private void assignNeuronDepth(Gene[] nodeGenes, int depth, Chromosome mutated) {
int i;
NEATNodeGene node;
// ArrayList nodeGenes = this.findOutputNodes(this.candidateNodes(genes));
for (i = 0; i < nodeGenes.length; i++) {
node = (NEATNodeGene) nodeGenes[i];
if (node.getType() == NEATNodeGene.OUTPUT) {
if (depth == 1) {
node.setDepth(depth);
this.assignNeuronDepth(
this.findSourceNodes(node.id(), mutated.genes()), depth + 1, mutated);
}
} else if (node.getType() == NEATNodeGene.HIDDEN) {
if (node.getDepth() == 0) {
// we have an unassigned depth
node.setDepth(depth);
this.assignNeuronDepth(
this.findSourceNodes(node.id(), mutated.genes()), depth + 1, mutated);
}
} else if (node.getType() == NEATNodeGene.INPUT) {
node.setDepth(Integer.MAX_VALUE);
}
}
}
private Gene[] ensureLegalLinks(Gene[] genes) {
ArrayList links;
NEATLinkGene link;
NEATNodeGene from;
NEATNodeGene to;
Gene[] newGenes = null;
ArrayList tmpGenes = new ArrayList();
int i;
// only need to prune if recurrency not allowed
if (!this.recurrencyAllowed) {
// only return enabled links
links = this.candidateLinks(genes, false);
for (i = 0; i < genes.length; i++) {
if (genes[i] instanceof NEATLinkGene) {
link = (NEATLinkGene) genes[i];
from = this.findNode(link.getFromId(), genes);
to = this.findNode(link.getToId(), genes);
if (from.getDepth() > to.getDepth()) {
// not recurrent - so keep
tmpGenes.add(genes[i]);
}
} else {
tmpGenes.add(genes[i]);
}
}
newGenes = new Gene[tmpGenes.size()];
for (i = 0; i < newGenes.length; i++) {
newGenes[i] = (Gene) tmpGenes.get(i);
}
} else {
newGenes = genes;
}
return (newGenes);
}