public ProteinSequence(string rawSequence, AlphabetType desiredProteinAlphabet, GeneticCode geneticCode = GeneticCode.Standard)
{
switch (desiredProteinAlphabet)
{
case AlphabetType.ExtendedProtein:
break;
case AlphabetType.StandardProtein:
break;
default:
throw new ArgumentException(String.Format(ProteinAlphabet.InvalidProteinAlphabet, desiredProteinAlphabet));
}
_proteinAlphabet = new ProteinAlphabet(desiredProteinAlphabet, geneticCode);
ActiveAlphabet = desiredProteinAlphabet;
AllowedSymbols = AlphabetDataProvider.GetAllowedProteinSymbols(ActiveAlphabet);
_aminoCounts = new Dictionary <AminoAcid, long>(AllowedSymbols.Count);
foreach (var symbol in AllowedSymbols)
{
_aminoCounts.Add(symbol, 0);
}
var trimmedRaw = rawSequence.Trim();
foreach (var aminoCharacter in trimmedRaw)
{
var typedAmino = (AminoAcid)Char.ToUpperInvariant(aminoCharacter);
if (!AllowedSymbols.Contains(typedAmino))
{
throw new ArgumentException(String.Format(_invalidAminoAcidCharacter, aminoCharacter, _proteinAlphabet));
}
_aminoCounts[typedAmino]++;
}
Sequence = trimmedRaw;
}
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]);
}
}