static public HlaToLength GetInstanceABMixed(string hlaPattern)
{
HlaToLength aHlaToLength = new HlaToLength();
aHlaToLength.HlaResolution = HlaResolution.ABMixed;
if (HlaResolution.TwoDigitHlaPatternIsOK(hlaPattern))
{
aHlaToLength._hlaClass = hlaPattern.Substring(0, 1);
aHlaToLength._hlaNumberToLength = int.Parse(hlaPattern.Substring(1));
SpecialFunctions.CheckCondition(aHlaToLength._hlaClass != "B" || aHlaToLength._hlaNumberToLength != 15); //!!!raise error
SpecialFunctions.CheckCondition(aHlaToLength._hlaClass != "A" || aHlaToLength._hlaNumberToLength != 68); //!!!raise error
}
else
{
HlaToLength hlaToLengthFour = GetInstanceFour(hlaPattern);
int twoDigits = hlaToLengthFour.TwoDigits();
if ((twoDigits == 15 && hlaToLengthFour.HlaClass == "B") || (twoDigits == 68 && hlaToLengthFour.HlaClass == "A"))
{
aHlaToLength._hlaClass = hlaToLengthFour.HlaClass;
aHlaToLength._hlaNumberToLength = hlaToLengthFour._hlaNumberToLength;
}
else
{
aHlaToLength._hlaClass = hlaToLengthFour.HlaClass;
aHlaToLength._hlaNumberToLength = twoDigits;
}
}
return(aHlaToLength);
}
static public HlaToLength GetInstance(string hlaPattern, HlaResolution hlaResolution)
{
HlaToLength aHlaToLength = hlaResolution.GetHlaLengthInstance(hlaPattern);
SpecialFunctions.CheckCondition(aHlaToLength != null);
return(aHlaToLength);
}
public override HlaToLength GetHlaLengthInstance(string hlaPattern)
{
if (!HlaPatternIsOK(hlaPattern))
{
return(null);
}
return(HlaToLength.GetInstanceFour(hlaPattern));
}
private static System.Collections.Generic.IEnumerable <HlaToLength> HlaCollection(string hlaCollection, HlaResolution hlaResolution)
{
foreach (string sHlaPattern in hlaCollection.Split('/'))
{
HlaToLength hlaToLength = HlaToLength.GetInstanceOrNull(sHlaPattern, hlaResolution);
SpecialFunctions.CheckCondition(hlaToLength != null); //!!!raise error
yield return(hlaToLength);
}
}
static internal HlaToLength GetInstanceFour(string hlaPattern)
{
HlaToLength aHlaToLength = new HlaToLength();
aHlaToLength.HlaResolution = HlaResolution.Four;
aHlaToLength._hlaClass = hlaPattern.Substring(0, 1);
SpecialFunctions.CheckCondition(hlaPattern.Length == 5, String.Format("Expected 4-digit HLA (not {0})", hlaPattern));
aHlaToLength._hlaNumberToLength = int.Parse(hlaPattern.Substring(hlaPattern.Length - 4));
return(aHlaToLength);
}
public override HlaToLength GetHlaLengthInstance(string hlaPattern)
{
if (!HlaPatternIsOK(hlaPattern))
{
Debug.Fail("fix up");
return(null);
}
return(HlaToLength.GetInstanceABMixed(hlaPattern));
}
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));
}
}
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 override string HlaToLengthString(HlaToLength hlaToLength)
{
if (IsA68OrB15(hlaToLength))
{
return(string.Format("{0}{1:0000}", hlaToLength.HlaClass, hlaToLength.HlaNumberToLength));
}
else
{
return(string.Format("{0}{1:00}", hlaToLength.HlaClass, hlaToLength.HlaNumberToLength));
}
}
public override bool Equals(object obj)
{
HlaToLength other = obj as HlaToLength;
if ((other as object) == null)
{
return(false);
}
else
{
bool b = other._hlaNumberToLength == _hlaNumberToLength &&
other._hlaClass == _hlaClass &&
other.HlaResolution == HlaResolution;
return(b);
}
}
static internal HlaToLength GetInstanceTwo(string hlaPattern)
{
HlaToLength aHlaToLength = new HlaToLength();
aHlaToLength.HlaResolution = HlaResolution.Two;
if (HlaResolution.TwoDigitHlaPatternIsOK(hlaPattern))
{
aHlaToLength._hlaClass = hlaPattern.Substring(0, 1);
aHlaToLength._hlaNumberToLength = int.Parse(hlaPattern.Substring(1));
}
else
{
HlaToLength hlaToLengthFour = GetInstanceFour(hlaPattern);
aHlaToLength._hlaClass = hlaToLengthFour.HlaClass;
aHlaToLength._hlaNumberToLength = hlaToLengthFour.TwoDigits();
}
return(aHlaToLength);
}
public override string HlaToLengthString(HlaToLength hlaToLength)
{
return(string.Format("{0}{1:0000}", hlaToLength.HlaClass, hlaToLength.HlaNumberToLength));
}
public abstract string HlaToLengthString(HlaToLength hlaToLength);
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 abstract string HlaToLengthStringWithLeading0(HlaToLength hlaToLength);
public abstract HlaGroup PossibleHlaGroup(HlaToLength hlaToLength);
private bool IsA68OrB15(HlaToLength hlaToLength)
{
return(IsA68(hlaToLength) || IsB15(hlaToLength));
}
public override HlaGroup PossibleHlaGroup(HlaToLength hlaToLength)
{
return(HlaGroup.GetInstance(hlaToLength.HlaClass, hlaToLength.HlaNumberToLength));
}
public override string HlaToLengthStringWithLeading0(HlaToLength hlaToLength)
{
return(string.Format("{0}{1}", hlaToLength.HlaClass, hlaToLength.HlaNumberToLength));
}
private bool IsA68(HlaToLength hlaToLength)
{
return(hlaToLength.HlaClass == "A" && TwoDigits(hlaToLength.HlaNumberToLength) == 68);
}
//!!!some code in common with BMixed
internal bool IsB15(HlaToLength hlaToLength)
{
return(hlaToLength.HlaClass == "B" && TwoDigits(hlaToLength.HlaNumberToLength) == 15);
}
