public override void GetFitScores(IEnumerable <IsosResult> isosResults)
{
foreach (var result in isosResults)
{
//create a temporary mass tag, as a data object for storing relevant info, and using the CalculateMassesForIsotopicProfile() method.
var mt = new PeptideTarget
{
ChargeState = (short)result.IsotopicProfile.ChargeState,
MonoIsotopicMass = result.IsotopicProfile.MonoIsotopicMass
};
mt.MZ = (mt.MonoIsotopicMass / mt.ChargeState) + Globals.PROTON_MASS;
//TODO: use Josh's isotopicDistribution calculator after confirming averagine formula
mt.EmpiricalFormula = _tomIsotopicPatternGenerator.GetClosestAvnFormula(result.IsotopicProfile.MonoIsotopicMass, false);
mt.IsotopicProfile = _tomIsotopicPatternGenerator.GetIsotopePattern(mt.EmpiricalFormula, _tomIsotopicPatternGenerator.aafIsos);
TheorIsotopicProfile = mt.IsotopicProfile;
mt.CalculateMassesForIsotopicProfile(mt.ChargeState);
var theorXYData = mt.IsotopicProfile.GetTheoreticalIsotopicProfileXYData(result.IsotopicProfile.GetFWHM());
offsetDistribution(theorXYData, mt.IsotopicProfile, result.IsotopicProfile);
// Obsolete Class-wide variable: MercuryDistributionCreator distributionCreator;
//
//double resolution = result.IsotopicProfile.GetMZofMostAbundantPeak() / result.IsotopicProfile.GetFWHM();
//distributionCreator.CreateDistribution(result.IsotopicProfile.MonoIsotopicMass, result.IsotopicProfile.ChargeState, resolution);
//distributionCreator.OffsetDistribution(result.IsotopicProfile);
//XYData theorXYData = distributionCreator.Data;
var areaFitter = new AreaFitter();
var fitVal = areaFitter.GetFit(theorXYData, result.Run.XYData, 0.1, out _);
if (double.IsNaN(fitVal) || fitVal > 1)
{
result.IsotopicProfile.Score = 1;
}
else
{
result.IsotopicProfile.Score = fitVal;
}
}
}
public double CalculateFitScore(IsotopicProfile theorProfile, IsotopicProfile observedProfile, XYData massSpecXYData)
{
if (observedProfile == null || observedProfile.Peaklist == null || observedProfile.Peaklist.Count == 0)
{
return(1.0); // this is the worst possible fit score. ( 0.000 is the best possible fit score); Maybe we want to return a '-1' to indicate a failure...
}
var indexOfMostAbundantTheorPeak = theorProfile.GetIndexOfMostIntensePeak();
var indexOfCorrespondingObservedPeak = PeakUtilities.getIndexOfClosestValue(observedProfile.Peaklist,
theorProfile.getMostIntensePeak().XValue, 0, observedProfile.Peaklist.Count - 1, 0.1);
if (indexOfCorrespondingObservedPeak < 0) // most abundant peak isn't present in the actual theoretical profile... problem!
{
return(1.0);
}
var mzOffset = observedProfile.Peaklist[indexOfCorrespondingObservedPeak].XValue - theorProfile.Peaklist[indexOfMostAbundantTheorPeak].XValue;
var theorXYData = theorProfile.GetTheoreticalIsotopicProfileXYData(observedProfile.GetFWHM());
//theorXYData.Display();
theorXYData.OffSetXValues(mzOffset); //May want to avoid this offset if the masses have been aligned using LCMS Warp
//theorXYData.Display();
var areafitter = new AreaFitter();
int ionCountUsed;
var fitval = areafitter.GetFit(theorXYData, massSpecXYData, 0.1, out ionCountUsed);
if (double.IsNaN(fitval) || fitval > 1)
{
fitval = 1;
}
return(fitval);
}
