[401] | 1 |
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[559] | 2 | function create_genotype(proculus_size, number_of_chambers, rgbstring, lastchambergrowth) //lastchambergrowth is 0..1
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[557] | 3 | {
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[847] | 4 | const shift = 0.7;
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| 5 | const angle_delta = 0.8;
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| 6 | const angle_delta_delta = -0.01;
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| 7 | const growing = 1.07; //7% growth
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| 8 |
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[1074] | 9 | var str = "//0s\nm:Vstyle=foram\n";
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[847] | 10 | var size = proculus_size;
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| 11 | for(var i = 0; i < number_of_chambers; i++)
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[557] | 12 | {
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[847] | 13 | var effectivesize = size; //'effectivesize' is introduced only to consider the last chamber
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| 14 | if (i == number_of_chambers - 1) //last chamber
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[559] | 15 | {
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[847] | 16 | effectivesize *= lastchambergrowth;
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| 17 | size = size * (1.35 - 0.35 * lastchambergrowth); //last iteration: 'size' is only used for shifting (dx). The last chamber emerges at the surface of the previous one
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| 18 | if (lastchambergrowth < 1)
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| 19 | rgbstring = "0.9,0.9,0.9,i=\"growing=%g\"" % lastchambergrowth; //when the last chamber is growing, make it bright gray and add extra information in its "i" field
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[559] | 20 | }
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[567] | 21 | str += "p:sh=1,sx=%g,sy=%g,sz=%g,rz=3.14159265358979,vr=%s\n" % effectivesize % effectivesize % effectivesize % rgbstring;
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[847] | 22 | if (i > 0)
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| 23 | str += "j:%d,%d,sh=1,dx=%g,rz=%g\n" % (i - 1) % i % (size * shift) % (angle_delta + i * angle_delta_delta);
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| 24 | size *= growing;
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[557] | 25 | }
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| 26 | return str;
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| 27 | }
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| 28 |
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[422] | 29 | function setGenotype(mode)
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| 30 | {
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[554] | 31 | if (mode->opt == "growth")
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[422] | 32 | {
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[554] | 33 | mode->cr.data->genes = mode->parent_genes;
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| 34 | mode->cr.data->lifeparams = mode->parent_lifeparams;
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[422] | 35 | }
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[554] | 36 |
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| 37 | else if (mode->opt == "birth")
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[422] | 38 | {
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[567] | 39 | foram_uid += 1;
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[847] | 40 | var new_id = "c" + string(foram_uid);
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[554] | 41 | mode->cr.data->genes = String.deserialize(String.serialize(mode->genes));
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[847] | 42 | 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, "uid" : new_id};
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[554] | 43 |
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[567] | 44 | var oper = "cloning";
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[573] | 45 | var inherit = [1.0];
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[567] | 46 | if (mode->parentsuids.size > 1)
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[847] | 47 | {
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[567] | 48 | oper = "cross-over";
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[573] | 49 | inherit = [0.5, 0.5];
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[567] | 50 | }
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[847] | 51 |
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| 52 | var dict = {"Time": Simulator.stepNumber, "FromIDs": mode->parentsuids, "ID": new_id, "Inherited": inherit, "Operation": oper, "Kind" : mode->gen};
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[1100] | 53 | if (ExpProperties.print_evol_progress == 1)
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[1098] | 54 | Simulator.print("[OFFSPRING] " + String.serialize(dict));
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[422] | 55 | }
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| 56 | }
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| 57 |
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[567] | 58 | function getEnergy0(radius)
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| 59 | {
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[847] | 60 | return energyFromVolume(micronsToFrams(radius), 1);
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[567] | 61 | }
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| 62 |
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[479] | 63 | function gametsDivision(parent_energy, energy0)
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| 64 | {
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| 65 | var number = 1;
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| 66 | var result = parent_energy;
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[847] | 67 | while ((result - ExpProperties.divisionCost) >= energy0)
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[479] | 68 | {
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[847] | 69 | result = (result - ExpProperties.divisionCost) / 2;
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[567] | 70 | number *= 2;
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[479] | 71 | }
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| 72 | //Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number);
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| 73 | return {"energy" : result, "number" : number};
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| 74 | }
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| 75 |
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[422] | 76 | function reproduce_haploid(parent, parent2, clone)
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[847] | 77 | {
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[476] | 78 | var number, energy0, new_genes, gen;
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[422] | 79 | if (clone == 1)
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| 80 | {
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[847] | 81 | var offspring = gametsDivision(parent.energy, getEnergy0(getGene(parent, "energies0", 0)[0]));
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[479] | 82 | energy0 = offspring->energy;
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| 83 | number = offspring->number;
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[476] | 84 | new_genes = parent.data->genes;
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| 85 | parent.data->lifeparams->gen = 1 - parent.data->lifeparams->gen; //because of reversal of "gen" in createOffspring function
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| 86 | gen = parent.data->lifeparams->gen;
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[422] | 87 | }
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| 88 | else
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| 89 | {
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[847] | 90 | var offspring1 = gametsDivision(parent.energy, getEnergy0(getGene(parent, "energies0", 0)[1]));
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| 91 | var offspring2 = gametsDivision(parent2.energy, getEnergy0(getGene(parent2, "energies0", 0)[1]));
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| 92 | energy0 = (offspring1->energy + offspring2->energy);
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| 93 | number = ExpProperties.gametSuccessRate * (offspring1->number + offspring2->number) / 2;
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[476] | 94 | new_genes = [parent.data->genes, parent2.data->genes];
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| 95 | gen = 1 - parent.data->lifeparams->gen;
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[493] | 96 |
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| 97 | if (ExpProperties.logging == 1)
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| 98 | {
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[847] | 99 | log(createLogVector(parent, parent.energy), ExpProperties.logPref + "repro_energies_log.txt");
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| 100 | log(createLogVector(parent2, parent2.energy), ExpProperties.logPref + "repro_energies_log.txt");
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| 101 | log(createLogVector(parent, number), ExpProperties.logPref + "repro_num_log.txt");
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| 102 | log(createLogVector(parent, parent.lifespan), ExpProperties.logPref + "lifespan_log.txt");
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| 103 | log(createLogVector(parent2, parent2.lifespan), ExpProperties.logPref + "lifespan_log.txt");
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| 104 | }
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[422] | 105 | }
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| 106 |
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[567] | 107 | //Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0);
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[422] | 108 |
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[418] | 109 | for (var j = 0; j < number; j++)
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[401] | 110 | {
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[567] | 111 | createOffspring(create_genotype(ExpProperties.chamber_proculus_diplo, 1, colors[1], 1), energy0, new_genes, parent.data->lifeparams, [parent.data->lifeparams->uid, parent2.data->lifeparams->uid]);
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[401] | 112 | }
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| 113 | }
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| 114 |
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[418] | 115 | function reproduce_diploid(parent)
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[401] | 116 | {
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[847] | 117 | var offspring = gametsDivision(parent.energy, getEnergy0(getGene(parent, "energies0", 0)[0]));
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| 118 | var energy0 = offspring->energy;
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[510] | 119 | var number = offspring->number;
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[422] | 120 |
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[847] | 121 | if (ExpProperties.logging == 1)
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| 122 | {
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| 123 | log(createLogVector(parent, parent.energy), ExpProperties.logPref + "repro_energies_log.txt");
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| 124 | log(createLogVector(parent, number), ExpProperties.logPref + "repro_num_log.txt");
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| 125 | log(createLogVector(parent, parent.lifespan), ExpProperties.logPref + "lifespan_log.txt");
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| 126 | }
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[493] | 127 |
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[567] | 128 | //Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);
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[422] | 129 |
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[418] | 130 | for (var j = 0; j < number / 2; j++)
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[401] | 131 | {
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[418] | 132 | var crossed = 0;
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| 133 | //crossover
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[486] | 134 | if (Math.rnd01 < ExpProperties.crossprob)
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[418] | 135 | {
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[422] | 136 | crossover(parent, "min_repro_energies");
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[418] | 137 | crossed = 1;
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| 138 | }
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[401] | 139 |
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[418] | 140 | for (var k = 0; k < 2; k++)
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[404] | 141 | {
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[847] | 142 | createOffspring(create_genotype(ExpProperties.chamber_proculus_haplo, 1, colors[0], 1), energy0, parent.data->genes[0], parent.data->lifeparams, [parent.data->lifeparams->uid]);
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[404] | 143 | }
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| 144 |
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[418] | 145 | //reverse of crossover for fossilization
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| 146 | if (crossed == 1)
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[401] | 147 | {
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[422] | 148 | crossover(parent, "min_repro_energies");
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[418] | 149 | crossed = 0;
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[401] | 150 | }
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[847] | 151 |
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[401] | 152 | }
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[404] | 153 | }
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| 154 |
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[422] | 155 | function reproduce_parents(species)
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[404] | 156 | {
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[847] | 157 | var parent1 = null;
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| 158 | var parent2 = null;
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| 159 | var pop = Populations[0];
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| 160 | for (var i = pop.size - 1; i >= 0; i--)
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| 161 | {
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| 162 | if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species)
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[401] | 163 | {
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[847] | 164 | if ((pop[i].data->lifeparams->gen == 1) || ((pop[i].data->lifeparams->gen == 0) && ExpProperties.stress == 0))
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| 165 | {
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| 166 | continue;
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| 167 | }
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| 168 | else if (parent1 == null)
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| 169 | {
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| 170 | parent1 = pop[i];
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| 171 | }
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| 172 | else if (parent2 == null)
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| 173 | {
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| 174 | parent2 = pop[i];
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| 175 | }
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| 176 | if (parent1 != null && parent2 != null)
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| 177 | {
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| 178 | //when parents are ready for reproduction start gametogenesis
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| 179 | if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1)
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[401] | 180 | {
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[847] | 181 | var time = int(secToSimSteps(ExpProperties.gametoPeriodSec));
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| 182 | parent1.data->lifeparams->division_time = time;
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| 183 | parent2.data->lifeparams->division_time = time;
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| 184 | parent1.idleen = 0;
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| 185 | parent2.idleen = 0;
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| 186 | //Simulator.print("parents "+parent1.uid + " " + parent2.uid + " ready to repro: "+Simulator.stepNumber);
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[401] | 187 | }
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[847] | 188 | //when gametogenesis is finished fuse gamets
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| 189 | else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0)
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[401] | 190 | {
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[847] | 191 | reproduce_haploid(parent1, parent2, 0);
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| 192 | //print_repro_info(parent1);
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| 193 | //print_repro_info(parent2);
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| 194 | pop.kill(parent1);
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| 195 | pop.kill(parent2);
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| 196 | parent1 = null;
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| 197 | parent2 = null;
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[401] | 198 | }
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[847] | 199 | }
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[401] | 200 | }
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[847] | 201 | }
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[422] | 202 | }
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| 203 |
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| 204 | function readyToRepro(cr)
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| 205 | {
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| 206 | var reproduced = 1;
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[567] | 207 |
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[476] | 208 | if (cr.data->lifeparams->gen == 1)
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[422] | 209 | {
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| 210 | reproduce_diploid(cr);
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[401] | 211 | }
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| 212 |
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[486] | 213 | else if (ExpProperties.stress == 0)
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[401] | 214 | {
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[422] | 215 | reproduce_haploid(cr, null, 1);
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| 216 | }
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| 217 |
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| 218 | else
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| 219 | {
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| 220 | if (cr.signals.size == 0)
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[401] | 221 | {
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[847] | 222 | cr.signals.add("repro" + cr.data->lifeparams->species);
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[422] | 223 | cr.signals[0].power = 1;
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[401] | 224 | }
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[422] | 225 | reproduced = 0;
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[476] | 226 | cr.data->lifeparams->reproduce = 1;
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[401] | 227 | }
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[422] | 228 |
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| 229 | if (reproduced == 1)
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| 230 | {
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[567] | 231 | //print_repro_info(cr);
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[422] | 232 | Populations[0].kill(cr);
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| 233 | }
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| 234 |
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| 235 | return reproduced;
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[401] | 236 | }
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| 237 |
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[422] | 238 | function foramReproduce(cr)
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| 239 | {
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[847] | 240 | var properEnergy = cr.energy >= getGene(cr, "min_repro_energies", 0)[cr.data->lifeparams->gen];
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| 241 | var reproduced = 0;
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[422] | 242 |
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| 243 | //if creature has proper energy
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[590] | 244 | if ( properEnergy )
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[422] | 245 | {
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| 246 | //reproduce with probability repro_prob
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[486] | 247 | if (Math.rnd01 <= ExpProperties.repro_prob) //TODO env trigger
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[421] | 248 | {
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[422] | 249 | reproduced = readyToRepro(cr);
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[421] | 250 | }
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[847] | 251 | else if (cr.signals.receive("repro" + cr.data->lifeparams->species) > 0)
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[421] | 252 | {
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[422] | 253 | reproduced = readyToRepro(cr);
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[421] | 254 | }
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[422] | 255 | if (reproduced == 1)
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[847] | 256 | return 1;
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[421] | 257 | }
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| 258 |
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[422] | 259 | else if (!properEnergy)
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[421] | 260 | {
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[422] | 261 | cr.signals.clear();
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[847] | 262 | cr.data->lifeparams->reproduce = 0;
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[421] | 263 | }
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[430] | 264 |
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| 265 | return 0;
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[422] | 266 | }
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[421] | 267 |
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[422] | 268 | function crossover(parent, gene)
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| 269 | {
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[476] | 270 | var tmp = parent.data->genes[0][gene];
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| 271 | parent.data->genes[0][gene] = parent.data->genes[1][gene];
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| 272 | parent.data->genes[1][gene] = tmp;
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[422] | 273 | }
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[421] | 274 |
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[567] | 275 | function createOffspring(geno, energy, parent_genes, parent_lifeparams, parentsuids)
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[422] | 276 | {
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[847] | 277 | curColor = colors[1 - parent_lifeparams->gen];
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| 278 | var cr = createAndRotate(geno, 0, 2 * Math.pi, 0);
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[422] | 279 | cr.energy0 = energy;
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| 280 | cr.energy = cr.energy0;
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[567] | 281 | setGenotype({"opt" : "birth", "cr" : cr, "gen" : 1 - parent_lifeparams->gen, "species" : parent_lifeparams->species, "energy0" : cr.energy0, "genes" : parent_genes, "parentsuids" : parentsuids});
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[422] | 282 | placeRandomlyNotColliding(cr);
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[421] | 283 | }
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[567] | 284 |
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| 285 | function print_repro_info(cr)
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| 286 | {
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[1100] | 287 | if (ExpProperties.print_evol_progress == 1)
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[1098] | 288 | Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy);
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[567] | 289 | }
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