private PValueDetails CreateAPValueDetail(int nullIndex, string peptide, Dictionary <string, Set <Hla> > pidToHlaSetAll, Set <Hla> knownHlaSet, Set <Hla> bestHlaSetSoFar, Hla hla)
{
//Dictionary<string, Dictionary<string, double>> reactTableCustom;
Dictionary <string, Set <Hla> > pidToHlaSetCustom =
CreatePidToHlaSetCustom(pidToHlaSetAll, bestHlaSetSoFar, hla, knownHlaSet);
//out pidToHlaSetCustom, out reactTableCustom);
//!!!could cache both calls to FindBestParams
double scoreBase;
OptimizationParameterList baseParams = FindBestParams(peptide, bestHlaSetSoFar, Set <Hla> .GetInstance(), pidToHlaSetCustom, out scoreBase);
double scoreWithOneMore;
OptimizationParameterList withMoreMoreParams = FindBestParams(peptide, bestHlaSetSoFar.Union(hla), Set <Hla> .GetInstance(), pidToHlaSetCustom, out scoreWithOneMore);
PValueDetails pValueDetails = PValueDetails.GetInstance(SelectionName, nullIndex, peptide, hla,
scoreWithOneMore, scoreBase, knownHlaSet, bestHlaSetSoFar, withMoreMoreParams["leakProbability"].Value, withMoreMoreParams["link" + hla].Value, withMoreMoreParams);
//Debug.Write(String.Format("{0}/{1}\t", hla, scoreWithOneMore));
return(pValueDetails);
}
internal override Dictionary <Hla, PValueDetails> CreateHlaToPValueDetails(int nullIndex, string peptide, Dictionary <string, Set <Hla> > pidToHlaSet, Set <Hla> candidateHlaSet, TextWriter writer)
{
Dictionary <string, double> pidToReactValue = ReactTableUnfiltered[peptide];
Set <Hla> knownHlaSet = KnownTable(peptide);
double scoreKnown;
OptimizationParameterList knownParams = FindBestParams(peptide, Set <Hla> .GetInstance(), Set <Hla> .GetInstance(), pidToHlaSet, out scoreKnown);
Dictionary <Hla, PValueDetails> hlaToPValueDetails = new Dictionary <Hla, PValueDetails>();
foreach (Hla hla in candidateHlaSet.Subtract(knownHlaSet)) //!!!only look at hla's of patients with reactivity to this peptide (how effects nulls?)
{
double scoreWithOne;
OptimizationParameterList withHlaParams = FindBestParams(peptide, Set <Hla> .GetInstance(hla), Set <Hla> .GetInstance(), pidToHlaSet, out scoreWithOne);
PValueDetails pValueDetails = PValueDetails.GetInstance(SelectionName, nullIndex, peptide, hla, scoreWithOne, scoreKnown, knownHlaSet, null, withHlaParams["leakProbability"].Value, withHlaParams["link" + hla].Value, withHlaParams);
hlaToPValueDetails.Add(hla, pValueDetails);
writer.WriteLine(pValueDetails);
Debug.WriteLine(pValueDetails);
writer.Flush();
}
return(hlaToPValueDetails);
}