//size versus energy
//real proportions

function init_chambers()
{
	colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
	chambers = [ ["0.0,0.0,0.0,",  //coiled
	"1.08020961284637, -0.0597195439040661, -0.0393781512975693,",
	"1.08020961284637, -0.0597195439040661, -0.0393781512975693,",
	"0.615013539791107, 0.778662621974945, 0.535521030426025,",
	"0.488581955432892, 0.826426684856415, -0.381044268608093,",
	"0.732419908046722, -0.0084995785728097, -1.02214300632477,",
	"1.35288727283478, 0.875738024711609, -1.03719782829285,",
	"0.342692613601685, 0.938660383224487, -1.45657968521118,",
	"1.0958571434021, 0.316927701234818, -1.813929438591,",
	"0.903768002986908, 1.11856341362, -2.53161096572876,",
	"0.21014116704464, 0.295340299606323, -2.45328187942505,"],
        ["0.0,0.0,0.0,", //longitudal
	"0.98089325428009, 0.00591040402650833, 0.00389722990803421,",
	"1.90962779521942, -0.256769120693207, -0.16194811463356,",
	"2.63965249061584, -0.727959632873535, -0.609036147594452,",
	"3.17575979232788, -1.34843015670776, -1.14828503131866,",
	"3.55273032188416, -2.22369408607483, -1.3917418718338,",
	"3.64916682243347, -3.11888360977173, -1.01666414737701,",
	"3.50461649894714, -3.84039807319641, -0.377427101135254,",
	"3.15921688079834, -4.50001525878906, 0.261153399944305,",
	"2.51528453826904, -5.16421365737915, 0.59241509437561,"]];
}

function createForamGenotype(gen, species, chamber_num)
{
	var rad = getProperty(gen, "chamber_proculus"); 
	var geno = "//0\np:" + chambers[species][0] + "sh=1,sx=" + rad + ",sy=" + rad + ",sz=" + rad + ", rz=3.14159265358979,vr=" + colors[gen];

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

	for (var i = 0; i < chamber_num; i++)
	{
		rad = getProperty(gen, "chamber_proculus") + getProperty(gen, "chamber_difference") * (i + 1);
		geno += "\n" + "p:" + chambers[species][i+1] + "sh=1,sx=" + rad + ",sy=" + rad + ",sz=" + rad + ",vr=" + colors[gen];
	}

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

	if (species == 0) geno += "\nn:p=0,d=\"S\"";

	return geno;
}

function setGenotype(mode)
{
	if (mode["opt"] == 0) //initial
	{
		mode["cr"].user1 = {"min_repro_energies" : [max_chamber_energ[0][getProperty(0, "min_repro_energ")], max_chamber_energ[1][getProperty(1, "min_repro_energ")]], "hibernation" : mode["species"]};
		mode["cr"].user2 = {"max_energy_level" : getProperty(0,"energies0"), "gen" : 0,  "hibernated" : 0, "species" : mode["species"], "reproduce" : 0, "dir" : randomDir()};
	}
	else if (mode["opt"]  == 1) //child
	{
		mode["cr"].user2 = {"max_energy_level" : getProperty(1 - mode["parent_user2"]["gen"],"energies0"), "gen" : 1 - mode["parent_user2"]["gen"],  "hibernated" : 0, "species" : mode["parent_user2"]["species"], "reproduce" : 0, "dir" : randomDir()};
		mode["cr"].user1 = mode["parent_user1"];
	}
	else //grow
	{
		mode["cr"].user1 = mode["parent_user1"];
		mode["cr"].user2 = mode["parent_user2"];
	}
}

function reproduce_haploid(parent, parent2, clone)
{	
	var number, energy0, new_user1, gen;
	if (clone == 1)
	{
		energy0 = getProperty(0,"energies0");
		number = (( 1 - getProperty(1, "e_repro_cost")) * parent.energy) / energy0;
		new_user1 = parent.user1;
		parent.user2["gen"] = 1 - parent.user2["gen"]; //because of reversal of "gen" in createOffspring function
		gen = parent.user2["gen"];
	}
	else
	{
		energy0 = getProperty(1,"energies0"); 
		number = (((1 - getProperty(parent.user2["gen"], "e_repro_cost")) * parent.energy) + ((1 -(getProperty(parent.user2["gen"], "e_repro_cost"))) * parent2.energy)) / energy0;
		new_user1 = [parent.user1, parent2.user1];
		gen = 1 - parent.user2["gen"];
	}

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

	for (var j = 0; j < number; j++)
	{
		createOffspring(createForamGenotype(gen, parent.user2["species"], 0), energy0, new_user1, parent.user2); 
	}
}

function reproduce_diploid(parent)
{
	var energy0 = getProperty(0,"energies0");
	var number = ((1 - (getProperty(parent.user2["gen"], "e_repro_cost"))) * parent.energy) / energy0;

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

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

		for (var k = 0; k < 2; k++)
		{
			createOffspring(createForamGenotype(1 - parent.user2["gen"], parent.user2["species"], 0), energy0, parent.user1[0], parent.user2); 
		}

		//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].user2["reproduce"] == 1 && pop[i].user2["species"] == species) 
   			{ 
				if ((pop[i].user2["gen"]==1) || ((pop[i].user2["gen"]==0) && ExpParams.stress == 0))
				{
					continue;
				}
      				else if (parent1 == null)
				{
					parent1 = pop[i];
				}
				else if (parent2 == null)
				{
					parent2 = pop[i];
				}  
				if (parent1 != null && parent2 != null)
				{
					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.user2["gen"] == 1)
	{
		reproduce_diploid(cr);
	}

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

	else
	{
		if (cr.signals.size == 0)
		{
			cr.signals.add("repro"+cr.user2["species"]);
			cr.signals[0].power = 1;
		}
		reproduced = 0;
		cr.user2["reproduce"] = 1;
	}

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

	return reproduced;
}

function print_repro_info(cr)
{
	Simulator.print("Reproduced " + cr.user2["gen"] + " of species " + cr.user2["species"] + " energy: " + cr.energy);
}



function foramReproduce(cr)
{
	var properEnergy = 0;
	var reproduced = 0;

	if (cr.user2["gen"] == 0)
	{
		properEnergy = ( cr.energy >= cr.user1["min_repro_energies"][cr.user2["gen"]] );
	}
	else
	{
		properEnergy = ( cr.energy >= cr.user1[0]["min_repro_energies"][cr.user2["gen"]] ); //TODO gene selection
	}

	//if creature has proper energy
	if ( properEnergy && cr.signals.size == 0)
	{
		//reproduce with probability repro_prob
		if (Math.rnd01 <= ExpParams.repro_prob) //TODO env trigger
		{
			reproduced = readyToRepro(cr);
		}
		else if (cr.signals.receive("repro"+cr.user2["species"]) > 0)
		{
			reproduced = readyToRepro(cr);
		}
		if (reproduced == 1)
				return 1;
	}

	else if (!properEnergy)
	{
		cr.signals.clear();
		cr.user2["reproduce"] = 0; 
	}

	return 0;
}

function crossover(parent, gene)
{
	var tmp = parent.user1[0][gene];
	parent.user1[0][gene] = parent.user1[1][gene];
	parent.user1[1][gene] = tmp;
}

function createOffspring(geno, energy, parent_user1, parent_user2)
{
	var cr = Populations[0].add(geno);
	cr.energy0 = energy;
	cr.energy = cr.energy0;
	setGenotype({"cr" : cr, "parent_user1" : parent_user1, "parent_user2" : parent_user2, "opt" : 1});
	placeRandomlyNotColliding(cr);
}