public static long CalculateHammingDistance(NucleotideSequence a, NucleotideSequence b)
{
if (a.Sequence.Length != b.Sequence.Length)
{
throw new ArgumentException("Sequences are of unequal length!");
}
if (a.ActiveAlphabet != b.ActiveAlphabet)
{
throw new ArgumentException("Sequences are not using the same nucleotide alphabet!");
}
if (a.GetType() != b.GetType())
{
throw new ArgumentException(String.Format("Sequence types do not match. ({0} vs {1})", a.GetType(), b.GetType()));
}
return(a.Sequence.Where((t, i) => t != b.Sequence[i]).Count());
}
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 virtual long CalculateHammingDistance(NucleotideSequence comparisonSequence)
{
return(CalculateHammingDistance(this, comparisonSequence));
}
