public static HlaAssignmentsToConsider GetInstance(QmmrModelOnePeptide qmmrModelOnePeptide)
{
EveryHlaAssignmentToConsiderBitFlip aEveryHlaAssignmentToConsiderBitFlip = new EveryHlaAssignmentToConsiderBitFlip();
aEveryHlaAssignmentToConsiderBitFlip.QmmrModelOnePeptide = qmmrModelOnePeptide;
return(aEveryHlaAssignmentToConsiderBitFlip);
}
public static HlaAssignmentsToConsider GetInstance(QmmrModelOnePeptide qmmrModelOnePeptide)
{
EveryHlaAssignmentToConsiderReplace1s aEveryHlaAssignmentToConsiderReplace1s = new EveryHlaAssignmentToConsiderReplace1s();
aEveryHlaAssignmentToConsiderReplace1s.QmmrModelOnePeptide = qmmrModelOnePeptide;
return(aEveryHlaAssignmentToConsiderReplace1s);
}
public static HlaAssignmentsToConsider GetInstance(QmmrModelOnePeptide qmmrModelOnePeptide, int depth)
{
SpecialFunctions.CheckCondition(depth > 0); //!!!raise error
EveryHlaAssignmentOfThisDepth aEveryHlaAssignmentOfThisDepth = new EveryHlaAssignmentOfThisDepth();
aEveryHlaAssignmentOfThisDepth.QmmrModelOnePeptide = qmmrModelOnePeptide;
aEveryHlaAssignmentOfThisDepth.Depth = depth;
return(aEveryHlaAssignmentOfThisDepth);
}
private double FindBestHlaAssignmentSet(QmrrPartialModelCollection qmrrPartialModelCollection, double depth)
{
double sumScore = 0.0;
PeptideToBestHlaAssignmentSoFar = new Dictionary <string, BestSoFar <double, TrueCollection> >();
foreach (QmrrPartialModel qmrrPartialModel in qmrrPartialModelCollection)
{
QmmrModelOnePeptide aQmmrModelOnePeptide = QmmrModelOnePeptideGetInstance(qmrrPartialModel, BestParamsSoFar.Champ, depth);
aQmmrModelOnePeptide.FindBestHlaAssignment();
sumScore += aQmmrModelOnePeptide.BestHlaAssignmentSoFar.ChampsScore;
PeptideToBestHlaAssignmentSoFar.Add(qmrrPartialModel.Peptide, aQmmrModelOnePeptide.BestHlaAssignmentSoFar);
}
return(sumScore);
}
protected QmmrModelOnePeptide QmmrModelOnePeptideGetInstance(QmrrPartialModel qmrrPartialModel, OptimizationParameterList qmrrParams, double depth)
{
QmmrModelOnePeptide aQmmrModelOnePeptide = new QmmrModelOnePeptide();
aQmmrModelOnePeptide.QmrrModelMissingAssignment = QmrrModelMissingAssignment.GetInstance(ModelLikelihoodFactories, qmrrPartialModel, qmrrParams);
aQmmrModelOnePeptide.CreateNoSwitchablesHlaAssignment();
if (depth == 0)
{
// do nothing
}
else if (depth == Math.Floor(depth))
{
SpecialFunctions.CheckCondition(depth > 0);
aQmmrModelOnePeptide.SetForDepthSearch((int)Math.Floor(depth));
}
else
{
SpecialFunctions.CheckCondition(depth == 1.5);
aQmmrModelOnePeptide.SetForBitFlipsAnd1Replacement();
}
return(aQmmrModelOnePeptide);
}
