[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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[558] | 4 | const shift=0.7;
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| 5 | const angle_delta=0.8;
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[561] | 6 | const angle_delta_delta=-0.01;
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| 7 | const growing=1.07; //7% growth
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[557] | 8 |
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[593] | 9 | var str="//0\nm:Vstyle=foram\n";
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[557] | 10 | var size=proculus_size;
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| 11 | for(var i=0;i<number_of_chambers;i++)
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| 12 | {
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[559] | 13 | var effectivesize=size; //'effectivesize' is introduced only to consider the last chamber
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[575] | 14 | if (i==number_of_chambers-1) //last chamber
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[559] | 15 | {
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| 16 | effectivesize*=lastchambergrowth;
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[560] | 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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[575] | 18 | if (lastchambergrowth<1)
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[581] | 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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[557] | 22 | if (i>0)
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[567] | 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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[557] | 24 | size*=growing;
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| 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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| 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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[567] | 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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| 47 | {
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| 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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| 51 |
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[573] | 52 | var dict={"Time":Simulator.stepNumber,"FromIDs":mode->parentsuids,"ID":new_id, "Inherited":inherit, "Operation": oper, "Kind" : mode->gen};
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[567] | 53 | Simulator.print("[OFFSPRING] " + String.serialize(dict));
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[422] | 54 | }
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| 55 | }
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| 56 |
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[567] | 57 | function getEnergy0(radius)
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| 58 | {
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| 59 | return energyFromVolume(micronsToFrams(radius),1);
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| 60 | }
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| 61 |
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[479] | 62 | function gametsDivision(parent_energy, energy0)
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| 63 | {
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| 64 | var number = 1;
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| 65 | var result = parent_energy;
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[486] | 66 | while ((result-ExpProperties.divisionCost) >= energy0)
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[479] | 67 | {
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[486] | 68 | result = (result-ExpProperties.divisionCost)/2;
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[567] | 69 | number *= 2;
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[479] | 70 | }
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| 71 | //Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number);
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| 72 | return {"energy" : result, "number" : number};
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| 73 | }
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| 74 |
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[422] | 75 | function reproduce_haploid(parent, parent2, clone)
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| 76 | {
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[476] | 77 | var number, energy0, new_genes, gen;
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[422] | 78 | if (clone == 1)
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| 79 | {
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[487] | 80 | var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0",0)[0]));
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[479] | 81 | energy0 = offspring->energy;
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| 82 | number = offspring->number;
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[476] | 83 | new_genes = parent.data->genes;
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| 84 | parent.data->lifeparams->gen = 1 - parent.data->lifeparams->gen; //because of reversal of "gen" in createOffspring function
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| 85 | gen = parent.data->lifeparams->gen;
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[422] | 86 | }
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| 87 | else
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| 88 | {
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[487] | 89 | var offspring1 = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[1]));
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| 90 | var offspring2 = gametsDivision(parent2.energy,getEnergy0(getGene(parent2,"energies0", 0)[1]));
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[479] | 91 | energy0 = (offspring1->energy+offspring2->energy);
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[486] | 92 | number = ExpProperties.gametSuccessRate*(offspring1->number+offspring2->number)/2;
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[476] | 93 | new_genes = [parent.data->genes, parent2.data->genes];
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| 94 | gen = 1 - parent.data->lifeparams->gen;
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[493] | 95 |
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| 96 | if (ExpProperties.logging == 1)
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| 97 | {
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| 98 | log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
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| 99 | log(createLogVector(parent2, parent2.energy),ExpProperties.logPref+"repro_energies_log.txt");
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| 100 | log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
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[552] | 101 | log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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| 102 | log(createLogVector(parent2, parent2.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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[493] | 103 | }
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[422] | 104 | }
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| 105 |
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[567] | 106 | //Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0);
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[422] | 107 |
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[418] | 108 | for (var j = 0; j < number; j++)
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[401] | 109 | {
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[567] | 110 | 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] | 111 | }
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| 112 | }
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| 113 |
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[418] | 114 | function reproduce_diploid(parent)
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[401] | 115 | {
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[510] | 116 | var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[0]));
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| 117 | var energy0 = offspring->energy;
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| 118 | var number = offspring->number;
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[422] | 119 |
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[493] | 120 | if (ExpProperties.logging == 1)
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| 121 | {
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| 122 | log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
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| 123 | log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
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[552] | 124 | log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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[493] | 125 | }
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| 126 |
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[567] | 127 | //Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);
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[422] | 128 |
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[418] | 129 | for (var j = 0; j < number / 2; j++)
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[401] | 130 | {
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[418] | 131 | var crossed = 0;
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| 132 | //crossover
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[486] | 133 | if (Math.rnd01 < ExpProperties.crossprob)
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[418] | 134 | {
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[422] | 135 | crossover(parent, "min_repro_energies");
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[418] | 136 | crossed = 1;
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| 137 | }
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[401] | 138 |
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[418] | 139 | for (var k = 0; k < 2; k++)
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[404] | 140 | {
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[567] | 141 | 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] | 142 | }
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| 143 |
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[418] | 144 | //reverse of crossover for fossilization
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| 145 | if (crossed == 1)
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[401] | 146 | {
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[422] | 147 | crossover(parent, "min_repro_energies");
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[418] | 148 | crossed = 0;
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[401] | 149 | }
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[418] | 150 |
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[401] | 151 | }
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[404] | 152 | }
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| 153 |
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[422] | 154 | function reproduce_parents(species)
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[404] | 155 | {
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[418] | 156 | var parent1 = null;
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| 157 | var parent2 = null;
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| 158 | var pop = Populations[0];
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| 159 | for (var i = pop.size-1; i >= 0; i--)
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[401] | 160 | {
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[476] | 161 | if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species)
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[418] | 162 | {
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[486] | 163 | if ((pop[i].data->lifeparams->gen==1) || ((pop[i].data->lifeparams->gen==0) && ExpProperties.stress == 0))
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[401] | 164 | {
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[422] | 165 | continue;
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[401] | 166 | }
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[418] | 167 | else if (parent1 == null)
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[401] | 168 | {
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[418] | 169 | parent1 = pop[i];
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[401] | 170 | }
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[418] | 171 | else if (parent2 == null)
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| 172 | {
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| 173 | parent2 = pop[i];
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| 174 | }
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[430] | 175 | if (parent1 != null && parent2 != null)
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[418] | 176 | {
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[479] | 177 | //when parents are ready for reproduction start gametogenesis
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| 178 | if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1)
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| 179 | {
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[554] | 180 | var time = int(secToSimSteps(ExpProperties.gametoPeriodSec));
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[479] | 181 | parent1.data->lifeparams->division_time = time;
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| 182 | parent2.data->lifeparams->division_time = time;
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| 183 | parent1.idleen = 0;
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| 184 | parent2.idleen = 0;
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| 185 | //Simulator.print("parents "+parent1.uid + " " + parent2.uid + " ready to repro: "+Simulator.stepNumber);
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| 186 | }
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| 187 | //when gametogenesis is finished fuse gamets
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| 188 | else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0)
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| 189 | {
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| 190 | reproduce_haploid(parent1, parent2, 0);
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[567] | 191 | //print_repro_info(parent1);
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| 192 | //print_repro_info(parent2);
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[479] | 193 | pop.kill(parent1);
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| 194 | pop.kill(parent2);
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| 195 | parent1 = null;
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| 196 | parent2 = null;
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| 197 | }
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[430] | 198 | }
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[418] | 199 | }
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[401] | 200 | }
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[422] | 201 | }
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| 202 |
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| 203 | function readyToRepro(cr)
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| 204 | {
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| 205 | var reproduced = 1;
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[567] | 206 |
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[476] | 207 | if (cr.data->lifeparams->gen == 1)
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[422] | 208 | {
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| 209 | reproduce_diploid(cr);
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[401] | 210 | }
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| 211 |
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[486] | 212 | else if (ExpProperties.stress == 0)
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[401] | 213 | {
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[422] | 214 | reproduce_haploid(cr, null, 1);
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| 215 | }
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| 216 |
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| 217 | else
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| 218 | {
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| 219 | if (cr.signals.size == 0)
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[401] | 220 | {
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[476] | 221 | cr.signals.add("repro"+cr.data->lifeparams->species);
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[422] | 222 | cr.signals[0].power = 1;
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[401] | 223 | }
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[422] | 224 | reproduced = 0;
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[476] | 225 | cr.data->lifeparams->reproduce = 1;
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[401] | 226 | }
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[422] | 227 |
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| 228 | if (reproduced == 1)
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| 229 | {
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[567] | 230 | //print_repro_info(cr);
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[422] | 231 | Populations[0].kill(cr);
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| 232 | }
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| 233 |
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| 234 | return reproduced;
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[401] | 235 | }
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| 236 |
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[422] | 237 | function foramReproduce(cr)
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| 238 | {
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[567] | 239 | var properEnergy = cr.energy >= getGene(cr, "min_repro_energies",0)[cr.data->lifeparams->gen];
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[487] | 240 | var reproduced = 0;
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[422] | 241 |
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| 242 | //if creature has proper energy
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[590] | 243 | if ( properEnergy )
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[422] | 244 | {
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| 245 | //reproduce with probability repro_prob
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[486] | 246 | if (Math.rnd01 <= ExpProperties.repro_prob) //TODO env trigger
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[421] | 247 | {
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[422] | 248 | reproduced = readyToRepro(cr);
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[421] | 249 | }
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[476] | 250 | else if (cr.signals.receive("repro"+cr.data->lifeparams->species) > 0)
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[421] | 251 | {
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[422] | 252 | reproduced = readyToRepro(cr);
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[421] | 253 | }
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[422] | 254 | if (reproduced == 1)
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[430] | 255 | return 1;
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[421] | 256 | }
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| 257 |
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[422] | 258 | else if (!properEnergy)
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[421] | 259 | {
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[422] | 260 | cr.signals.clear();
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[476] | 261 | cr.data->lifeparams->reproduce = 0;
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[421] | 262 | }
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[430] | 263 |
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| 264 | return 0;
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[422] | 265 | }
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[421] | 266 |
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[422] | 267 | function crossover(parent, gene)
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| 268 | {
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[476] | 269 | var tmp = parent.data->genes[0][gene];
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| 270 | parent.data->genes[0][gene] = parent.data->genes[1][gene];
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| 271 | parent.data->genes[1][gene] = tmp;
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[422] | 272 | }
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[421] | 273 |
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[567] | 274 | function createOffspring(geno, energy, parent_genes, parent_lifeparams, parentsuids)
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[422] | 275 | {
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[579] | 276 | curColor = colors[1-parent_lifeparams->gen];
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[422] | 277 | var cr = Populations[0].add(geno);
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| 278 | cr.energy0 = energy;
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| 279 | cr.energy = cr.energy0;
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[567] | 280 | 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] | 281 | placeRandomlyNotColliding(cr);
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[421] | 282 | }
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[567] | 283 |
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| 284 | function print_repro_info(cr)
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| 285 | {
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| 286 | Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy);
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| 287 | }
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