public override void Execute(ResultCollection resultList)
{
Check.Require(resultList.Run.CurrentMassTag != null, this.Name + " failed. MassTag was not defined.");
var currentResult = resultList.GetTargetedResult(resultList.Run.CurrentMassTag);
if (msgen == null)
{
msgen = MSGeneratorFactory.CreateMSGenerator(resultList.Run.MSFileType);
msgen.IsTICRequested = false;
}
var currentTarget = resultList.Run.CurrentMassTag;
// Set the MS Generator to use a window around the target so that we do not grab a lot of unecessary data from the UIMF file
msgen.MinMZ = currentTarget.MZ - 10;
msgen.MaxMZ = currentTarget.MZ + 10;
float normalizedElutionTime;
if (currentResult.Run.CurrentMassTag.ElutionTimeUnit == DeconTools.Backend.Globals.ElutionTimeUnit.ScanNum)
{
normalizedElutionTime = resultList.Run.CurrentMassTag.ScanLCTarget / (float)currentResult.Run.GetNumMSScans();
}
else
{
normalizedElutionTime = resultList.Run.CurrentMassTag.NormalizedElutionTime;
}
//collect Chrom peaks that fall within the NET tolerance
var peaksWithinTol = new List <ChromPeak>(); //
foreach (ChromPeak peak in resultList.Run.PeakList)
{
if (Math.Abs(peak.NETValue - normalizedElutionTime) <= Parameters.NETTolerance) //peak.NETValue was determined by the ChromPeakDetector or a future ChromAligner Task
{
peaksWithinTol.Add(peak);
}
}
var peakQualityList = new List <ChromPeakQualityData>();
//iterate over peaks within tolerance and score each peak according to MSFeature quality
#if DEBUG
var tempMinScanWithinTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime - Parameters.NETTolerance);
var tempMaxScanWithinTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime + Parameters.NETTolerance);
var tempCenterTol = (int)resultList.Run.NetAlignmentInfo.GetScanForNet(normalizedElutionTime);
Console.WriteLine("SmartPeakSelector --> NETTolerance= " + Parameters.NETTolerance + "; chromMinCenterMax= " + tempMinScanWithinTol + "\t" + tempCenterTol + "" +
"\t" + tempMaxScanWithinTol);
Console.WriteLine("MT= " + currentResult.Target.ID + ";z= " + currentResult.Target.ChargeState + "; mz= " + currentResult.Target.MZ.ToString("0.000") + "; ------------------------- PeaksWithinTol = " + peaksWithinTol.Count);
#endif
currentResult.NumChromPeaksWithinTolerance = peaksWithinTol.Count;
currentResult.NumQualityChromPeaks = -1;
ChromPeak bestChromPeak;
if (currentResult.NumChromPeaksWithinTolerance > _parameters.NumChromPeaksAllowed)
{
bestChromPeak = null;
}
else
{
foreach (var chromPeak in peaksWithinTol)
{
var pq = new ChromPeakQualityData(chromPeak);
peakQualityList.Add(pq);
// TODO: Currently hard-coded to sum only 1 scan
resultList.Run.CurrentScanSet = ChromPeakUtilities.GetLCScanSetForChromPeakUIMF(chromPeak, resultList.Run, 1);
//This resets the flags and the scores on a given result
currentResult.ResetResult();
//generate a mass spectrum
msgen.Execute(resultList);
//find isotopic profile
TargetedMSFeatureFinder.Execute(resultList);
//get fit score
fitScoreCalc.Execute(resultList);
//get i_score
resultValidator.Execute(resultList);
//collect the results together
AddScoresToPeakQualityData(pq, currentResult);
#if DEBUG
pq.Display();
#endif
}
//run a algorithm that decides, based on fit score mostly.
bestChromPeak = determineBestChromPeak(peakQualityList, currentResult);
}
currentResult.ChromPeakQualityList = peakQualityList;
resultList.Run.CurrentScanSet = ChromPeakUtilities.GetLCScanSetForChromPeakUIMF(bestChromPeak, resultList.Run, Parameters.NumScansToSum);
UpdateResultWithChromPeakAndLCScanInfo(currentResult, bestChromPeak);
}
/// <summary>
/// Calculates Metrics based on ChromPeakIqTarget
/// NET Error, Mass Error, Isotopic Fit, & Isotope Correlation
/// </summary>
protected override void ExecuteWorkflow(IqResult result)
{
result.IsExported = false;
if (MSGenerator == null)
{
MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType);
MSGenerator.IsTICRequested = false;
}
var target = result.Target as ChromPeakIqTarget;
if (target == null)
{
throw new NullReferenceException("The ChromPeakAnalyzerIqWorkflow only works with the ChromPeakIqTarget.");
}
var lcscanset = _chromPeakUtilities.GetLCScanSetForChromPeak(target.ChromPeak, Run, WorkflowParameters.SmartChromPeakSelectorNumMSSummed);
//Generate a mass spectrum
var massSpectrumXYData = MSGenerator.GenerateMS(Run, lcscanset);
massSpectrumXYData = massSpectrumXYData.TrimData(result.Target.MZTheor - 5, result.Target.MZTheor + 15);
//Find isotopic profile
List <Peak> mspeakList;
result.ObservedIsotopicProfile = TargetedMSFeatureFinder.IterativelyFindMSFeature(massSpectrumXYData, target.TheorIsotopicProfile, out mspeakList);
//Default Worst Scores
double iscore = 1;
//Get NET Error
var netError = target.ChromPeak.NETValue - target.ElutionTimeTheor;
var leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
var peakToTheLeft = leftOfMonoPeakLooker.LookforPeakToTheLeftOfMonoPeak(target.TheorIsotopicProfile.getMonoPeak(), target.ChargeState, mspeakList);
var hasPeakTotheLeft = peakToTheLeft != null;
if (result.ObservedIsotopicProfile == null)
{
result.IsotopicProfileFound = false;
result.FitScore = 1;
}
else
{
//Get fit score O16 profile
var observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Take(4).ToList(); //first 4 peaks excludes the O18 double label peak (fifth peak)
var theorPeakList = target.TheorIsotopicProfile.Peaklist.Select(p => (Peak)p).Take(4).ToList();
result.FitScore = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
// fit score O18 profile
var o18Iso = ((O16O18IqResult)result).ConvertO16ProfileToO18(target.TheorIsotopicProfile, 4);
theorPeakList = o18Iso.Peaklist.Select(p => (Peak)p).ToList();
observedIsoList = result.ObservedIsotopicProfile.Peaklist.Cast <Peak>().Skip(4).ToList(); //skips the first 4 peaks and thus includes the O18 double label isotopic profile
((O16O18IqResult)result).FitScoreO18Profile = PeakFitter.GetFit(theorPeakList, observedIsoList, 0.05, WorkflowParameters.MSToleranceInPPM);
//get i_score
iscore = InterferenceScorer.GetInterferenceScore(result.ObservedIsotopicProfile, mspeakList);
//get ppm error
var massErrorInDaltons = TheorMostIntensePeakMassError(target.TheorIsotopicProfile, result.ObservedIsotopicProfile, target.ChargeState);
var ppmError = (massErrorInDaltons / target.MonoMassTheor) * 1e6;
//Get Isotope Correlation
var scan = lcscanset.PrimaryScanNumber;
var sigma = target.ChromPeak.Width / 2.35;
var chromScanWindowWidth = 4 * sigma;
//Determines where to start and stop chromatogram correlation
var startScan = scan - (int)Math.Round(chromScanWindowWidth / 2, 0);
var stopScan = scan + (int)Math.Round(chromScanWindowWidth / 2, 0);
result.CorrelationData = ChromatogramCorrelator.CorrelateData(Run, result, startScan, stopScan);
result.LcScanObs = lcscanset.PrimaryScanNumber;
result.ChromPeakSelected = target.ChromPeak;
result.LCScanSetSelected = new ScanSet(lcscanset.PrimaryScanNumber);
result.IsotopicProfileFound = true;
result.InterferenceScore = iscore;
result.IsIsotopicProfileFlagged = hasPeakTotheLeft;
result.NETError = netError;
result.MassErrorBefore = ppmError;
result.IqResultDetail.MassSpectrum = massSpectrumXYData;
result.Abundance = GetAbundance(result);
}
}
