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 void FindBestQmrrParams(QmrrPartialModelCollection qmrrPartialModelCollection)
{
SpecialFunctions.CheckCondition(false, "Regression test this to be sure that switch to new optimization method didn't change anything important - cmk 5/1/2006");
QmrrlModelMissingParametersCollection aQmrrlModelMissingParametersCollection =
QmrrlModelMissingParametersCollection.GetInstance(ModelLikelihoodFactories, qmrrPartialModelCollection, PeptideToBestHlaAssignmentSoFar);
double score;
OptimizationParameterList qmrrParamsEnd = aQmrrlModelMissingParametersCollection.FindBestParams(BestParamsSoFar.Champ, out score);
BestParamsSoFar.Compare(score, qmrrParamsEnd);
}
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);
}
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);
}
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);
}
private void SearchForBestParamsAndHlaAssignments(QmrrPartialModelCollection qmrrPartialModelCollection, double depth)
{
int cStep = 100;
double eps = 1e-7;
OptimizationParameterList oldQmrrParams = null;
Debug.WriteLine(SpecialFunctions.CreateTabString("depth", "dataset", QmrrParamsStart.ToStringHeader(), "Step", "After", QmrrParamsStart.ToStringHeader(), "Score"));
for (int iStep = 0; iStep < cStep && !(BestParamsSoFar.Champ.IsClose(oldQmrrParams, eps)); ++iStep)
{
oldQmrrParams = BestParamsSoFar.Champ.Clone();
double hlaAssignmentSumScore = FindBestHlaAssignmentSet(qmrrPartialModelCollection, depth);
Debug.WriteLine(SpecialFunctions.CreateTabString(depth, qmrrPartialModelCollection.DatasetName,
QmrrParamsStart, iStep + 1, "AfterHla", BestParamsSoFar.Champ,
hlaAssignmentSumScore));
FindBestQmrrParams(qmrrPartialModelCollection);
Debug.WriteLine(SpecialFunctions.CreateTabString(depth, qmrrPartialModelCollection.DatasetName,
QmrrParamsStart, iStep + 1, "AfterParam", BestParamsSoFar.Champ, BestParamsSoFar.ChampsScore));
}
}
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);
}
//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);
}