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;
}
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]);
}
}
