public NucleotideSequence Complement()
{
if (String.IsNullOrEmpty(_rawComplement))
{
_rawComplement = GetComplementString();
}
//Transform the symbol counts table T count becomes A count, etc.
var _newSymbolCounts = new Dictionary <Nucleotide, long>(SymbolCounts.Count);
foreach (var symbol in SymbolCounts)
{
if (_newSymbolCounts.ContainsKey(symbol.Key))
{
continue;
}
var nucleotide = symbol.Key;
var countToBeSwapped = SymbolCounts[nucleotide];
var complement = ComplementTable[nucleotide];
var newCount = SymbolCounts[complement];
_newSymbolCounts.Add(nucleotide, newCount);
_newSymbolCounts.Add(complement, countToBeSwapped);
}
if (GetType() == typeof(DnaSequence))
{
return(DnaSequence.FastDnaSequence(_rawComplement, ActiveAlphabet, GeneticCode, _newSymbolCounts));
}
return(RnaSequence.FastRnaSequence(_rawComplement, ActiveAlphabet, GeneticCode, _newSymbolCounts));
}
public override NucleotideSequence Transcribe()
{
var alphabet = ActiveAlphabet == AlphabetType.StrictRna ? AlphabetType.StrictDna : AlphabetType.AmbiguousDna;
var newSymbolCounts = new Dictionary <Nucleotide, long>(SymbolCounts);
var count = SymbolCounts[Nucleotide.Uracil];
newSymbolCounts.Remove(Nucleotide.Uracil);
newSymbolCounts.Add(Nucleotide.Thymine, count);
var newSequence = Sequence.Replace((char)Nucleotide.Uracil, (char)Nucleotide.Thymine);
return(DnaSequence.FastDnaSequence(newSequence, alphabet, GeneticCode, newSymbolCounts));
}
public NucleotideSequence ReverseComplement()
{
if (String.IsNullOrEmpty(_rawComplement))
{
_rawComplement = GetComplementString();
}
var complementArray = _rawComplement.ToCharArray();
Array.Reverse(complementArray);
var reversed = new string(complementArray);
if (GetType() == typeof(DnaSequence))
{
return(DnaSequence.FastDnaSequence(reversed, ActiveAlphabet, GeneticCode, SymbolCounts));
}
else
{
return(RnaSequence.FastRnaSequence(reversed, ActiveAlphabet, GeneticCode, SymbolCounts));
}
}
public ProteinSequence Translate(DnaSequence dna, AlphabetType desiredProteinAlphabet)
{
return(new ProteinSequence(dna));
}