//private static OptimizationParameterList CreateQmrrParamsX(double causePrior, double leakProbability, Set<string> candidateHlaSet)
//{
// List<Parameter> parameterCollection = new List<Parameter>();
// parameterCollection.Add(Parameter.GetProbabilityInstance("causePrior", causePrior, false));
// foreach (string hla in candidateHlaSet)
// {
// if (hla == "B1599")
// {
// Parameter aParameter = Parameter.GetProbabilityInstance("link" + hla, 0, false);
// parameterCollection.Add(aParameter);
// }
// else
// {
// Parameter aParameter = Parameter.GetProbabilityInstance("link" + hla, .5, true);
// parameterCollection.Add(aParameter);
// }
// }
// parameterCollection.Add(Parameter.GetProbabilityInstance("leakProbability", leakProbability, false));
// parameterCollection.Add(Parameter.GetPositiveFactorInstance("useKnownList", 1, false));
// OptimizationParameterList qmrrParamsStart = OptimizationParameterList.GetInstance2(parameterCollection);
// return qmrrParamsStart;
//}
//private static Dictionary<string, string> LoadOriginalParameters(string directory)
//{
// string parameterFileName = string.Format(@"{0}\{1}", directory, "NoisyOr.Parameters.TwoCause.UseKnown.txt");//!!!const
// string header = "dataset varyFitFactor score causePrior fitFactor leakProbability link useKnownList";
// foreach (Dictionary<string, string> row in SpecialFunctions.TabFileTable(parameterFileName, header, false))
// {
// bool varyFitFactor = bool.Parse(row["varyFitFactor"]);
// if (!varyFitFactor)
// {
// return row;
// }
// }
// Debug.Fail("Didn't find expected line");
// return null;
//}
//static Dictionary<string, Set<string>> LoadOriginalPeptideToHlaSet(string directory)
//{
// string fileName = string.Format(@"{0}\{1}", directory, @"NoisyOr.HlasPerPeptide.hivmodel.TwoCauseFalse.UseKnownTrue.txt");
// Dictionary<string, Set<string>> originalPeptideToHlaSet = new Dictionary<string, Set<string>>();
// string header = "Peptide HLAAssignment LogLikelihood";
// foreach (Dictionary<string, string> row in SpecialFunctions.TabFileTable(fileName, header, false))
// {
// string peptide = row["Peptide"];
// Set<string> hlaSet = Set<string>.GetInstance(row["HLAAssignment"].Split(';'));
// originalPeptideToHlaSet.Add(peptide, hlaSet);
// }
// return originalPeptideToHlaSet;
//}
public static QmrrModelAllPeptides CreateSimpleModel(string directory, string casename, bool useKnownList)
{
OptimizationParameterList qmrrParamsStart = OptimizationParameterList.GetInstance(
OptimizationParameter.GetProbabilityInstance("causePrior", .01, true),
OptimizationParameter.GetProbabilityInstance("link", .5, true),
OptimizationParameter.GetProbabilityInstance("leakProbability", .003, true),
OptimizationParameter.GetPositiveFactorInstance("useKnownList", useKnownList ? 1 : 0, false)
);
ModelLikelihoodFactories modelLikelihoodFactories = ModelLikelihoodFactories.GetInstanceThreeParamSlow(qmrrParamsStart);
double depth = 1.5;
string dataset = string.Format(@"{0}\{1}", directory, casename);
QmrrModelAllPeptides qmrrModel = QmrrModelAllPeptides.GetInstance(modelLikelihoodFactories, dataset, qmrrParamsStart, depth, "noConstraints");
return(qmrrModel);
}
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);
}