/// <summary>
/// Read table from http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html
/// </summary>
private void ReadTheGeneticCode()
{
Debug.Assert(CodonToAminoAcid == null); // real assert
CodonToAminoAcid = new Dictionary <string, GeneticCodeMapping>();
AminoAcidCollection = new Dictionary <string, bool>();
//!!!could load these into memory instead of reading them over and over again
string sTheGenenicCodeFile = @"GeneticCodeDna.txt"; //!!!const
using (StreamReader streamreaderTheGenenicCodeFile = OpenResource(sTheGenenicCodeFile))
{
string sLine = null;
while (null != (sLine = streamreaderTheGenenicCodeFile.ReadLine()))
{
string[] rgFields = sLine.Split('\t');
SpecialFunctions.CheckCondition(rgFields.Length == 3); //!!!raise error
string sCodon = rgFields[0];
SpecialFunctions.CheckCondition(sCodon.Length == 3); //!!!raise error
string sAminoAcid = rgFields[1];
bool bNormal = bool.Parse(rgFields[2]); //!!!could raise error
GeneticCodeMapping aGeneticCodeMapping = new GeneticCodeMapping(sCodon, sAminoAcid, bNormal);
CodonToAminoAcid.Add(sCodon, aGeneticCodeMapping);
if (!AminoAcidCollection.ContainsKey(sAminoAcid))
{
AminoAcidCollection.Add(sAminoAcid, true);
}
}
}
}
public string GenticCode(string codon, out bool bAcidOrStop)
{
SpecialFunctions.CheckCondition(codon.Length == 3); //!!!raise error
//If unambiguous, look it up and return it
if (CodonToAminoAcid.ContainsKey(codon))
{
GeneticCodeMapping aGeneticCodeMapping = (GeneticCodeMapping)CodonToAminoAcid[codon];
string sAminoAcid = aGeneticCodeMapping.AminoAcid;
bAcidOrStop = true;
return(sAminoAcid);
}
//If ambiguous, try every possiblity for this 1st ambiguity and see if the results are the same (this is recursive)
for (int i = 0; i < codon.Length; ++i)
{
char c = codon[i];
if (Ambiguous1LetterNucCodeToChoices.ContainsKey(c))
{
string sAminoAcidAll = null;
bAcidOrStop = false;
foreach (char cNucleotide in (string)Ambiguous1LetterNucCodeToChoices[c])
{
string sNewCodon = string.Format("{0}{1}{2}", codon.Substring(0, i), cNucleotide, codon.Substring(i + 1));
Debug.Assert(sNewCodon.Length == 3); //real assert
Debug.Assert(sNewCodon != codon); // real assert
string sAminoAcid = GenticCode(sNewCodon, out bAcidOrStop);
if (!bAcidOrStop)
{
goto CantFixAmbiguity;
}
if (sAminoAcidAll == null)
{
sAminoAcidAll = sAminoAcid;
}
else
{
if (sAminoAcidAll != sAminoAcid)
{
//goto CantFixAmbiguity;
sAminoAcidAll = "Ambiguous Amino Acid"; //!!!const
}
}
}
Debug.Assert(sAminoAcidAll != null); //!!!???
return(sAminoAcidAll);
}
}
CantFixAmbiguity:
bAcidOrStop = false;
return("Not an amino acid: '" + codon + "'");
}
public void GenticCode(string codon, ref SimpleAminoAcidSet aminoAcidCollection)
{
SpecialFunctions.CheckCondition(codon.Length == 3); //!!!raise error
Debug.Assert(aminoAcidCollection != null); //real assert
//If unambiguous, look it up and return it
if (CodonToAminoAcid.ContainsKey(codon))
{
GeneticCodeMapping aGeneticCodeMapping = (GeneticCodeMapping)CodonToAminoAcid[codon];
string sAminoAcid = aGeneticCodeMapping.AminoAcid;
aminoAcidCollection.AddOrCheck(sAminoAcid);
return;
}
//If ambiguous, try every possiblity for this 1st ambiguity and see if the results are the same (this is recursive)
int iFirstAmbiguity = 0;
char c = char.MinValue;
for (; iFirstAmbiguity < codon.Length; ++iFirstAmbiguity)
{
c = codon[iFirstAmbiguity];
if (Ambiguous1LetterNucCodeToChoices.ContainsKey(c))
{
break;
}
SpecialFunctions.CheckCondition("ATCG".Contains(c.ToString()), string.Format("Illegal nucleotide of '{0}'", c));
}
SpecialFunctions.CheckCondition(iFirstAmbiguity < codon.Length); //!!!raise error - Is CodonToAminoAcid table missing a value?
foreach (char cNucleotide in (string)Ambiguous1LetterNucCodeToChoices[c])
{
string sNewCodon = string.Format("{0}{1}{2}", codon.Substring(0, iFirstAmbiguity), cNucleotide, codon.Substring(iFirstAmbiguity + 1));
Debug.Assert(sNewCodon.Length == 3); //real assert
Debug.Assert(sNewCodon != codon); // real assert
GenticCode(sNewCodon, ref aminoAcidCollection);
}
}
