public override HlaGroup PossibleHlaGroup(HlaToLength hlaToLength)
{
if (IsA68OrB15(hlaToLength))
{
return(HlaGroup.GetInstance(hlaToLength.HlaClass, hlaToLength.HlaNumberToLength));
}
else
{
return(HlaGroup.GetInstance(hlaToLength.HlaClass, hlaToLength.HlaNumberToLength * 100));
}
}
//!!!rename Class to Locus
//!!!rename HLa to HlaAllele
static public HlaGroup GetInstance(string hlaClass, int hlaNumber)
{
string name = CreateName(hlaClass, hlaNumber);
if (SingletonHlaCollection.ContainsKey(name))
{
return(SingletonHlaCollection[name]);
}
HlaGroup hlaGroup = new HlaGroup(hlaClass, hlaNumber);
SingletonHlaCollection.Add(hlaGroup.ToString(), hlaGroup);
return(hlaGroup);
}
internal static string XHlaGroupString(HlaGroup hlaGroup)
{
int twoDigits = hlaGroup.TwoDigits();
if (twoDigits == 15)
{
return(hlaGroup.ToString());
}
else
{
return(string.Format("{0}{1:00}", hlaGroup.HlaClass, twoDigits));
}
}
public string Evaluate(KmerDefinition kmerDefinition,
string featureString, bool isPositive, int rowId, int groupId, string sOperator,
string[] rgKmer, HlaGroup hlaGroup /*, int lengthOfOriginalLanlEpitopeOrLongMin*/)
{
for (int iProperty = 0; iProperty < AAPropertyCollection.Length; ++iProperty)
{
string sAAProperty = (string)AAPropertyCollection[iProperty];
if (featureString.StartsWith(sAAProperty))
{
char chBEA;
int iPos = GetPos(kmerDefinition, featureString, out chBEA);
SpecialFunctions.CheckCondition(iPos != -1); //!!! raise error
string sAminoAcid = rgKmer[iPos];
bool? goalValue = GoalValue(sAminoAcid, iProperty);
switch (goalValue)
{
case true:
return("1");
case false:
return("0");
case null:
return("#");
}
}
}
//!!!switch to switch
if (featureString == "RowId")
{
return(rowId.ToString());
}
if (featureString == "Operator")
{
return(sOperator);
}
if (featureString == "GroupId")
{
return(groupId.ToString());
}
if (featureString == "Immunogenic")
{
return(isPositive ? "1" : "0");
}
//if (featureString == "KmerLength")
//{
// Debug.Assert(lengthOfOriginalLanlEpitopeOrLongMin != int.MinValue);
// return lengthOfOriginalLanlEpitopeOrLongMin.ToString();
//}
if (featureString.StartsWith("amino"))
{
char chBEA;
int iPos = GetPos(kmerDefinition, featureString, out chBEA);
SpecialFunctions.CheckCondition(iPos != -1); //!!! raise error
string sAminoAcid = rgKmer[iPos];
string sGoalValue = AANumberAsGoalValue(sAminoAcid);
return(sGoalValue);
}
//if(featureString == "HLA") //HLA,HLA2digits,HLALetter //HLA-A*0201,HLA-A*02,A
//{
// string sGoalValue = string.Format("HLA-{0}*{1:0000}", hlaGroup.HlaClass, hlaGroup.HlaNumber);
// return sGoalValue;
//}
//if(featureString == "HLA2digits") //HLA,HLA2digits,HLALetter //HLA-A*0201,HLA-A*02,A
//{
// string sGoalValue = string.Format("HLA-{0}*{1:00}",hlaGroup.HlaClass, hlaGroup.TwoDigits());
// return sGoalValue;
//}
//else if(featureString == "HLALetter") //HLA,HLA2digits,HLALetter //HLA-A*0201,HLA-A*02,A
//{
// return hlaGroup.HlaClass;
//}
//if (featureString == "HLAHarvard") //HLA,HLA2digits,HLALetter //HLA-A*0201,HLA-A*02,A
//{
// return BMixedHlaResolution.HlaGroupString(hlaGroup);
//}
//if (featureString.StartsWith(OldStyleEpitopeTrainingData.HlaHarvardFeatureString)) //!!!const
//{
// string goal = featureString.Substring(OldStyleEpitopeTrainingData.HlaHarvardFeatureString.Length);
// string value = BMixedHlaResolution.HlaGroupString(hlaGroup);
// return (goal == value) ? "1" : "0";
//}
//if (featureString == "Supertype") //HLA,HLA2digits,HLALetter //HLA-A*0201,HLA-A*02,A
//{
// return SupertypeMapping.HlaGroupString(hlaGroup);
//}
Debug.Assert(false); //!!!need code
return(null);
}
static public HlaToLength GetInstanceOrNull(HlaGroup hlaGroup, HlaResolution hlaResolution)
{
HlaToLength hlaToLength = HlaToLength.GetInstanceOrNull(hlaGroup.ToString(), hlaResolution);
return(hlaToLength);
}
public bool Consistant(HlaGroup hlaGroup)
{
bool b = (this == HlaToLength.GetInstanceOrNull(hlaGroup, HlaResolution));
return(b);
}
public override HlaGroup PossibleHlaGroup(HlaToLength hlaToLength)
{
return(HlaGroup.GetInstance(hlaToLength.HlaClass, hlaToLength.HlaNumberToLength));
}