organism.cpp

#include "organism.h"
#include "noveltyset.h"
#include <cstring>

using namespace NEAT;

Organism::Organism(double fit, Genome *g,int gen, const char* md) {
	noveltypoint=NULL;
	fitness=fit;
	orig_fitness=fitness;
	gnome=g;
	net=gnome->genesis(gnome->genome_id);
	species=0;  //Start it in no Species
	expected_offspring=0;
	generation=gen;
	eliminate=false;
	error=0;
	winner=false;
	champion=false;
	super_champ_offspring=0;

	// If md is null, then we don't have metadata, otherwise we do have metadata so copy it over
	if(md == 0) {
		strcpy(metadata, "");
	} else {
		strncpy(metadata, md, 128);
	}

	time_alive=0;

	//DEBUG vars
	pop_champ=false;
	pop_champ_child=false;
	high_fit=0;
	mut_struct_baby=0;
	mate_baby=0;

	modified = true;
}

Organism::Organism(const Organism& org)
{
	noveltypoint=NULL;
	fitness = org.fitness;
	orig_fitness = org.orig_fitness;
	if(org.noveltypoint)
	{
		noveltypoint=new noveltyitem(*(org.noveltypoint));
	}
	gnome = new Genome(*(org.gnome));	// Associative relationship
	//gnome = org.gnome->duplicate(org.gnome->genome_id);
	net = new Network(*(org.net)); // Associative relationship
	species = org.species;	// Delegation relationship
	expected_offspring = org.expected_offspring;
	generation = org.generation;
	eliminate = org.eliminate;
	error = org.error;
	winner = org.winner;
	champion = org.champion;
	super_champ_offspring = org.super_champ_offspring;

	strcpy(metadata, org.metadata);
	//printf("copying %s did it work? %s", org.metadata, metadata);

	time_alive = org.time_alive;
	pop_champ = org.pop_champ;
	pop_champ_child = org.pop_champ_child;
	high_fit = org.high_fit;
	mut_struct_baby = org.mut_struct_baby;
	mate_baby = org.mate_baby;

	modified = false;
}

Organism::~Organism() {
	delete net;
	delete gnome;
	if(noveltypoint)
	{
		if(!noveltypoint->added)
			delete noveltypoint;
	}
}

void Organism::update_phenotype() {

	//First, delete the old phenotype (net)
	delete net;

	//Now, recreate the phenotype off the new genotype
	net=gnome->genesis(gnome->genome_id);

	modified = true;
}

bool Organism::print_to_file(char *filename) {
	
	std::ofstream oFile(filename);

	return write_to_file(oFile);
}

bool Organism::write_to_file(std::ostream &outFile) {
	
	char tempbuf2[1024];
	if(modified == true) {
		sprintf(tempbuf2, "/* Organism #%d Fitness: %f Time: %d */\n", (gnome)->genome_id, orig_fitness, time_alive);
	} else {
		sprintf(tempbuf2, "/* %s */\n", metadata);
	}
	outFile << tempbuf2;
	gnome->print_to_file(outFile);
	return 1;
}

//// Print the Organism's genome to a file preceded by a comment             
////   detailing the organism's species, number, and fitness
//bool Organism::print_to_file(char *filename) {
//
//ofstream oFile(filename,ios::out);
//
//cout<<"FILENAME: "<<filename<<endl;
//
////Make sure it worked
//if (!oFile) {
//cerr<<"Can't open "<<filename<<" for output"<<endl;
//return 0;
//}
//
////Put the fitness and other information for each organism in a comment
//oFile<<endl<<"/* Organism #"<<gnome->genome_id<<" Fitness: "<<fitness<<" *///"<<endl;
//
//gnome->print_to_file(oFile);
//
//return 1;
//}

bool NEAT::order_orgs(Organism *x, Organism *y) {
	return (x)->fitness > (y)->fitness;
}

bool NEAT::order_orgs_by_adjusted_fit(Organism *x, Organism *y) {
	return (x)->fitness / (x->species)->organisms.size()  > (y)->fitness / (y->species)->organisms.size();
}