protected void VerifyAndInitializeNucleotides(string rawNucleotides)
{
if (String.IsNullOrWhiteSpace(rawNucleotides))
{
throw new ArgumentException("Empty nucleotide sequence!");
}
SymbolCounts = new Dictionary <Nucleotide, long>(AllowedSymbols.Count);
foreach (var basePair in AllowedSymbols)
{
SymbolCounts.Add(basePair, 0);
}
foreach (var nucleotide in rawNucleotides)
{
var typedNucleotide = (Nucleotide)Char.ToUpperInvariant(nucleotide);
if (!AllowedSymbols.Contains(typedNucleotide))
{
throw new ArgumentException(nucleotide + " is not a recognized nucleotide");
}
SymbolCounts[typedNucleotide]++;
}
}
public long AminoCount(AminoAcid aminoAcid)
{
if (!AllowedSymbols.Contains(aminoAcid))
{
throw new ArgumentException(String.Format(_invalidAminoAcidCharacter, aminoAcid, _proteinAlphabet));
}
return(_aminoCounts[aminoAcid]);
}
public virtual long NucleotideCount(Nucleotide nucleotide)
{
if (!AllowedSymbols.Contains(nucleotide))
{
throw new ArgumentException(String.Format(InvalidNucleotideForAlphabetType, nucleotide, ActiveAlphabet));
}
return(!SymbolCounts.ContainsKey(nucleotide) ? 0 : SymbolCounts[nucleotide]);
}
public override bool Equals(object obj)
{
var anotherObject = obj as Language;
return(Keywords.SequenceEqual(anotherObject.Keywords) &&
Delimiters.SequenceEqual(anotherObject.Delimiters) &&
AllowedSymbols.SequenceEqual(anotherObject.AllowedSymbols) &&
Digits.SequenceEqual(anotherObject.Digits) &&
ComplexDelimiters.SequenceEqual(anotherObject.ComplexDelimiters));
}
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;
}
