//!!!Yikes tons of repeated code and stuff re-run
internal static HlaAssignmentWithResponses CreateHlaAssignment(Quickscore <Hla, int> quickscore, string hlaListAsString, ICollection <int> patientsWhoRespond)
{
Qmrr.HlaFactory hlaFactory = Qmrr.HlaFactory.GetFactory("noConstraint");
//!!!this code is repeated elsewhere
Dictionary <Hla, List <int> > hlaToRespondingPatientsUnfiltered = quickscore.CreateCauseToSubsetOfEffects(patientsWhoRespond);
Dictionary <Hla, List <int> > hlaToRespondingPatients = Filter9xs(hlaToRespondingPatientsUnfiltered);
List <Hla> hlaListFromRepondingPatients = new List <Hla>(hlaToRespondingPatients.Keys);
Dictionary <Hla, bool> hlaAssignmentDicationary = new Dictionary <Hla, bool>();
foreach (string hlaName in hlaListAsString.Split(';'))
{
Hla hla = hlaFactory.GetGroundInstance(hlaName);
hlaAssignmentDicationary[hla] = true;
}
List <int> indexCollection = new List <int>();
for (int hlaIndex = 0; hlaIndex < hlaListFromRepondingPatients.Count; ++hlaIndex)
{
Hla hla = hlaListFromRepondingPatients[hlaIndex];
if (hlaAssignmentDicationary.ContainsKey(hla))
{
indexCollection.Add(hlaIndex);
}
}
HlaAssignmentWithResponses hlaAssignment = HlaAssignmentWithResponses.GetInstance(quickscore, hlaListFromRepondingPatients,
indexCollection, hlaToRespondingPatients);
return(hlaAssignment);
}
//private Dictionary<string, bool> GetAList(Dictionary<string, string> row)
//{
// Dictionary<string, bool> alist = new Dictionary<string, bool>();
// string alistValue = row["HLA In Fixed List"];
// foreach (string hla in alistValue.Split(' '))
// {
// Debug.Assert((hla.Length == 3 && !hla.StartsWith("B15")) || (hla.Length == 5 && hla.StartsWith("B15")));
// alist.Add(hla, true);
// }
// return alist;
//}
public static HlaAssignmentWithResponses CreateHlaAssignment(List <Dictionary <string, string> > rowsOfThisPeptide, IEnumerable <Hla> hlaList, HlaResolution hlaResolution, Quickscore <Hla, int> quickscore, List <int> patientsWhoRespond)
{
//!!!this code is repeated elsewhere
Dictionary <Hla, List <int> > hlaToRespondingPatientsUnfiltered = quickscore.CreateCauseToSubsetOfEffects(patientsWhoRespond);
Dictionary <Hla, List <int> > hlaToRespondingPatients = Filter9xs(hlaToRespondingPatientsUnfiltered);
List <Hla> hlaListFromRepondingPatients = new List <Hla>(hlaToRespondingPatients.Keys);
Dictionary <Hla, bool> hlaAssignmentDicationary = new Dictionary <Hla, bool>();
foreach (Dictionary <string, string> causeAssignmentRow in rowsOfThisPeptide)
{
Hla hla = GetHlaFromRow(causeAssignmentRow, hlaResolution);
hlaAssignmentDicationary[hla] = true;
}
HlaAssignmentWithResponses hlaAssignment = HlaAssignmentWithResponses.GetInstance(hlaAssignmentDicationary.Keys, quickscore, hlaListFromRepondingPatients,
hlaToRespondingPatients);
return(hlaAssignment);
}
//!!!Yikes tons of repeated code and stuff re-run
public static HlaAssignmentWithResponses CreateHlaAssignment(List <Dictionary <string, string> > rowsOfThisPeptide, IEnumerable <Hla> hlaList, HlaResolution hlaResolution, Quickscore <Hla, int> quickscore, List <int> patientsWhoRespond, Hla hlaToReplace, Hla hlaWithWhichToReplaceItOrNull)
{
//!!!this code is repeated elsewhere
Dictionary <Hla, List <int> > hlaToRespondingPatientsUnfiltered = quickscore.CreateCauseToSubsetOfEffects(patientsWhoRespond);
Dictionary <Hla, List <int> > hlaToRespondingPatients = Filter9xs(hlaToRespondingPatientsUnfiltered);
List <Hla> hlaListFromRepondingPatients = new List <Hla>(hlaToRespondingPatients.Keys);
Dictionary <Hla, bool> hlaAssignmentDicationary = new Dictionary <Hla, bool>();
foreach (Dictionary <string, string> causeAssignmentRow in rowsOfThisPeptide)
{
Hla hla = GetHlaFromRow(causeAssignmentRow, hlaResolution);
hlaAssignmentDicationary[hla] = true;
}
hlaAssignmentDicationary.Remove(hlaToReplace);
if (hlaWithWhichToReplaceItOrNull != null)
{
hlaAssignmentDicationary.Add(hlaWithWhichToReplaceItOrNull, true);
}
List <int> indexCollection = new List <int>();
for (int hlaIndex = 0; hlaIndex < hlaListFromRepondingPatients.Count; ++hlaIndex)
{
Hla hla = hlaListFromRepondingPatients[hlaIndex];
if (hlaAssignmentDicationary.ContainsKey(hla))
{
indexCollection.Add(hlaIndex);
}
}
HlaAssignmentWithResponses hlaAssignment = HlaAssignmentWithResponses.GetInstance(quickscore, hlaListFromRepondingPatients,
indexCollection, hlaToRespondingPatients);
return(hlaAssignment);
}
