static public QmrrPartialModel GetInstance(ModelLikelihoodFactories modelLikelihoodFactories,
string peptide,
Dictionary <string, double> patientToAnyReaction,
Set <Hla> knownHlaSet,
Dictionary <string, Set <Hla> > patientList,
OptimizationParameterList qmrrParamsStart
)
{
QmrrPartialModel aQmrrPartialModel = new QmrrPartialModel();
aQmrrPartialModel.QmrrParamsStart = qmrrParamsStart;
aQmrrPartialModel.Peptide = peptide;
aQmrrPartialModel.PatientToAnyReaction = patientToAnyReaction;
aQmrrPartialModel.PatientList = patientList;
aQmrrPartialModel.KnownHlaSet = knownHlaSet;
aQmrrPartialModel.CreateHlaList();
aQmrrPartialModel.CreateSwitchableHlasWithRespondingPatients();
aQmrrPartialModel.ModelLikelihoodFactories = modelLikelihoodFactories;
if (modelLikelihoodFactories != null)
{
aQmrrPartialModel.LogLikelihoodOfCompleteModelConditionedOnKnownHlas = modelLikelihoodFactories.PartialModelDelegateFactory(aQmrrPartialModel);
}
else
{
aQmrrPartialModel.LogLikelihoodOfCompleteModelConditionedOnKnownHlas = null;
}
return(aQmrrPartialModel);
}
public static QmrrModelAllPeptides GetInstance(ModelLikelihoodFactories modelLikelihoodFactories, string datasetName, OptimizationParameterList qmrrParamsStart, double depth, string hlaFactoryName)
{
QmrrModelAllPeptides aQmrrModelAllPeptides = new QmrrModelAllPeptides();
aQmrrModelAllPeptides.QmrrPartialModelCollection = QmrrPartialModelCollection.GetInstance(modelLikelihoodFactories, datasetName, qmrrParamsStart, hlaFactoryName);
aQmrrModelAllPeptides.BestParamsAndHlaAssignments = BestParamsAndHlaAssignments.GetInstance(modelLikelihoodFactories, qmrrParamsStart, aQmrrModelAllPeptides.QmrrPartialModelCollection, depth);
aQmrrModelAllPeptides.ModelLikelihoodFactories = modelLikelihoodFactories;
return(aQmrrModelAllPeptides);
}
internal static QmrrlModelMissingParameters GetInstance(ModelLikelihoodFactories modelLikelihoodFactories, QmrrPartialModel qmrrPartialModel, BestSoFar <double, TrueCollection> bestSoFar)
{
QmrrlModelMissingParameters aQmrrlModelMissingParameters = new QmrrlModelMissingParameters();
aQmrrlModelMissingParameters.QmrrPartialModel = qmrrPartialModel;
aQmrrlModelMissingParameters.TrueCollection = bestSoFar.Champ;
aQmrrlModelMissingParameters.ModelLikelihoodFactories = modelLikelihoodFactories;
aQmrrlModelMissingParameters.LogLikelihoodOfCompleteModelConditionedOnKnownHlas = modelLikelihoodFactories.MissingParametersDelegateFactory(qmrrPartialModel, bestSoFar.Champ);
return(aQmrrlModelMissingParameters);
}
//private BestParamsAndHlaAssignments(OptimizationParameterList qmrrParamsStart)
//{
// QmrrParamsStart = qmrrParamsStart;
// CreateBestParamsSoFar();
// PeptideToBestHlaAssignmentSoFar = null;
//}
public static BestParamsAndHlaAssignments GetInstance(ModelLikelihoodFactories modelLikelihoodFactories, OptimizationParameterList qmrrParamsStart, QmrrPartialModelCollection qmrrPartialModelCollection, double depth)
{
BestParamsAndHlaAssignments aBestParamsAndHlaAssignments = new BestParamsAndHlaAssignments();
aBestParamsAndHlaAssignments.QmrrParamsStart = qmrrParamsStart;
aBestParamsAndHlaAssignments.CreateBestParamsSoFar();
aBestParamsAndHlaAssignments.ModelLikelihoodFactories = modelLikelihoodFactories;
aBestParamsAndHlaAssignments.SearchForBestParamsAndHlaAssignments(qmrrPartialModelCollection, depth);
return(aBestParamsAndHlaAssignments);
}
public static QmrrlModelMissingParametersCollection GetInstance(ModelLikelihoodFactories modelLikelihoodFactories, QmrrPartialModelCollection qmrrPartialModelCollection, Dictionary <string, BestSoFar <double, TrueCollection> > PeptideToBestHlaAssignmentSoFar)
{
QmrrlModelMissingParametersCollection aQmrrlModelMissingParametersCollection = new QmrrlModelMissingParametersCollection();
foreach (QmrrPartialModel qmrrPartialModel in qmrrPartialModelCollection)
{
QmrrlModelMissingParameters aQmrrlModelMissingParameters = QmrrlModelMissingParameters.GetInstance(modelLikelihoodFactories, qmrrPartialModel, PeptideToBestHlaAssignmentSoFar[qmrrPartialModel.Peptide]);
aQmrrlModelMissingParametersCollection.Collection.Add(aQmrrlModelMissingParameters);
}
aQmrrlModelMissingParametersCollection.GridSearch = GridSearch.GetInstance("Grid");
return(aQmrrlModelMissingParametersCollection);
}
static public QmrrPartialModelCollection GetInstance(ModelLikelihoodFactories modelLikelihoodFactories, string datasetName, OptimizationParameterList qmrrParams, string hlaFactoryName)
{
QmrrPartialModelCollection aQmrrPartialModelCollection = new QmrrPartialModelCollection();
aQmrrPartialModelCollection.HlaFactory = Qmrr.HlaFactory.GetFactory(hlaFactoryName);
aQmrrPartialModelCollection.OptimizationParameterList = qmrrParams;
aQmrrPartialModelCollection.SetFileNames(datasetName);
aQmrrPartialModelCollection.ReadTables();
aQmrrPartialModelCollection.ModelLikelihoodFactories = modelLikelihoodFactories;
aQmrrPartialModelCollection.CreateList();
return(aQmrrPartialModelCollection);
}
public static QmrrModelMissingAssignment GetInstance(ModelLikelihoodFactories modelLikelihoodFactories, QmrrPartialModel qmrrPartialModel, OptimizationParameterList qmrrParams)
{
QmrrModelMissingAssignment aQmrrModelMissingAssignment = new QmrrModelMissingAssignment();
aQmrrModelMissingAssignment.QmrrPartialModel = qmrrPartialModel;
aQmrrModelMissingAssignment.OptimizationParameterList = qmrrParams;
aQmrrModelMissingAssignment.KnownHlaSet = qmrrPartialModel.KnownHlaSet;
aQmrrModelMissingAssignment.SwitchableHlasOfRespondingPatients = qmrrPartialModel.SwitchableHlasOfRespondingPatients;
aQmrrModelMissingAssignment.ModelLikelihoodFactories = modelLikelihoodFactories;
aQmrrModelMissingAssignment.LogLikelihoodOfCompleteModelConditionedOnKnownHlas = modelLikelihoodFactories.MissingAssignmentDelegateFactory(qmrrPartialModel, qmrrParams);
return(aQmrrModelMissingAssignment);
//SetOfAllHlasCount = qmrrPartialModel.HlaList.Count;
}
public static QmrrPartialModelCollection GetInstance(string peptide,
ModelLikelihoodFactories modelLikelihoodFactories,
OptimizationParameterList qmrrParamsStart,
Dictionary <string, Set <Hla> > patientList,
Dictionary <string, Dictionary <string, double> > reactTable,
Dictionary <string, Set <Hla> > knownTable,
string hlaFactoryName
)
{
QmrrPartialModelCollection aQmrrPartialModelCollection = new QmrrPartialModelCollection();
aQmrrPartialModelCollection.HlaFactory = Qmrr.HlaFactory.GetFactory(hlaFactoryName);
aQmrrPartialModelCollection.OptimizationParameterList = qmrrParamsStart;
aQmrrPartialModelCollection.SetFileNamesToNull();
aQmrrPartialModelCollection.PeptideList = new List <string>(new string[] { peptide });
aQmrrPartialModelCollection.PatientList = patientList;
aQmrrPartialModelCollection.ReactTable = reactTable;
aQmrrPartialModelCollection._knownTable = knownTable;
aQmrrPartialModelCollection.ModelLikelihoodFactories = modelLikelihoodFactories;
aQmrrPartialModelCollection.CreateList();
return(aQmrrPartialModelCollection);
}
