function create_genotype(proculus_size, number_of_chambers, rgbstring)
{
	const shift=0.7;
	const angle_delta=0.8;
	const angle_delta_delta=-0.015;
	const growing=1.05;
	
	var str="//0\n";
	var size=proculus_size;
	for(var i=0;i<number_of_chambers;i++)
	{
		str+="p:sh=1,sx=%g,sy=%g,sz=%g,vr=%s\n" % size % size % size % rgbstring;
		if (i>0)
			str+="j:%d,%d,sh=1,dx=%g,ry=%g\n" % (i-1) % i % (size*shift) % (angle_delta+i*angle_delta_delta);
		size*=growing;
	}
	return str;
}

function init_chambers()
{
	colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
	retColors = ["1.0,1.0,1.0", "1.0,1.0,0.0"];
	chambers = [ ["p:sh=1, sx=0.2, sy=0.2, sz=0.2, rz=3.14159265358979,",
"p:0.18421219587326, 0.13, sh=1, sx=0.21, sy=0.21, sz=0.21,",
"p:0.323935478925705, 0.195192575454712, -0.0246672090142965, sh=1, sx=0.2205, sy=0.2205, sz=0.2205,",
"p:0.467822402715683, 0.258204102516174, -0.0246672090142965, sh=1, sx=0.231525, sy=0.231525, sz=0.231525,",
"p:0.664101362228394, 0.309014827013016, -0.0246672090142965, sh=1, sx=0.24310125, sy=0.24310125, sz=0.24310125,",
"p:0.860512733459473, 0.274790525436401, -0.0246672090142965, sh=1, sx=0.2552563125, sy=0.2552563125, sz=0.2552563125,",
"p:1.0273220539093, 0.1655353307724, -0.0246672090142965, sh=1, sx=0.268019128125, sy=0.268019128125, sz=0.268019128125,",
"p:1.13825333118439, -0.000509921927005053, -0.0246672090142965, sh=1, sx=0.28142008453125, sy=0.28142008453125, sz=0.28142008453125,",
"p:1.17569863796234, -0.196833491325378, -0.0246672090142965, sh=1, sx=0.295491088757813, sy=0.295491088757813, sz=0.295491088757813,",
"p:1.13369226455688, -0.392314255237579, -0.0246672090142965, sh=1, sx=0.310265643195703, sy=0.310265643195703, sz=0.310265643195703,"],
        ["p:sh=1, sx=0.1, sy=0.1, sz=0.1, rz=3.14159265358979,",
"p:0.110527315735817, -0.0167302016913891, sh=1, sx=0.105, sy=0.105, sz=0.105, rx=3.63519277003091e-33,",
"p:0.207026958465576, -0.080698736011982, 1.17627548103266e-17, sh=1, sx=0.11025, sy=0.11025, sz=0.11025,",
"p:0.271191358566284, -0.169948443770409, 1.17627548103266e-17, sh=1, sx=0.1157625, sy=0.1157625, sz=0.1157625,",
"p:0.291628688573837, -0.286643952131271, 1.17627548103266e-17, sh=1, sx=0.121550625, sy=0.121550625, sz=0.121550625,",
"p:0.264833927154541, -0.403534322977066, 1.17627548103266e-17, sh=1, sx=0.12762815625, sy=0.12762815625, sz=0.12762815625,",
"p:0.194418027997017, -0.500668346881866, 1.17627548103266e-17, sh=1, sx=0.1340095640625, sy=0.1340095640625, sz=0.1340095640625,",
"p:0.091719962656498, -0.562735974788666, 1.17627548103266e-17, sh=1, sx=0.140710042265625, sy=0.140710042265625, sz=0.140710042265625,",
"p:-0.0270438715815544, -0.57991486787796, 1.17627548103266e-17, sh=1, sx=0.147745544378906, sy=0.147745544378906, sz=0.147745544378906,",
"p:-0.143122747540474, -0.549489378929138, 1.17627548103266e-17, sh=1, sx=0.155132821597852, sy=0.155132821597852, sz=0.155132821597852,"]];
}

function createForamMorphology(morphotype, gen, chamber_num)
{
	var geno = "//0\nm:Vstyle=foram\n" + chambers[morphotype][0] + "vr=" + colors[gen];

	chamber_num = Math.min(chamber_num, chambers[morphotype].size - 1);

	for (var i = 0; i < chamber_num; i++)
	{
		geno += "\n" + chambers[morphotype][i+1]  + "vr=" +  colors[gen];
	}

	for (var i = 0; i < chamber_num; i++)
	{
		geno += "\n" +  "j:"+ i +", "+ (i+1) +", sh=1";
	}

	return geno;
}

function setGenotype(mode)
{
	if (mode->opt == "growth")
	{
		mode->cr.data->genes = mode->parent_genes;
		mode->cr.data->lifeparams = mode->parent_lifeparams;
	}

	else if (mode->opt == "birth")
	{
		mode->cr.data->genes = String.deserialize(String.serialize(mode->genes));
		mode->cr.data->lifeparams = {"max_energy_level" : mode->energy0, "gen" : mode->gen,  "hibernated" : 0, "species" : mode->species, "reproduce" : 0, "dir" : randomDir(), "dir_counter" : Math.random(int(secToSimSteps(ExpProperties.dir_change_sec))), "chamber_growth" : -1, "division_time" : -1};			

	}
}

function gametsDivision(parent_energy, energy0)
{
	var number = 1;
	var result = parent_energy;
	while ((result-ExpProperties.divisionCost) >= energy0)
	{
		result = (result-ExpProperties.divisionCost)/2;
		number *= 2; 
	}
	//Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number);
	return {"energy" : result, "number" : number};
}

function getEnergy0(radius)
{
	return energyFromVolume(micronsToFrams(radius),1);
}

function reproduce_haploid(parent, parent2, clone)
{	
	var number, energy0, new_genes, gen;
	if (clone == 1)
	{
		var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0",0)[0])); 
		energy0 = offspring->energy;
		number = offspring->number;
		new_genes = parent.data->genes;
		parent.data->lifeparams->gen = 1 - parent.data->lifeparams->gen; //because of reversal of "gen" in createOffspring function
		gen = parent.data->lifeparams->gen;
	}
	else
	{
		var offspring1 = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[1])); 
		var offspring2 = gametsDivision(parent2.energy,getEnergy0(getGene(parent2,"energies0", 0)[1])); 
		energy0 = (offspring1->energy+offspring2->energy); 
		number = ExpProperties.gametSuccessRate*(offspring1->number+offspring2->number)/2;
		new_genes = [parent.data->genes, parent2.data->genes];
		gen = 1 - parent.data->lifeparams->gen;

		if (ExpProperties.logging == 1)
		{
				log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
				log(createLogVector(parent2, parent2.energy),ExpProperties.logPref+"repro_energies_log.txt");
				log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
				log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
				log(createLogVector(parent2, parent2.lifespan),ExpProperties.logPref+"lifespan_log.txt");
		}	
	}

	Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0);

	for (var j = 0; j < number; j++)
	{
		createOffspring(createForamMorphology(gen, gen, 0), energy0, new_genes, parent.data->lifeparams); 
	}
}

function reproduce_diploid(parent)
{
	var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[0]));
	var energy0 = offspring->energy; 
	var number = offspring->number;

		if (ExpProperties.logging == 1)
		{
			log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
			log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
			log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
		}	

	Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);

	for (var j = 0; j < number / 2; j++)
	{
		var crossed = 0;
		//crossover
		if (Math.rnd01 < ExpProperties.crossprob)
		{
			crossover(parent, "min_repro_energies");
			crossed = 1;
		}

		for (var k = 0; k < 2; k++)
		{
			createOffspring(createForamMorphology(1 - parent.data->lifeparams->gen, 1 - parent.data->lifeparams->gen, 0), energy0, parent.data->genes[0], parent.data->lifeparams); 
		}

		//reverse of crossover for fossilization
		if (crossed == 1)
		{
			crossover(parent, "min_repro_energies");
			crossed = 0;
		}
			
	}
}

function reproduce_parents(species)
{
		var parent1 = null;
		var parent2 = null;
		var pop = Populations[0];
		for (var i = pop.size-1; i >= 0; i--)
		{
   			if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species) 
   			{ 
				if ((pop[i].data->lifeparams->gen==1) || ((pop[i].data->lifeparams->gen==0) && ExpProperties.stress == 0))
				{
					continue;
				}
      				else if (parent1 == null)
				{
					parent1 = pop[i];
				}
				else if (parent2 == null)
				{
					parent2 = pop[i];
				}  
				if (parent1 != null && parent2 != null)
				{
					//when parents are ready for reproduction start gametogenesis
					if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1)
					{
						var time = int(secToSimSteps(ExpProperties.gametoPeriodSec));
						parent1.data->lifeparams->division_time = time;
						parent2.data->lifeparams->division_time = time;
						parent1.idleen = 0;
						parent2.idleen = 0;
						//Simulator.print("parents "+parent1.uid + " " + parent2.uid + " ready to repro: "+Simulator.stepNumber);
					}
					//when gametogenesis is finished fuse gamets 
					else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0)
					{
						reproduce_haploid(parent1, parent2, 0);
						print_repro_info(parent1);
						print_repro_info(parent2);
						pop.kill(parent1);
						pop.kill(parent2);
						parent1 = null;
						parent2 = null;
					}
				}	
   			} 
		}
}

function readyToRepro(cr)
{
	var reproduced = 1;
	
	
	if (cr.data->lifeparams->gen == 1)
	{
		reproduce_diploid(cr);
	}

	else if (ExpProperties.stress == 0)
	{
		reproduce_haploid(cr, null, 1);
	}

	else
	{
		if (cr.signals.size == 0)
		{
			cr.signals.add("repro"+cr.data->lifeparams->species);
			cr.signals[0].power = 1;
		}
		reproduced = 0;
		cr.data->lifeparams->reproduce = 1;
	}

	if (reproduced == 1)
	{
		print_repro_info(cr);
		Populations[0].kill(cr);
	}

	return reproduced;
}

function print_repro_info(cr)
{
	Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy);
}

function foramReproduce(cr)
{
	var properEnergy = cr.energy >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][getGene(cr, "min_repro_energies",0)[cr.data->lifeparams->gen]],0);
	var reproduced = 0;	

	//if creature has proper energy
	if ( properEnergy && cr.signals.size == 0)
	{
		//reproduce with probability repro_prob
		if (Math.rnd01 <= ExpProperties.repro_prob) //TODO env trigger
		{
			reproduced = readyToRepro(cr);
		}
		else if (cr.signals.receive("repro"+cr.data->lifeparams->species) > 0)
		{
			reproduced = readyToRepro(cr);
		}
		if (reproduced == 1)
				return 1;
	}

	else if (!properEnergy)
	{
		cr.signals.clear();
		cr.data->lifeparams->reproduce = 0; 
	}

	return 0;
}

function crossover(parent, gene)
{
	var tmp = parent.data->genes[0][gene];
	parent.data->genes[0][gene] = parent.data->genes[1][gene];
	parent.data->genes[1][gene] = tmp;
}

function createOffspring(geno, energy, parent_genes, parent_lifeparams)
{
	curColor = retColors[1-parent_lifeparams->gen];
	var cr = Populations[0].add(geno);
	cr.energy0 = energy;
	cr.energy = cr.energy0;
	setGenotype({"opt" : "birth", "cr" : cr, "gen" : 1 - parent_lifeparams->gen, "species" : parent_lifeparams->species, "energy0" : cr.energy0, "genes" : parent_genes});
	placeRandomlyNotColliding(cr);
}