static public KmerDefinition GetInstance(int b, int e, int a)
{
KmerDefinition aKmerDefinition = new KmerDefinition();
aKmerDefinition.BeforeMerCount = b;
aKmerDefinition.EpitopeMerCount = e;
aKmerDefinition.AfterMerCount = a;
aKmerDefinition.NumberOfEAt1stPosition = 1;
Debug.Assert(aKmerDefinition.NumberOfEAt1stPosition == 1 || aKmerDefinition.BeforeMerCount == 0); //!!! these two cases are the only ones tested
return(aKmerDefinition);
}
public static MerAndHlaToLength GetInstance(string aaSequence, HlaToLength aHlaToLength, KmerDefinition kmerDefinition)
{
SpecialFunctions.CheckCondition(aaSequence.Length > 0 && char.IsUpper(aaSequence[0])); //Spot check that all upper
MerAndHlaToLength aMerAndHlaToLength = new MerAndHlaToLength();
aMerAndHlaToLength.Mer = aaSequence;
aMerAndHlaToLength.HlaToLength = aHlaToLength;
//aMerAndHlaToLength.Study = study;
aMerAndHlaToLength.KmerDefinition = kmerDefinition;
return(aMerAndHlaToLength);
}
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);
}
public int GetPos(KmerDefinition kmerDefinition, string sVariable, out char chBEA)
{
int iLetter;
for (iLetter = sVariable.Length - 1; iLetter >= 0; --iLetter)
{
if (char.IsLetter(sVariable[(int)iLetter]))
{
break;
}
}
Debug.Assert(0 < iLetter && iLetter < sVariable.Length - 1); // real assert
chBEA = sVariable[(int)iLetter];
int iNum = int.Parse(sVariable.Substring((int)iLetter + 1));
int iPos;
switch (chBEA)
{
case 'B':
{
// e.g.KmerDefinition.BeforeMerCount is 6, -6 to -1 are positions 0 to 5
iPos = kmerDefinition.BeforeMerCount + iNum;
if (!(0 <= iPos && iPos < kmerDefinition.BeforeMerCount))
{
chBEA = ' ';
}
}
break;
case 'E':
{
// e.g.KmerDefinition.BeforeMerCount is 6, NumberOfEAt1stPosition=1, 1 to 8 are positions 6 to 13
// e.g.KmerDefinition.BeforeMerCount is 0, NumberOfEAt1stPosition=4, 4 to 11 are positions 0 to 7
iPos = iNum + kmerDefinition.BeforeMerCount - kmerDefinition.NumberOfEAt1stPosition;
if (!(kmerDefinition.BeforeMerCount <= iPos && iPos < kmerDefinition.BeforeMerCount + kmerDefinition.EpitopeMerCount))
{
chBEA = ' ';
}
}
break;
case 'A':
{
// e.g.KmerDefinition.BeforeMerCount is 6, NumberOfEAt1stPosition=1, KmerDefinition.EpitopeMerCount = 8, 1 to 6 are positions 14 to 19
// e.g.KmerDefinition.BeforeMerCount is 0, NumberOfEAt1stPosition=4, KmerDefinition.EpitopeMerCount = 8, 1 to 6 are positions 8 to 13
iPos = iNum + kmerDefinition.BeforeMerCount + kmerDefinition.EpitopeMerCount - 1;
if (!(kmerDefinition.BeforeMerCount + kmerDefinition.EpitopeMerCount <= iPos && iPos < kmerDefinition.FullMerCount))
{
chBEA = ' ';
}
}
break;
default:
iPos = -1;
SpecialFunctions.CheckCondition(false); //!!!raise error
break;
}
return(iPos);
}
private static string FillInKmerOrNull(string aaSequence, string sProtein, int aa1, KmerDefinition kmerDefinition)
{
SpecialFunctions.CheckCondition(kmerDefinition.BeforeMerCount == 0 && kmerDefinition.AfterMerCount == 0, "look at old code to see how to handle other cases");
if (aaSequence.Length == kmerDefinition.FullMerCount)
{
return(aaSequence);
}
else
{
return(null);
}
}