public override List<IGEPOrganism> Execute(IGEPEnvironment environment)
{
var dna = new GEPDNA();
var allele = new GEPAllele(dna);
var main = new GEPGene(environment: environment);
main.Add(allele);
var chromosome = new GEPChromosome(environment: environment, main: main);
var organism = new GEPOrganism(environment: environment) { chromosome };
organism.Parent = environment;
for (var i = 0; i < environment.GeneticCode.DNALength; i++)
allele.DNA.AddRandomNucleotide();
/*
var testAllele = new GEPAllele(new GEPDNA());
var testGene = new GEPGene(environment: environment);
testGene.Add(testAllele);
main.Add(testGene);
for (var i = 0; i < environment.GeneticCode.DNALength; i++)
testAllele.DNA.AddRandomNucleotide();
var test2Allele = new GEPAllele(new GEPDNA());
var test2Gene = new GEPGene(environment: environment);
test2Gene.Add(test2Allele);
main.Add(test2Gene);
for (var i = 0; i < environment.GeneticCode.DNALength; i++)
test2Allele.DNA.AddRandomNucleotide();
var test3Allele = new GEPAllele(new GEPDNA());
var test3Gene = new GEPGene(environment: environment);
test3Gene.Add(test3Allele);
test2Gene.Add(test3Gene);
for (var i = 0; i < environment.GeneticCode.DNALength; i++)
test3Allele.DNA.AddRandomNucleotide();
var test4Allele = new GEPAllele(new GEPDNA());
var test4Gene = new GEPGene(environment: environment);
test4Gene.Add(test4Allele);
main.Add(test4Gene);
for (var i = 0; i < environment.GeneticCode.DNALength; i++)
test4Allele.DNA.AddRandomNucleotide();
var test5Allele = new GEPAllele(new GEPDNA());
var test5Gene = new GEPGene(environment: environment);
test5Gene.Add(test5Allele);
test3Gene.Add(test5Gene);
for (var i = 0; i < environment.GeneticCode.DNALength; i++)
test5Allele.DNA.AddRandomNucleotide();
*/
return new List<IGEPOrganism>() { organism };
}
public override IChromosome ShallowCopy()
{
var mainCopy = (IGEPGene) this.Main.ShallowCopy();
var copy = new GEPChromosome(this.ParentEnvironment, mainCopy);
mainCopy.Parent = copy;
mainCopy.ReassignChildrenChromosomeParent();
return copy;
}
public override IOrganism ToOrganism(IEnvironment environment)
{
var gepEnvironment = (IGEPEnvironment) environment;
var organism = new GEPOrganism(environment: gepEnvironment)
{
Parent = gepEnvironment
};
// Get all of the "main" genes.
var lastChromosomeIndex = -1;
foreach(var unit in this)
{
if(unit.ChromosomeIndex != lastChromosomeIndex)
{
var mainGene = this.CreateGeneFromGenomeUnit(gepEnvironment: gepEnvironment, unit: unit);
var chromosome = new GEPChromosome(environment: gepEnvironment, main: mainGene);
organism.Add(chromosome);
lastChromosomeIndex = unit.ChromosomeIndex;
}
}
var chromosomeIndex = 0;
foreach (var chromosome in organism)
{
var lastProcessedGeneLevel = 1;
var mainGene = chromosome.Main;
var lastProcessedGene = mainGene;
foreach (var unit in this.Where(u => u.ChromosomeIndex == chromosomeIndex && u.GeneLevel >= 1))
{
var gene = this.CreateGeneFromGenomeUnit(gepEnvironment: gepEnvironment, unit: unit);
// If we're moving to the next level, add the gene to the next level
// and go down to see if there are any others on that level
if (unit.GeneLevel > lastProcessedGeneLevel)
{
lastProcessedGene = (IGEPGene)lastProcessedGene.GetChildGenes().Last();
lastProcessedGene.Add(gene);
}
// if we're up a level, go up to that level and add the gene
else if (unit.GeneLevel < lastProcessedGeneLevel)
{
while(unit.GeneLevel < lastProcessedGeneLevel)
{
lastProcessedGene = lastProcessedGene.ParentGene;
lastProcessedGeneLevel--;
}
lastProcessedGene.Add(gene);
}
// if we're at the same level, just add the gene.
else
{
lastProcessedGene.Add(gene);
}
lastProcessedGeneLevel = unit.GeneLevel;
}
chromosomeIndex++;
}
return organism;
}
