public NucleotideAlphabet(AlphabetType nucleotideAlphabet, GeneticCode geneticCode)
{
if (nucleotideAlphabet == AlphabetType.ExtendedProtein || nucleotideAlphabet == AlphabetType.StandardProtein)
{
throw new ArgumentException(String.Format(AlphabetDataProvider.InvalidNucleotideAlphabet, nucleotideAlphabet));
}
GeneticCode = geneticCode;
AllowedSymbols = AlphabetDataProvider.GetAllowedNucleotideSymbols(nucleotideAlphabet);
ComplementTable = AlphabetDataProvider.GetComplementTable(nucleotideAlphabet);
TranscriptionTable = AlphabetDataProvider.GetTranscriptionTable(nucleotideAlphabet);
TranslationTable = AlphabetDataProvider.GetTranslationTable(geneticCode, nucleotideAlphabet);
GcContentSymbols = AlphabetDataProvider.GcContentSymbols(nucleotideAlphabet);
}
internal ProteinSequence(NucleotideSequence seq)
{
if (seq.ActiveAlphabet == AlphabetType.StrictDna || seq.ActiveAlphabet == AlphabetType.StrictRna)
{
if (seq.Sequence.Length % 3 != 0)
{
throw new ArgumentException("Sequence length is not evenly divisible by three, which means it cannot be translated because you are using a strict nucleotide alphabet");
}
}
AlphabetType alphabet;
var allowedSymbols = new HashSet <AminoAcid> {
AminoAcid.Stop, AminoAcid.Gap
};
switch (seq.ActiveAlphabet)
{
case AlphabetType.AmbiguousDna:
alphabet = AlphabetType.ExtendedProtein;
allowedSymbols.UnionWith(AlphabetDataProvider.ExtendedProtein);
break;
case AlphabetType.AmbiguousRna:
alphabet = AlphabetType.ExtendedProtein;
allowedSymbols.UnionWith(AlphabetDataProvider.ExtendedProtein);
break;
default:
alphabet = AlphabetType.StandardProtein;
allowedSymbols.UnionWith(AlphabetDataProvider.StandardProtein);
break;
}
var translationTable = new Dictionary <string, AminoAcid>(AlphabetDataProvider.GetTranslationTable(seq.GeneticCode, seq.ActiveAlphabet));
//string safeSequence, AlphabetType alphabet, GeneticCode geneticCode, Dictionary<Nucleotide, long> symbolCounts
ActiveAlphabet = seq.ActiveAlphabet;
_proteinAlphabet = new ProteinAlphabet(alphabet, seq.GeneticCode);
var proteinBlob = Translate(seq.Sequence, translationTable);
Sequence = proteinBlob.Sequence;
_aminoCounts = proteinBlob.AminoCounts;
}