protected CodonBase(IGeneticCode geneticCode, ICodonIdentifier codonIdentifier, CodonType codonType,
IEnumerable<INucleotide> nucleotides)
{
this.CodonIdentifier = codonIdentifier;
this.CodonType = codonType;
this.Nucleotides = nucleotides as List<INucleotide> ?? nucleotides.ToList();
if (this.Nucleotides.Count() != geneticCode.CodonLength)
throw new GeneticCodeException("All Codons must be of the specified CodonLength in the Genetic Code.");
}
/// <summary> /// Retrieves the first IGEPCodon of the specified CodonType that primarily /// encodes for the IFunction as identified /// by the given IFunctionIdentifier. /// </summary> /// <param name="functionIdentifier"></param> /// <param name="codonType"></param> /// <returns></returns> public abstract IGEPCodon GetCodonEncodingFunction(IFunctionIdentifier functionIdentifier, CodonType codonType = CodonType.Standard);
public override void SetCodonType(ICodonIdentifier codonIdentifier, CodonType codonType)
{
Qry.Update(DM.Codon.CodonType, codonType.ToString())
.Where(DM.Codon.Name, codonIdentifier.ToString())
.Go();
}
public override IGEPCodon GetCodonEncodingFunction(IFunctionIdentifier functionIdentifier, CodonType codonType = CodonType.Standard)
{
var codonRow = new CodonRow();
Qry.SelectAllFrom(codonRow)
.InnerJoinSelectingAllOn(codonRow.FunctionPairRowColumn)
.InnerJoinOn(codonRow.FunctionPairRow.PrimaryFunctionRowColumn)
.Where(codonRow.CodonTypeColumn, codonType.ToString())
.Where(codonRow.FunctionPairRow.PrimaryFunctionRow.FunctionIdentifierColumn, functionIdentifier.ToString())
.GoAndExtract(ref codonRow);
return codonRow.ToGEPCodon(this);
}
/// <summary> /// Sets the ICodon as specified by the given ICodonIdentifier to the specified CodonType. /// </summary> /// <param name="codonIdentifier"></param> /// <param name="codonType"></param> public abstract void SetCodonType(ICodonIdentifier codonIdentifier, CodonType codonType);
public override void SetCodonType(ICodonIdentifier codonIdentifier, CodonType codonType)
{
this.Codons[codonIdentifier].CodonType = codonType;
}
public override IGEPCodon GetCodonEncodingFunction(IFunctionIdentifier functionIdentifier, CodonType codonType = CodonType.Standard)
{
return this.Codons.FirstOrDefault(c => c.Value.CodonType == codonType && c.Value.Functions.PrimaryFunction.Equals(functionIdentifier)).Value;
}
protected CodonBase(IGeneticCode geneticCode, ICodonIdentifier codonIdentifier, CodonType codonType,
IEnumerable<INucleotideIdentifier> nucleotides) :
this(geneticCode: geneticCode, codonIdentifier: codonIdentifier, codonType: codonType,
nucleotides: nucleotides.Select(i => geneticCode.Nucleotides[i]))
{
}
protected GEPCodonBase(IGEPGeneticCode geneticCode, ICodonIdentifier codonIdentifier,
CodonType codonType, IEnumerable<INucleotide> nucleotides, IFunctionPair functions)
: base(geneticCode, codonIdentifier, codonType, nucleotides)
{
this.Functions = functions;
}
