private static LinkedList1 <UOPair <HlaMsr1> > MakeUnphased(UOPair <LinkedList1 <HlaMsr1> > phaseGrounded)
{
LinkedList1 <UOPair <HlaMsr1> > unphased = null;
foreach (var pair in SpecialFunctions.EnumerateTwo(phaseGrounded.First, phaseGrounded.Second))
{
unphased = LinkedList1 <UOPair <HlaMsr1> > .GetInstance(UOPair <HlaMsr1> .GetInstance(pair.Key, pair.Value), unphased);
}
return(unphased);
}
internal void Prenormalize(PidAndHlaSet pidAndHlaSet, Linkdis linkdis)
{
PhaseToLogProb = new Dictionary <UOPair <LinkedList1 <HlaMsr1> >, double>();
UnphaseToLogProb = new Dictionary <LinkedList1 <UOPair <HlaMsr1> >, double>();
LogTotal = double.NegativeInfinity;
BadHlaMsr1NameOrNull = null;
UsedLowerResModel = false;
//CounterWithMessages abstractPhaseCounter = CounterWithMessages.GetInstance("\tabstract phase index = {0}", 1, null);
try
{
foreach (var phaseAbstract in pidAndHlaSet.GetPhasedEnumeration())
{
//abstractPhaseCounter.Increment();
var firstHlaListToProb = linkdis.CreateHlaListToProb(phaseAbstract.First);
var secondHlaListToProb = linkdis.CreateHlaListToProb(phaseAbstract.Second);
if (firstHlaListToProb.Count * secondHlaListToProb.Count > linkdis.CombinationLimit)
{
throw new CombinationLimitException("The combinationLimit was exceeded. " + linkdis.CombinationLimit.ToString());
}
CounterWithMessages groundPhaseCounter = CounterWithMessages.GetInstance("\t\tground phase index = {0}", 1000, null);
foreach (var firstHlaListAndProb in firstHlaListToProb)
{
foreach (var secondHlaListAndProb in secondHlaListToProb)
{
groundPhaseCounter.Increment();
var phaseGrounded = UOPair <LinkedList1 <HlaMsr1> > .GetInstance(firstHlaListAndProb.Key, secondHlaListAndProb.Key);
var unphasedGrounded = MakeUnphased(phaseGrounded);
double prob = firstHlaListAndProb.Value.Key * secondHlaListAndProb.Value.Key;
UsedLowerResModel |= firstHlaListAndProb.Value.Value || secondHlaListAndProb.Value.Value;
double logProb = Math.Log(prob);
LogSum(PhaseToLogProb, phaseGrounded, logProb);
LogSum(UnphaseToLogProb, unphasedGrounded, logProb);
LogTotal = SpecialFunctions.LogSum(LogTotal, logProb);
}
}
}
}
catch (HlaNotInModelException e)
{
CreateNoAnswerAnswer(pidAndHlaSet, e);
}
}
public static IEnumerable <PidAndHlaSet> GetEnumerationDense(TextReader inputTextReader)
{
foreach (var pidAndHlaRecord in SpecialFunctions.ReadDelimitedFile(inputTextReader, new { pid = "", A1 = "", A2 = "", B1 = "", B2 = "", C1 = "", C2 = "" }, new char[] { '\t' }, true))
{
PidAndHlaSet pidAndHlaSet = new PidAndHlaSet();
pidAndHlaSet.Pid = pidAndHlaRecord.pid;
pidAndHlaSet.WarningSet = new HashSet <string>();
pidAndHlaSet.HlaUopairList = LinkedList1 <UOPair <HlaMsr1> > .GetInstance(
UOPair <HlaMsr1> .GetInstance(CreateHla(pidAndHlaRecord.C1, ref pidAndHlaSet.WarningSet), CreateHla(pidAndHlaRecord.C2, ref pidAndHlaSet.WarningSet)),
UOPair <HlaMsr1> .GetInstance(CreateHla(pidAndHlaRecord.B1, ref pidAndHlaSet.WarningSet), CreateHla(pidAndHlaRecord.B2, ref pidAndHlaSet.WarningSet)),
UOPair <HlaMsr1> .GetInstance(CreateHla(pidAndHlaRecord.A1, ref pidAndHlaSet.WarningSet), CreateHla(pidAndHlaRecord.A2, ref pidAndHlaSet.WarningSet)));
pidAndHlaSet.ClassList = new List <string> {
"C", "B", "A"
};
yield return(pidAndHlaSet);
}
}
private void CreateNoAnswerAnswer(PidAndHlaSet pidAndHlaSet, HlaNotInModelException e)
{
PhaseToLogProb = new Dictionary <UOPair <LinkedList1 <HlaMsr1> >, double>();
UnphaseToLogProb = new Dictionary <LinkedList1 <UOPair <HlaMsr1> >, double>();
BadHlaMsr1NameOrNull = e.HlaName;
UsedLowerResModel = true;
var phaseGrounded = UOPair <LinkedList1 <HlaMsr1> > .GetInstance(
LinkedList1 <HlaMsr1> .GetInstanceFromList(pidAndHlaSet.HlaUopairList.Select(pair => pair.First).ToList()),
LinkedList1 <HlaMsr1> .GetInstanceFromList(pidAndHlaSet.HlaUopairList.Select(pair => pair.Second).ToList())
);
var unphasedGrounded = pidAndHlaSet.HlaUopairList;
double logProb = double.NaN;
LogSum(PhaseToLogProb, phaseGrounded, logProb);
LogSum(UnphaseToLogProb, unphasedGrounded, logProb);
}
private static PidAndHlaSet CreatePidAndHlaSet(string previousPid, Dictionary <string, List <HlaMsr1> > classToHlaList, HashSet <string> warningSet)
{
SpecialFunctions.CheckCondition(new HashSet <string>(classToHlaList.Keys).SetEquals(new HashSet <string> {
"A", "B", "C"
}), "Expect Hla's for exactly classes A,B, & C. " + previousPid);
SpecialFunctions.CheckCondition(classToHlaList.Values.All(list => list.Count == 2), "Expect two hla lines for each Hla class. " + previousPid);
PidAndHlaSet pidAndHlaSet = new PidAndHlaSet();
pidAndHlaSet.Pid = previousPid;
pidAndHlaSet.WarningSet = warningSet;
pidAndHlaSet.HlaUopairList = LinkedList1 <UOPair <HlaMsr1> > .GetInstance(
UOPair <HlaMsr1> .GetInstance(classToHlaList["C"][0], classToHlaList["C"][1]),
UOPair <HlaMsr1> .GetInstance(classToHlaList["B"][0], classToHlaList["B"][1]),
UOPair <HlaMsr1> .GetInstance(classToHlaList["A"][0], classToHlaList["A"][1]));
pidAndHlaSet.ClassList = new List <string> {
"C", "B", "A"
};
return(pidAndHlaSet);
}
