/// <summary>
/// Set values for codons around change.
/// </summary>
/// <param name="codonsLeft"></param>
/// <param name="codonsRight"></param>
public void SetCodonsAround(string codonsLeft, string codonsRight)
{
CodonsAroundOld = codonsLeft.ToLower(CultureInfo.InvariantCulture) + CodonsRef.ToUpper(CultureInfo.InvariantCulture) + codonsRight.ToLower(CultureInfo.InvariantCulture);
CodonsAroundNew = codonsLeft.ToLower(CultureInfo.InvariantCulture) + CodonsAlt.ToUpper(CultureInfo.InvariantCulture) + codonsRight.ToLower(CultureInfo.InvariantCulture);
// Amino acids surrounding the ones changed
string aasLeft = Translation.TranslateDnaCodon(codonsLeft, out byte aa1) ?
new string(new char[] { (char)aa1 }) :
"";
string aasRigt = Translation.TranslateDnaCodon(codonsRight, out byte aa2) ?
new string(new char[] { (char)aa2 }) :
"";
AroundOldAAs = aasLeft.ToLower(CultureInfo.InvariantCulture) + ReferenceAA.ToUpper(CultureInfo.InvariantCulture) + aasRigt.ToLower(CultureInfo.InvariantCulture);
AroundNewAAs = aasLeft.ToLower(CultureInfo.InvariantCulture) + AlternateAA.ToUpper(CultureInfo.InvariantCulture) + aasRigt.ToLower(CultureInfo.InvariantCulture);
}
/// <summary>
/// Return functional class of this effect (i.e. NONSENSE, MISSENSE, SILENT or NONE)
/// </summary>
/// <returns></returns>
public FunctionalClass GetFunctionalClass()
{
if (Variant.isSnv())
{
if (!AlternateAA.Equals(ReferenceAA))
{
Translation.TranslateDnaCodon(CodonsAlt, out byte aa);
return(aa == Alphabets.Protein.Ter ?
FunctionalClass.NONSENSE :
FunctionalClass.MISSENSE);
}
if (!CodonsAlt.Equals(CodonsRef))
{
return(FunctionalClass.SILENT);
}
}
return(FunctionalClass.NONE);
}
