/// <summary>
/// Translate 3 byte representations of DNA bases to an amino acid
/// </summary>
/// <param name="mitochondrial"></param>
/// <param name="base1"></param>ec
/// <param name="base2"></param>
/// <param name="base3"></param>
/// <param name="aminoAcid"></param>
/// <returns></returns>
public static bool TryTranslateBytes(bool mitochondrial, byte base1, byte base2, byte base3, out byte aminoAcid)
{
if (mitochondrial)
{
return(CodonsVertebrateMitochondrial.TryLookup(
Transcription.GetRnaComplement(base1),
Transcription.GetRnaComplement(base2),
Transcription.GetRnaComplement(base3),
out aminoAcid));
}
else
{
return(Codons.TryLookup(
Transcription.GetRnaComplement(base1),
Transcription.GetRnaComplement(base2),
Transcription.GetRnaComplement(base3),
out aminoAcid));
}
}
/// <summary>
/// Is the last codon a STOP codon?
/// </summary>
/// <returns></returns>
public bool isWarningStopCodon()
{
if (IsProteinCoding())
{
return(false);
} //!Config.get().isTreatAllAsProteinCoding() &&
// Not even one codon in this protein? Error
ISequence cds = RetrieveCodingSequence();
if (cds.Count < 3)
{
return(true);
}
ISequence codon = cds.GetSubSequence(cds.Count - GeneModel.CODON_SIZE, GeneModel.CODON_SIZE);
return(Codons.TryLookup(Transcription.Transcribe(codon), 0, out byte aa) && aa == Alphabets.Protein.Ter);
}
/// <summary>
/// Get AA for a single DNA codon
/// </summary>
/// <param name="codon"></param>
/// <param name="aa"></param>
/// <returns></returns>
public static bool TranslateDnaCodon(string codon, out byte aa)
{
ISequence rnaCodon = Transcription.Transcribe(new Sequence(Alphabets.DNA, codon.Select(c => (byte)c).ToArray()));
return(Codons.TryLookup(rnaCodon, 0, out aa));
}
