/// <summary>
/// '-' means delete and must be part of "---"
/// ' ' means missing and is treated just like 'N'
/// null means that it could be anything
/// </summary>
public SimpleAminoAcidSet GenticCode(int ifCodeHasBeenReviewedAndWorksOKWithDeleteAndSpaceAndDashAsMissingSetTo22, string codon, bool dashAsMissing)
{
Helper.CheckCondition(ifCodeHasBeenReviewedAndWorksOKWithDeleteAndSpaceAndDashAsMissingSetTo22 == 22, "Need to review code to be sure that it is OK to treat '---' as the amino acid DELETE");
if (codon.Contains("X") || codon.Contains("*") || codon.Contains("?"))
{
return(null);
}
if (codon.Contains("-"))
{
if (dashAsMissing)
{
return(null);
}
else
{
codon = "---";
}
}
//Get the set of values
SimpleAminoAcidSet aminoAcidCollection = SimpleAminoAcidSet.GetInstance();
GenticCode(codon, ref aminoAcidCollection);
if (aminoAcidCollection.PositiveCount == 21)
{
return(null);
}
return(aminoAcidCollection);
}
public bool AnyAminoAcidInCommon(SimpleAminoAcidSet aaCollection2)
{
foreach (string aminoAcid1 in Positives)
{
if (aaCollection2.Contains(aminoAcid1))
{
return(true);
}
}
return(false);
}
public bool AminoAcidSetEqual(SimpleAminoAcidSet aminoAcidCollection2)
{
if (PositiveCount != aminoAcidCollection2.PositiveCount)
{
return(false);
}
foreach (string sAminoAcid1 in Positives)
{
if (!aminoAcidCollection2.Contains(sAminoAcid1))
{
return(false);
}
}
return(true);
}
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());
}
}
public void GenticCode(string codon, ref SimpleAminoAcidSet aminoAcidCollection)
{
Helper.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) && Ambiguous1LetterNucCodeToChoices[c].Length > 1)
{
break;
}
Helper.CheckCondition("ATCG".Contains(c.ToString()), string.Format("Illegal nucleotide of '{0}'", c));
}
Helper.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);
}
}