internal override Dictionary <Hla, PValueDetails> CreateHlaToPValueDetails(int nullIndex, string peptide, Dictionary <string, Set <Hla> > pidToHlaSetAll, Set <Hla> setOfHlasToConsiderAdding, TextWriter writer)
{
Dictionary <Hla, PValueDetails> hlaToPValueDetails = new Dictionary <Hla, PValueDetails>();
if (setOfHlasToConsiderAdding.Count == 0)
{
return(hlaToPValueDetails);
}
Dictionary <string, double> pidToReactValue = ReactTableUnfiltered[peptide];
Set <Hla> knownHlaSet = KnownTable(peptide);
SpecialFunctions.CheckCondition(setOfHlasToConsiderAdding.Intersection(knownHlaSet).Count == 0);
Set <Hla> bestHlaSetSoFar = Set <Hla> .GetInstance();
while (setOfHlasToConsiderAdding.Count > 0)
{
BestSoFar <PValueDetails, Hla> bestHlaToAddSoFar = BestSoFar <PValueDetails, Hla> .GetInstance(delegate(PValueDetails pValueDetails1, PValueDetails pValueDetails2) { return(pValueDetails1.Diff.CompareTo(pValueDetails2.Diff)); });
foreach (Hla hla in setOfHlasToConsiderAdding) //!!!only look at hla's of patients with reactivity to this peptide (how effects nulls?)
{
PValueDetails pValueDetails = CreateAPValueDetail(nullIndex, peptide, pidToHlaSetAll, knownHlaSet, bestHlaSetSoFar, hla);
bestHlaToAddSoFar.Compare(pValueDetails, hla);
}
//Debug.WriteLine("");
PValueDetails bestPValueDetails = bestHlaToAddSoFar.ChampsScore; //!!!weird that PValue details is the score and the object
if (bestPValueDetails.PValue() > PValueCutOff)
{
break;
}
Hla hlaToAdd = bestHlaToAddSoFar.Champ;
setOfHlasToConsiderAdding.Remove(hlaToAdd);
bestHlaSetSoFar = bestHlaSetSoFar.Union(hlaToAdd);
hlaToPValueDetails.Add(hlaToAdd, bestPValueDetails);
writer.WriteLine(bestPValueDetails);
//Debug.WriteLine(bestPValueDetails);
writer.Flush();
}
return(hlaToPValueDetails);
}
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 static PValueDetails GetInstance(
string selectionName,
int nullIndex, string peptide, Hla hla,
double score1, double score2, Set <Hla> knownHlas, Set <Hla> bestHlaSetSoFar, double leakProbability, double linkProbability, OptimizationParameterList previousParams)
{
PValueDetails pValueDetails = new PValueDetails();
pValueDetails.SelectionName = selectionName;
pValueDetails.NullIndex = nullIndex;
pValueDetails.Peptide = peptide;
pValueDetails.Hla = hla;
pValueDetails.Score1 = score1;
pValueDetails.Score2 = score2;
pValueDetails.Diff = score1 - score2;
pValueDetails.KnownHlas = knownHlas;
pValueDetails.BestHlaSetSoFar = bestHlaSetSoFar;
pValueDetails.LeakProbability = leakProbability;
pValueDetails.LinkProbability = linkProbability;
pValueDetails.PreviousParams = previousParams;
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);
}
