static public ModelLikelihoodFactories GetInstanceTwoCausePriors(OptimizationParameterList qmrrParams, string dataset)
{
SpecialFunctions.CheckCondition(qmrrParams.Count == 5);
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("causePrior"));
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("fitFactor"));
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("link"));
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("leakProbability"));
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("useKnownList"));
SpecialFunctions.CheckCondition(!qmrrParams["useKnownList"].DoSearch);
SpecialFunctions.CheckCondition(qmrrParams["useKnownList"].Value == 0.0 || qmrrParams["useKnownList"].Value == 1.0);
TwoCausePriors aTwoCausePriors = new TwoCausePriors();
aTwoCausePriors.SetPeptideToFitUniverse(dataset);
return(aTwoCausePriors);
}
static public ModelLikelihoodFactories GetInstanceThreeParamSlow(OptimizationParameterList qmrrParams)
{
SpecialFunctions.CheckCondition(qmrrParams.Count == 4);
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("causePrior"));
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("link"));
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("leakProbability"));
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("useKnownList"));
SpecialFunctions.CheckCondition(!qmrrParams["useKnownList"].DoSearch);
SpecialFunctions.CheckCondition(qmrrParams["useKnownList"].Value == 0.0 || qmrrParams["useKnownList"].Value == 1.0);
ThreeParamSlow aThreeParamSlow = new ThreeParamSlow();
return(aThreeParamSlow);
}
internal static ModelLikelihoodFactories GetInstanceLinkPerHla(OptimizationParameterList qmrrParams, Set <Hla> candidateHlaSet)
{
SpecialFunctions.CheckCondition(qmrrParams.Count == 3 + candidateHlaSet.Count);
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("causePrior"));
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("leakProbability"));
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey("useKnownList"));
SpecialFunctions.CheckCondition(!qmrrParams["useKnownList"].DoSearch);
SpecialFunctions.CheckCondition(qmrrParams["useKnownList"].Value == 1.0);
foreach (Hla hla in candidateHlaSet)
{
string paramName = "link" + hla.ToString();
SpecialFunctions.CheckCondition(qmrrParams.ContainsKey(paramName));
}
LinkPerHla aLinkPerHla = new LinkPerHla();
return(aLinkPerHla);
}
public static ModelLikelihoodFactories GetInstanceCoverage(OptimizationParameterList qmrrParamsStart, string dataset)
{
SpecialFunctions.CheckCondition(qmrrParamsStart.Count == 1);
SpecialFunctions.CheckCondition(qmrrParamsStart.ContainsKey("useKnownList"));
SpecialFunctions.CheckCondition(!qmrrParamsStart["useKnownList"].DoSearch);
SpecialFunctions.CheckCondition(qmrrParamsStart["useKnownList"].Value == 0.0 || qmrrParamsStart["useKnownList"].Value == 1.0);
Coverage aCoverage = new Coverage();
return(aCoverage);
}