public bool Equals(ICodonIdentifier other)
{
if (other == null)
return false;
else if (other is CodonIdentifier)
return this.Identifier == ((CodonIdentifier)other).Identifier;
else
return false;
}
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.");
}
public int CompareTo(ICodonIdentifier other)
{
return this.Identifier.CompareTo(other.ToString());
}
public override void SetCodonType(ICodonIdentifier codonIdentifier, CodonType codonType)
{
Qry.Update(DM.Codon.CodonType, codonType.ToString())
.Where(DM.Codon.Name, codonIdentifier.ToString())
.Go();
}
public override ICodon GetCodon(ICodonIdentifier codonIdentifier)
{
var codonRow = new CodonRow();
Qry.SelectAllFrom(codonRow)
.InnerJoinSelectingAllOn(codonRow.FunctionPairRowColumn)
.Where(codonRow.NameColumn, codonIdentifier.ToString())
.GoAndExtract(ref codonRow);
return codonRow.ToGEPCodon(this);
}
/// <summary> /// Gets the ICodon as specified by the given ICodonIdentifier. /// </summary> /// <param name="codonIdentifier"></param> /// <returns></returns> public abstract ICodon GetCodon(ICodonIdentifier codonIdentifier);
/// <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 ICodon GetCodon(ICodonIdentifier codonIdentifier)
{
return this.Codons[codonIdentifier];
}
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;
}
