public string TranscriptAnnotation()
{
return("effect:" + GetFunctionalClass().ToString() + " " +
GetEffectType().ToString() + " " +
ReferenceAA + (CodonNum + 1).ToString() + AlternateAA + " " +
CodonsRef.ToLower(CultureInfo.InvariantCulture) + CodonNum.ToString() + CodonsAlt);
}
/// <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);
}
