public override ICodon GetRandomCodon()
{
// Construct a Codon (randomly).
var codonName = "";
for (var i = 0; i < this.CodonLength; i++)
{
var nucleotide = this.Nucleotides.Values.RandomElement();
codonName += nucleotide.Identifier.ToString();
}
var codonRow = new CodonRow();
Qry.SelectAllFrom(codonRow)
.InnerJoinSelectingAllOn(codonRow.FunctionPairRowColumn)
.Where(codonRow.NameColumn, codonName)
.GoAndExtract(ref codonRow);
return codonRow.ToGEPCodon(this);
}
public override IEnumerable<ICodon> GetStopCodons()
{
var codonRow = new CodonRow();
var codonRows = Qry.SelectAllFrom(codonRow)
.InnerJoinSelectingAllOn(codonRow.FunctionPairRowColumn)
.Where(codonRow.CodonTypeColumn, CodonType.Stop)
.GoAndExtractMultiple<CodonRow>();
return codonRows.Select(c => c.ToGEPCodon(this));
}
public override void AddCodon(IGEPCodon codon)
{
var functionPairRow = new FunctionPairRow();
var result = Qry.SelectAllFrom(functionPairRow)
.InnerJoinOn(functionPairRow.PrimaryFunctionRowColumn)
.InnerJoinOn(functionPairRow.ParameterlessFunctionRowColumn)
.Where(functionPairRow.PrimaryFunctionRow.FunctionIdentifierColumn, codon.Functions.PrimaryFunction.ToString())
.Where(functionPairRow.ParameterlessFunctionRow.FunctionIdentifierColumn, codon.Functions.ParameterlessFunction.ToString())
.Go();
if(result.IsEmpty)
this.InsertFunctionPairIfNecessary(ref functionPairRow, codon: codon);
else
result.ExtractStrongRow(ref functionPairRow);
var codonRow = new CodonRow(name: codon.CodonIdentifier.ToString(), geneticCode: this.GeneticCodePrimaryKey.Value,
functionPair: functionPairRow.PrimaryKey, codonType: codon.CodonType.ToCodonType());
codonRow.InsertIntoDatabase();
/*
var nucleotideRow = new NucleotideRow();
var nucleotideRows = Qry.SelectAllFrom(nucleotideRow)
.Where(nucleotideRow.GeneticCodeColumn, this.GeneticCodePrimaryKey.Value)
.GoAndExtractMultiple<NucleotideRow>();
foreach(var nucleotide in codon)
{
var codonNucleotideRow =
nucleotide.ToCodonNucleotideRow(
nucleotidePrimaryKey:
nucleotideRows.First(n => n.Name == nucleotide.Identifier.ToString()).PrimaryKey,
codonPrimaryKey: codonRow.PrimaryKey,
geneticCodePrimaryKey: this.GeneticCodePrimaryKey.Value);
codonNucleotideRow.InsertOnlyIfNecessary();
}
*/
}
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);
}
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);
}