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);
}
public ConsensusBuilder(IEnumerable <ISequence> sequences)
{
_sequences = sequences.ToList();
var firstElement = _sequences.First();
_sequenceLength = firstElement.Sequence.Length;
_alphabet = firstElement.ActiveAlphabet;
foreach (var sequence in _sequences)
{
if (sequence.Sequence.Length != _sequenceLength)
{
throw new ArgumentException("Sequences were not all of uniform length");
}
if (_alphabet != sequence.ActiveAlphabet)
{
throw new ArgumentException("Sequences must all be of the same type");
}
}
char[] alphabetChars;
switch (_alphabet)
{
case AlphabetType.StrictRna:
case AlphabetType.AmbiguousRna:
case AlphabetType.StrictDna:
case AlphabetType.AmbiguousDna:
{
var symbols = AlphabetDataProvider.GetAllowedNucleotideSymbols(_alphabet).ToArray();
alphabetChars = new char[symbols.Length];
for (var i = 0; i < symbols.Length; i++)
{
alphabetChars[i] = (char)symbols[i];
}
}
break;
case AlphabetType.ExtendedProtein:
case AlphabetType.StandardProtein:
{
var symbols = AlphabetDataProvider.GetAllowedProteinSymbols(_alphabet).ToArray();
alphabetChars = new char[symbols.Length];
for (var i = 0; i < symbols.Length; i++)
{
alphabetChars[i] = (char)symbols[i];
}
}
break;
default:
throw new ArgumentException("Unknown alphabet type");
}
_consensusMatrix = new Dictionary <char, int[]>(alphabetChars.Length);
foreach (var character in alphabetChars)
{
_consensusMatrix.Add(character, new int[_sequenceLength]);
}
}
