favChargeState + "\t" + result.LcScanObs + "\t" + rsquaredVal + "\t" + slope);
//now get the mass spectrum given the info from the favorite child charge state result
if (favResult != null)
{
var scanset = new ScanSetFactory().CreateScanSet(Run, favResult.LCScanSetSelected.PrimaryScanNumber,
WorkflowParameters.NumMSScansToSum);
var selectedChromPeak = favResult.ChromPeakSelected;
var sigma = selectedChromPeak.Width / 2.35;
var chromScanWindowWidth = 4 * sigma;
//Determines where to start and stop chromatogram correlation
var startScan = scanset.PrimaryScanNumber - (int)Math.Round(chromScanWindowWidth / 2, 0);
var stopScan = scanset.PrimaryScanNumber + (int)Math.Round(chromScanWindowWidth / 2, 0);
var massSpectrum = MSGenerator.GenerateMS(Run, scanset);
foreach (var iqTarget in children)
{
var childStateIqResult = (O16O18IqResult)iqTarget.GetResult();
childStateIqResult.IqResultDetail.MassSpectrum = massSpectrum.TrimData(iqTarget.MZTheor - 3, iqTarget.MZTheor + 8);
var mspeakList = _mspeakDetector.FindPeaks(childStateIqResult.IqResultDetail.MassSpectrum.Xvalues,
childStateIqResult.IqResultDetail.MassSpectrum.Yvalues);
childStateIqResult.CorrelationData = ChromatogramCorrelator.CorrelateData(Run, childStateIqResult, startScan, stopScan);
childStateIqResult.CorrelationO16O18SingleLabel = childStateIqResult.GetCorrelationO16O18SingleLabel();
childStateIqResult.CorrelationO16O18DoubleLabel = childStateIqResult.GetCorrelationO16O18DoubleLabel();
childStateIqResult.CorrelationBetweenSingleAndDoubleLabel = childStateIqResult.GetCorrelationBetweenSingleAndDoubleLabel();
childStateIqResult.RatioO16O18DoubleLabel = childStateIqResult.GetRatioO16O18DoubleLabel();
childStateIqResult.RatioO16O18SingleLabel = childStateIqResult.GetRatioO16O18SingleLabel();
childStateIqResult.RatioSingleToDoubleLabel = childStateIqResult.GetRatioSingleToDoubleLabel();
childStateIqResult.ObservedIsotopicProfile = MsfeatureFinder.IterativelyFindMSFeature(childStateIqResult.IqResultDetail.MassSpectrum,
iqTarget.TheorIsotopicProfile);
if (childStateIqResult.ObservedIsotopicProfile != null)
{
var observedIsoList = childStateIqResult.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Take(4).ToList(); //first 4 peaks excludes the O18 double label peak (fifth peak)
var theorPeakList = iqTarget.TheorIsotopicProfile.Peaklist.Select(p => (Peak)p).Take(4).ToList();
childStateIqResult.FitScore = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
var o18Iso = childStateIqResult.ConvertO16ProfileToO18(iqTarget.TheorIsotopicProfile, 4);
theorPeakList = o18Iso.Peaklist.Select(p => (Peak)p).ToList();
observedIsoList = childStateIqResult.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Skip(4).ToList(); //skips the first 4 peaks and thus includes the O18 double label isotopic profile
childStateIqResult.FitScoreO18Profile = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
childStateIqResult.InterferenceScore = InterferenceScorer.GetInterferenceScore(childStateIqResult.ObservedIsotopicProfile, mspeakList);
childStateIqResult.MZObs = childStateIqResult.ObservedIsotopicProfile.MonoPeakMZ;
childStateIqResult.MonoMassObs = childStateIqResult.ObservedIsotopicProfile.MonoIsotopicMass;
childStateIqResult.MZObsCalibrated = Run.GetAlignedMZ(childStateIqResult.MZObs);
childStateIqResult.MonoMassObsCalibrated = (childStateIqResult.MZObsCalibrated - DeconTools.Backend.Globals.PROTON_MASS) * childStateIqResult.Target.ChargeState;
childStateIqResult.ElutionTimeObs = ((ChromPeak)favResult.ChromPeakSelected).NETValue;
}
else
{
childStateIqResult.FitScore = -1;
childStateIqResult.InterferenceScore = -1;
}
getRsquaredVal(childStateIqResult, out rsquaredVal, out slope);
IqLogger.Log.Info("\t\t\t" + childStateIqResult.Target.ID + "\t" + childStateIqResult.Target.MZTheor.ToString("0.000") + "\t" + childStateIqResult.Target.ChargeState
+ "\t" + childStateIqResult.LcScanObs + "\t" + childStateIqResult.FitScore.ToString("0.000") + "\t" + rsquaredVal + "\t" + slope);
childStateIqResult.LCScanSetSelected = favResult.LCScanSetSelected;
childStateIqResult.LcScanObs = favResult.LcScanObs;
if (GraphsAreOutputted)
{
if (_graphGenerator == null)
{
_graphGenerator = new BasicGraphControl();
}
ExportGraphs(childStateIqResult);
}
}
}
}
