static public Hla TrimToHla2(Hla hlaIn)
{
string hlaName = hlaIn.ToString();
SpecialFunctions.CheckCondition(hlaName.Length >= 3, string.Format("Expected hla name to have length of at least 3 (a class and two digits), but it is '{0}'.", hlaName));
Hla hlaOut = SingletonSpecification.HlaFactoryNoConstraints.GetGroundInstance(hlaName.Substring(0, 3));
return(hlaOut);
}
//static PatchPatternFactory PatchPatternFactory = PatchPatternFactory.GetFactory("strings");
//private static PatchPattern CreateStringPatchPattern(string peptide)
//{
// PatchPatternBuilder aPatchPatternBuilder = PatchPatternFactory.GetBuilder();
// aPatchPatternBuilder.AppendGroundDisjunct(peptide);
// PatchPattern patchPattern = aPatchPatternBuilder.ToPatchPattern();
// return patchPattern;
//}
public double Predict(NEC nec, Hla hla, bool modelOnly, out string source)
{
Debug.Assert(HlaFactory.IsGroundOrAbstractInstance(hla.ToString())); // real assert
SpecialFunctions.CheckCondition(nec.N.Length == SampleNEC.N.Length && nec.E.Length == SampleNEC.E.Length && nec.C.Length == SampleNEC.C.Length,
string.Format("Length of peptide must be {0},{1},{2}", SampleNEC.N.Length, SampleNEC.E.Length, SampleNEC.C.Length));
Pair <NEC, Hla> necAndHla = new Pair <NEC, Hla>(nec, hla);
List <Pair <string, Hla> > sourceAndOriginalHlaCollection = ListAllSourcesContainingThisMerAndHlaToLength(necAndHla);
source = SpecialFunctions.Join("+", sourceAndOriginalHlaCollection); //Will be "" if list is empty
double probability = (sourceAndOriginalHlaCollection.Count == 0 || modelOnly) ? probability = (double)Logistic.EvaluateViaCache(necAndHla) : 1.0;
return(probability);
}