internal static HlaSeq GetInstance(int pos, bool treatHlaAsPrefix)
{
SpecialFunctions.CheckCondition(pos > 0, "pos must be 1 or greater");
HlaSeq hlaSeq = new HlaSeq();
hlaSeq.Pos = pos;
hlaSeq.TreatHlaAsPrefix = treatHlaAsPrefix;
return(hlaSeq);
}
private static void SetUpInterestingHlaPositionsForAAFeaturesTable(Dictionary <string, string> hlaNameToSequence)
{
int sumOfNonMaxMin = ReadSumOfNonMaxMin();
string firstSequence = SpecialFunctions.First(hlaNameToSequence.Values);
InterestingToAAExact = Set <HlaSeq> .GetInstance();
InterestingToAAAsPrefix = Set <HlaSeq> .GetInstance();
InterestingHlaSeqToPropertiesExact = new Dictionary <HlaSeq, Set <string> >();
InterestingHlaSeqToPropertiesAsPrefix = new Dictionary <HlaSeq, Set <string> >();
for (int posBase0 = 0; posBase0 < firstSequence.Length; ++posBase0)
{
Dictionary <char, int> aaToCount = new Dictionary <char, int>();
Dictionary <string, Dictionary <bool, int> > propertyToValueToCount = new Dictionary <string, Dictionary <bool, int> >();
foreach (string sequence in hlaNameToSequence.Values)
{
char aa = sequence[posBase0];
aaToCount[aa] = SpecialFunctions.GetValueOrDefault(aaToCount, aa) + 1;
//string aaAsString = Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter[aa];
foreach (KeyValuePair <string, Set <char> > propertyAndAASet in VirusCount.KmerProperties.GetInstance().PropertyToAACharSet)
{
string property = propertyAndAASet.Key;
Set <char> aaSet = propertyAndAASet.Value;
bool val = aaSet.Contains(aa);
Dictionary <bool, int> valueToCount = SpecialFunctions.GetValueOrDefault(propertyToValueToCount, property);
valueToCount[val] = 1 + SpecialFunctions.GetValueOrDefault(valueToCount, val);
}
}
if (SumOfNonMax(aaToCount.Values) >= sumOfNonMaxMin)
{
HlaSeq hlaSeqExact = HlaSeq.GetInstance(posBase0 + 1, false);
InterestingToAAExact.AddNew(hlaSeqExact);
HlaSeq hlaSeqAsPrefix = HlaSeq.GetInstance(posBase0 + 1, true);
InterestingToAAAsPrefix.AddNew(hlaSeqAsPrefix);
foreach (string property in propertyToValueToCount.Keys)
{
Dictionary <bool, int> valueToCount = propertyToValueToCount[property];
if (SumOfNonMax(valueToCount.Values) >= sumOfNonMaxMin)
{
Set <string> interestingPropertiesExact = SpecialFunctions.GetValueOrDefault(InterestingHlaSeqToPropertiesExact, hlaSeqExact);
interestingPropertiesExact.AddNew(property);
Set <string> interestingPropertiesAsPrefix = SpecialFunctions.GetValueOrDefault(InterestingHlaSeqToPropertiesAsPrefix, hlaSeqAsPrefix);
interestingPropertiesAsPrefix.AddNew(property);
}
}
}
}
}
internal static Set <string> InterestingProperties(HlaSeq featureHlaSeq)
{
if (featureHlaSeq.TreatHlaAsPrefix)
{
return(InterestingHlaSeqToPropertiesAsPrefix[featureHlaSeq]);
}
else
{
return(InterestingHlaSeqToPropertiesExact[featureHlaSeq]);
}
}
public override bool Equals(object obj)
{
HlaSeq other = obj as HlaSeq;
if (other == null)
{
return(false);
}
else
{
return(Pos == other.Pos && TreatHlaAsPrefix == other.TreatHlaAsPrefix);
}
}
