protected OptimizationParameterList FindBestParams(string peptide,
Set <Hla> candidateHlaSet,
Set <Hla> hlaWithLinkZero,
Dictionary <string, Set <Hla> > patientList,
//Dictionary<string, Dictionary<string,double>> reactTable,
out double score)
{
//SpecialFunctions.CheckCondition(false, "Regression test this to be sure that switch to new optimization method didn't change anything important - cmk 5/1/2006");
Set <Hla> knownHlaSet = KnownTable(peptide);
TrueCollection trueCollection = TrueCollection.GetInstance(candidateHlaSet, knownHlaSet);
OptimizationParameterList qmrrParamsThisPeptide = CreateQmrrParamsStartForTheseCandidateHlas(trueCollection.CreateHlaAssignmentAsSet(), hlaWithLinkZero);
//OptimizationParameterList qmrrParamsThisPeptide = CreateQmrrParamsX(causePrior, leakProbability, trueCollection.CreateHlaAssignmentAsSet());
ModelLikelihoodFactories modelLikelihoodFactories = ModelLikelihoodFactories.GetInstanceLinkPerHla(qmrrParamsThisPeptide, trueCollection.CreateHlaAssignmentAsSet());
QmrrPartialModelCollection singletonQmrrPartialModelCollection =
QmrrPartialModelCollection.GetInstance(
peptide,
modelLikelihoodFactories,
qmrrParamsThisPeptide,
patientList,
ReactTableUnfiltered,
_knownTable,
HlaFactory.Name //!!!would it be better to pass the actual factory???
);
BestSoFar <double, TrueCollection> bestSoFar = BestSoFar <double, TrueCollection> .GetInstance(SpecialFunctions.DoubleGreaterThan);
bestSoFar.Compare(double.NegativeInfinity, trueCollection);
Dictionary <string, BestSoFar <double, TrueCollection> > peptideToBestHlaAssignmentSoFar = new Dictionary <string, BestSoFar <double, TrueCollection> >();
peptideToBestHlaAssignmentSoFar.Add(peptide, bestSoFar);
QmrrlModelMissingParametersCollection aQmrrlModelMissingParametersCollection
= QmrrlModelMissingParametersCollection.GetInstance(modelLikelihoodFactories, singletonQmrrPartialModelCollection, peptideToBestHlaAssignmentSoFar);
OptimizationParameterList qmrrParamsEnd = aQmrrlModelMissingParametersCollection.FindBestParams(qmrrParamsThisPeptide, out score);
return(qmrrParamsEnd);
}
public override bool Remove(T item)
{
return(TrueCollection.Remove(item));
}
public override void Clear()
{
TrueCollection.Clear();
}
public override void Add(T item)
{
TrueCollection.Add(item);
}