protected override MBT.Escience.Set <char> GetResidueSetFromCharAndCheckThatValid(char ch)
{
char chUpper = char.ToUpper(ch);
Biology biology = Biology.GetInstance();
Set <char> result;
if (biology.Unambiguous1LetterNucCodes.Contains(chUpper))
{
result = new Set <char>(chUpper);
}
else if (biology.Ambiguous1LetterNucCodeToChoices.ContainsKey(chUpper))
{
string basesAsString = biology.Ambiguous1LetterNucCodeToChoices[chUpper];
result = new Set <char>();
foreach (char c in basesAsString)
{
result.AddNew(c);
}
}
else
{
throw new ArgumentException("Do not know dna base " + chUpper);
}
return(result);
}
public static char DnaSetAsChar(Set <char> dnas)
{
//if (dnas.Count == 1 && dnas.First() == '-')
//{
// return '-';
//}
if (dnas.Count == 1)
{
return(dnas.First());
}
return(Biology.GetInstance().NucSetToAmbiguous1LetterNucCode[HashableSet <char> .GetInstance(dnas)]);
}
/// <summary>
/// Returns the reverse complement. Throws an exception if IsDna() is false.
/// </summary>
/// <exception cref="Exception">If IsDna() is false.</exception>
/// <returns>The reverse complement</returns>
public NamedSequence ReverseCompelement()
{
Helper.CheckCondition(IsDna(), "Cannot take the reverse complement of a sequence that is not DNA.");
Biology Biology = Biology.GetInstance();
StringBuilder revComp = new StringBuilder(Sequence.Length);
for (int i = Sequence.Length - 1; i >= 0; i--)
{
Helper.CheckCondition(Biology.DnaComplementarityCode.ContainsKey(Sequence[i]), "Cannot compute complement for " + Sequence[i]);
char comp = Biology.DnaComplementarityCode[Sequence[i]];
revComp.Append(comp);
}
return(new NamedSequence(Name, Protein, revComp.ToString()));
}
protected virtual Set <char> GetResidueSetFromCharAndCheckThatValid(char ch)
{
ch = char.ToUpper(ch);
//!!!move this to Biology?
Helper.CheckCondition(Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter.ContainsKey(ch),
string.Format("The character {0} is not an amino acid", ch));
string aminoAcid = Biology.GetInstance().OneLetterAminoAcidAbbrevTo3Letter[ch];
Helper.CheckCondition(Biology.GetInstance().KnownAminoAcid(aminoAcid),
string.Format("The character {0} is not a standard amino acid", ch));
Set <char> charAsSet = Set <char> .GetInstance(ch);
return(charAsSet);
}
static public string CodonToAACharSetString(string sCodon, bool dashAsMissing)
{
sCodon = sCodon.ToUpper();
SimpleAminoAcidSet rgAminoAcid = Biology.GetInstance().GenticCode(22, sCodon, dashAsMissing);
if (rgAminoAcid == null)
{
return("?");
}
else
{
StringBuilder sb = new StringBuilder();
foreach (string aminoAcid in rgAminoAcid.Positives)
{
char aaChar = Biology.GetInstance().ThreeLetterAminoAcidAbbrevTo1Letter[aminoAcid];
sb.Append(aaChar);
}
return(sb.ToString());
}
}
