public static Quickscore <Hla, int> CreateQuickscore(string fileName, string header, double causePrior, double linkProbability, double leakProbability, HlaResolution hlaResolution)
{
Qmrr.HlaFactory hlaFactory = Qmrr.HlaFactory.GetFactory("noConstraint");
Quickscore <Hla, int> quickscore = Quickscore <Hla, int> .GetInstance(hlaFactory.GetGroundInstance(""));
foreach (Dictionary <string, string> row in QuickScoreOptimalsTable(fileName, header))
{
foreach (string column in CreateHlaColumns(header))
{
Hla hla = GetHlaValue(row, column, hlaResolution);
int patient = GetPatient(row);
quickscore.SetCause(hla, causePrior);
quickscore.SetLeak(patient, leakProbability);
quickscore.SetLink(hla, patient, linkProbability);
}
}
return(quickscore);
}
//double ScoreWithNewParameters(Dictionary<string, SearchHlaAssignmentsResult> peptideToResults, int iParameter, double parameter)
//{
// double totalLogLikelihood = 0.0;
// Quickscore<string, int> quickScore = null;
// foreach (SearchHlaAssignmentsResult searchHlaAssignmentsResult in peptideToResults.Values)
// {
// //!!!don't create these structures from scratch on every call
// //!!!don't create a whole new quickscore
// if (quickScore == null)
// {
// quickScore = CloneQuickScoreWithNewParameter(searchHlaAssignmentsResult.Quickscore, iParameter, parameter);
// }
// HlaAssignmentWithResponses hlaAssignment = searchHlaAssignmentsResult.BestLogLikelihoodSoFar.Champ;
// totalLogLikelihood +=
// //!!!speed up: don't compute whole loglikelihood - only part that changes with the parameters
// quickScore.LogLikelihoodOfModelWithCompleteAssignments(
// searchHlaAssignmentsResult.PatientsWhoRespond,
// searchHlaAssignmentsResult.PatientsWhoDoNotRespond,
// hlaAssignment.AsDictionary, searchHlaAssignmentsResult.PatientWeightTableOrNull);
// }
// return totalLogLikelihood;
//}
//double ScoreWithNewParameters(Dictionary<string, SearchHlaAssignmentsResult> peptideToResults, int iParameter, double parameter)
//{
// Quickscore<string, int> quickScore = CloneQuickScoreWithNewParameter(searchHlaAssignmentsResult.Quickscore, iParameter, parameter);
// double totalLogLiklihood = ScoreModelAgainstPeptideSolutions(peptideToResults, quickScore);
// return totalLogLiklihood;
//}
//private static double ScoreModelAgainstPeptideSolutions(Dictionary<string, SearchHlaAssignmentsResult> peptideToResults, Quickscore<string, int> quickScore)
//{
// double totalLogLiklihood = 0.0;
// foreach (SearchHlaAssignmentsResult searchHlaAssignmentsResult in peptideToResults.Values)
// {
// //!!!don't create these structures from scratch on every call
// //!!!don't create a whole new quickscore
// HlaAssignment hlaAssignment = searchHlaAssignmentsResult.BestLogLikelihoodSoFar.Champ;
// totalLogLiklihood +=
// //!!!speed up: don't compute whole loglikelihood - only part that changes with the parameters
// quickScore.LogLikelihoodOfModelWithCompleteAssignments(
// searchHlaAssignmentsResult.PatientsWhoRespond,
// searchHlaAssignmentsResult.PatientsWhoDoNotRespond,
// hlaAssignment.AsDictionary, searchHlaAssignmentsResult.PatientWeightTableOrNull);
// }
// return totalLogLiklihood;
//}
private Quickscore <string, int> CloneQuickScoreWithNewParameter(Quickscore <string, int> quickscoreIn, int iParameter, double parameter)
{
double causePrior = CausePrior;
double linkProbability = LinkProbability;
double leakProbability = LeakProbability;
switch (iParameter)
{
case 0:
causePrior = parameter;
break;
case 1:
linkProbability = parameter;
break;
case 2:
leakProbability = parameter;
break;
default:
SpecialFunctions.CheckCondition(false);
break;
}
Quickscore <string, int> quickscoreOut = Quickscore <string, int> .GetInstance("");
foreach (string cause in quickscoreIn.CauseList())
{
quickscoreOut.SetCause(cause, causePrior);
foreach (int effect in quickscoreIn.EffectListForCause(cause))
{
quickscoreOut.SetLink(cause, effect, linkProbability);
quickscoreOut.SetLeak(effect, leakProbability);
}
}
return(quickscoreOut);
}
