[401] | 1 | //size versus energy
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| 2 | //real proportions
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| 3 |
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[557] | 4 | function create_genotype(proculus_size, number_of_chambers)
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| 5 | {
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| 6 | const shift=0.75;
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| 7 | const angle_delta=0.7;
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| 8 | const angle_delta_delta=-0.018;
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| 9 | const growing=1.05;
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| 10 |
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| 11 | var str="//0\n";
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| 12 | var size=proculus_size;
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| 13 | for(var i=0;i<number_of_chambers;i++)
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| 14 | {
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| 15 | str+="p:sh=1,sx=%g,sy=%g,sz=%g\n" % size % size % size;
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| 16 | if (i>0)
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| 17 | str+="j:%d,%d,sh=1,dx=%g,ry=%g\n" % (i-1) % i % (size*shift) % (angle_delta+i*angle_delta_delta);
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| 18 | size*=growing;
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| 19 | }
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| 20 | return str;
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| 21 | }
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| 22 |
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[422] | 23 | function init_chambers()
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| 24 | {
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| 25 | colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
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[552] | 26 | retColors = ["1.0,1.0,1.0", "1.0,1.0,0.0"];
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[496] | 27 | chambers = [ ["p:sh=1, sx=0.2, sy=0.2, sz=0.2, rz=3.14159265358979,",
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| 28 | "p:0.18421219587326, 0.13, sh=1, sx=0.21, sy=0.21, sz=0.21,",
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| 29 | "p:0.323935478925705, 0.195192575454712, -0.0246672090142965, sh=1, sx=0.2205, sy=0.2205, sz=0.2205,",
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| 30 | "p:0.467822402715683, 0.258204102516174, -0.0246672090142965, sh=1, sx=0.231525, sy=0.231525, sz=0.231525,",
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| 31 | "p:0.664101362228394, 0.309014827013016, -0.0246672090142965, sh=1, sx=0.24310125, sy=0.24310125, sz=0.24310125,",
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| 32 | "p:0.860512733459473, 0.274790525436401, -0.0246672090142965, sh=1, sx=0.2552563125, sy=0.2552563125, sz=0.2552563125,",
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| 33 | "p:1.0273220539093, 0.1655353307724, -0.0246672090142965, sh=1, sx=0.268019128125, sy=0.268019128125, sz=0.268019128125,",
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| 34 | "p:1.13825333118439, -0.000509921927005053, -0.0246672090142965, sh=1, sx=0.28142008453125, sy=0.28142008453125, sz=0.28142008453125,",
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| 35 | "p:1.17569863796234, -0.196833491325378, -0.0246672090142965, sh=1, sx=0.295491088757813, sy=0.295491088757813, sz=0.295491088757813,",
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| 36 | "p:1.13369226455688, -0.392314255237579, -0.0246672090142965, sh=1, sx=0.310265643195703, sy=0.310265643195703, sz=0.310265643195703,"],
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| 37 | ["p:sh=1, sx=0.1, sy=0.1, sz=0.1, rz=3.14159265358979,",
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| 38 | "p:0.110527315735817, -0.0167302016913891, sh=1, sx=0.105, sy=0.105, sz=0.105, rx=3.63519277003091e-33,",
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| 39 | "p:0.207026958465576, -0.080698736011982, 1.17627548103266e-17, sh=1, sx=0.11025, sy=0.11025, sz=0.11025,",
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| 40 | "p:0.271191358566284, -0.169948443770409, 1.17627548103266e-17, sh=1, sx=0.1157625, sy=0.1157625, sz=0.1157625,",
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| 41 | "p:0.291628688573837, -0.286643952131271, 1.17627548103266e-17, sh=1, sx=0.121550625, sy=0.121550625, sz=0.121550625,",
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| 42 | "p:0.264833927154541, -0.403534322977066, 1.17627548103266e-17, sh=1, sx=0.12762815625, sy=0.12762815625, sz=0.12762815625,",
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| 43 | "p:0.194418027997017, -0.500668346881866, 1.17627548103266e-17, sh=1, sx=0.1340095640625, sy=0.1340095640625, sz=0.1340095640625,",
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| 44 | "p:0.091719962656498, -0.562735974788666, 1.17627548103266e-17, sh=1, sx=0.140710042265625, sy=0.140710042265625, sz=0.140710042265625,",
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| 45 | "p:-0.0270438715815544, -0.57991486787796, 1.17627548103266e-17, sh=1, sx=0.147745544378906, sy=0.147745544378906, sz=0.147745544378906,",
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| 46 | "p:-0.143122747540474, -0.549489378929138, 1.17627548103266e-17, sh=1, sx=0.155132821597852, sy=0.155132821597852, sz=0.155132821597852,"]];
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[422] | 47 | }
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[401] | 48 |
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[487] | 49 | function createForamMorphology(morphotype, gen, chamber_num)
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[401] | 50 | {
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[496] | 51 | var geno = "//0\nm:Vstyle=foram\n" + chambers[morphotype][0] + "vr=" + colors[gen];
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[401] | 52 |
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[487] | 53 | chamber_num = Math.min(chamber_num, chambers[morphotype].size - 1);
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[422] | 54 |
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| 55 | for (var i = 0; i < chamber_num; i++)
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| 56 | {
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[496] | 57 | geno += "\n" + chambers[morphotype][i+1] + "vr=" + colors[gen];
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[422] | 58 | }
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| 59 |
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| 60 | for (var i = 0; i < chamber_num; i++)
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| 61 | {
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| 62 | geno += "\n" + "j:"+ i +", "+ (i+1) +", sh=1";
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| 63 | }
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[430] | 64 |
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[422] | 65 | return geno;
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| 66 | }
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| 67 |
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| 68 | function setGenotype(mode)
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| 69 | {
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[554] | 70 | if (mode->opt == "growth")
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[422] | 71 | {
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[554] | 72 | mode->cr.data->genes = mode->parent_genes;
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| 73 | mode->cr.data->lifeparams = mode->parent_lifeparams;
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[422] | 74 | }
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[554] | 75 |
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| 76 | else if (mode->opt == "birth")
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[422] | 77 | {
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[554] | 78 | mode->cr.data->genes = String.deserialize(String.serialize(mode->genes));
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| 79 | 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};
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| 80 |
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[422] | 81 | }
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| 82 | }
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| 83 |
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[479] | 84 | function gametsDivision(parent_energy, energy0)
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| 85 | {
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| 86 | var number = 1;
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| 87 | var result = parent_energy;
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[486] | 88 | while ((result-ExpProperties.divisionCost) >= energy0)
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[479] | 89 | {
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[486] | 90 | result = (result-ExpProperties.divisionCost)/2;
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[479] | 91 | number *= 2;
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| 92 | }
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| 93 | //Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number);
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| 94 | return {"energy" : result, "number" : number};
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| 95 | }
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| 96 |
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[487] | 97 | function getEnergy0(radius)
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| 98 | {
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| 99 | return energyFromVolume(micronsToFrams(radius),1);
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| 100 | }
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| 101 |
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[422] | 102 | function reproduce_haploid(parent, parent2, clone)
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| 103 | {
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[476] | 104 | var number, energy0, new_genes, gen;
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[422] | 105 | if (clone == 1)
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| 106 | {
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[487] | 107 | var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0",0)[0]));
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[479] | 108 | energy0 = offspring->energy;
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| 109 | number = offspring->number;
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[476] | 110 | new_genes = parent.data->genes;
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| 111 | parent.data->lifeparams->gen = 1 - parent.data->lifeparams->gen; //because of reversal of "gen" in createOffspring function
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| 112 | gen = parent.data->lifeparams->gen;
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[422] | 113 | }
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| 114 | else
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| 115 | {
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[487] | 116 | var offspring1 = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[1]));
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| 117 | var offspring2 = gametsDivision(parent2.energy,getEnergy0(getGene(parent2,"energies0", 0)[1]));
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[479] | 118 | energy0 = (offspring1->energy+offspring2->energy);
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[486] | 119 | number = ExpProperties.gametSuccessRate*(offspring1->number+offspring2->number)/2;
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[476] | 120 | new_genes = [parent.data->genes, parent2.data->genes];
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| 121 | gen = 1 - parent.data->lifeparams->gen;
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[493] | 122 |
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| 123 | if (ExpProperties.logging == 1)
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| 124 | {
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| 125 | log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
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| 126 | log(createLogVector(parent2, parent2.energy),ExpProperties.logPref+"repro_energies_log.txt");
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| 127 | log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
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[552] | 128 | log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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| 129 | log(createLogVector(parent2, parent2.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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[493] | 130 | }
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[422] | 131 | }
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| 132 |
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[430] | 133 | Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0);
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[422] | 134 |
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[418] | 135 | for (var j = 0; j < number; j++)
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[401] | 136 | {
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[496] | 137 | createOffspring(createForamMorphology(gen, gen, 0), energy0, new_genes, parent.data->lifeparams);
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[401] | 138 | }
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| 139 | }
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| 140 |
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[418] | 141 | function reproduce_diploid(parent)
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[401] | 142 | {
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[510] | 143 | var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[0]));
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| 144 | var energy0 = offspring->energy;
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| 145 | var number = offspring->number;
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[422] | 146 |
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[493] | 147 | if (ExpProperties.logging == 1)
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| 148 | {
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| 149 | log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
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| 150 | log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
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[552] | 151 | log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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[493] | 152 | }
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| 153 |
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[430] | 154 | Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);
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[422] | 155 |
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[418] | 156 | for (var j = 0; j < number / 2; j++)
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[401] | 157 | {
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[418] | 158 | var crossed = 0;
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| 159 | //crossover
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[486] | 160 | if (Math.rnd01 < ExpProperties.crossprob)
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[418] | 161 | {
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[422] | 162 | crossover(parent, "min_repro_energies");
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[418] | 163 | crossed = 1;
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| 164 | }
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[401] | 165 |
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[418] | 166 | for (var k = 0; k < 2; k++)
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[404] | 167 | {
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[496] | 168 | createOffspring(createForamMorphology(1 - parent.data->lifeparams->gen, 1 - parent.data->lifeparams->gen, 0), energy0, parent.data->genes[0], parent.data->lifeparams);
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[404] | 169 | }
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| 170 |
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[418] | 171 | //reverse of crossover for fossilization
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| 172 | if (crossed == 1)
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[401] | 173 | {
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[422] | 174 | crossover(parent, "min_repro_energies");
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[418] | 175 | crossed = 0;
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[401] | 176 | }
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[418] | 177 |
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[401] | 178 | }
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[404] | 179 | }
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| 180 |
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[422] | 181 | function reproduce_parents(species)
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[404] | 182 | {
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[418] | 183 | var parent1 = null;
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| 184 | var parent2 = null;
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| 185 | var pop = Populations[0];
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| 186 | for (var i = pop.size-1; i >= 0; i--)
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[401] | 187 | {
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[476] | 188 | if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species)
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[418] | 189 | {
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[486] | 190 | if ((pop[i].data->lifeparams->gen==1) || ((pop[i].data->lifeparams->gen==0) && ExpProperties.stress == 0))
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[401] | 191 | {
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[422] | 192 | continue;
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[401] | 193 | }
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[418] | 194 | else if (parent1 == null)
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[401] | 195 | {
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[418] | 196 | parent1 = pop[i];
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[401] | 197 | }
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[418] | 198 | else if (parent2 == null)
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| 199 | {
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| 200 | parent2 = pop[i];
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| 201 | }
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[430] | 202 | if (parent1 != null && parent2 != null)
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[418] | 203 | {
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[479] | 204 | //when parents are ready for reproduction start gametogenesis
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| 205 | if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1)
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| 206 | {
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[554] | 207 | var time = int(secToSimSteps(ExpProperties.gametoPeriodSec));
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[479] | 208 | parent1.data->lifeparams->division_time = time;
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| 209 | parent2.data->lifeparams->division_time = time;
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| 210 | parent1.idleen = 0;
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| 211 | parent2.idleen = 0;
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| 212 | //Simulator.print("parents "+parent1.uid + " " + parent2.uid + " ready to repro: "+Simulator.stepNumber);
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| 213 | }
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| 214 | //when gametogenesis is finished fuse gamets
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| 215 | else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0)
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| 216 | {
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| 217 | reproduce_haploid(parent1, parent2, 0);
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| 218 | print_repro_info(parent1);
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| 219 | print_repro_info(parent2);
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| 220 | pop.kill(parent1);
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| 221 | pop.kill(parent2);
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| 222 | parent1 = null;
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| 223 | parent2 = null;
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| 224 | }
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[430] | 225 | }
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[418] | 226 | }
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[401] | 227 | }
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[422] | 228 | }
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| 229 |
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| 230 | function readyToRepro(cr)
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| 231 | {
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| 232 | var reproduced = 1;
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| 233 |
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| 234 |
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[476] | 235 | if (cr.data->lifeparams->gen == 1)
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[422] | 236 | {
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| 237 | reproduce_diploid(cr);
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[401] | 238 | }
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| 239 |
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[486] | 240 | else if (ExpProperties.stress == 0)
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[401] | 241 | {
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[422] | 242 | reproduce_haploid(cr, null, 1);
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| 243 | }
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| 244 |
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| 245 | else
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| 246 | {
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| 247 | if (cr.signals.size == 0)
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[401] | 248 | {
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[476] | 249 | cr.signals.add("repro"+cr.data->lifeparams->species);
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[422] | 250 | cr.signals[0].power = 1;
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[401] | 251 | }
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[422] | 252 | reproduced = 0;
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[476] | 253 | cr.data->lifeparams->reproduce = 1;
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[401] | 254 | }
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[422] | 255 |
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| 256 | if (reproduced == 1)
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| 257 | {
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| 258 | print_repro_info(cr);
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| 259 | Populations[0].kill(cr);
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| 260 | }
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| 261 |
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| 262 | return reproduced;
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[401] | 263 | }
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| 264 |
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[422] | 265 | function print_repro_info(cr)
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[421] | 266 | {
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[476] | 267 | Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy);
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[422] | 268 | }
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[421] | 269 |
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[422] | 270 | function foramReproduce(cr)
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| 271 | {
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[488] | 272 | var properEnergy = cr.energy >= energyFromVolume(max_chamber_volume[cr.data->lifeparams->gen][getGene(cr, "min_repro_energies",0)[cr.data->lifeparams->gen]],0);
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[487] | 273 | var reproduced = 0;
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[422] | 274 |
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| 275 | //if creature has proper energy
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| 276 | if ( properEnergy && cr.signals.size == 0)
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| 277 | {
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| 278 | //reproduce with probability repro_prob
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[486] | 279 | if (Math.rnd01 <= ExpProperties.repro_prob) //TODO env trigger
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[421] | 280 | {
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[422] | 281 | reproduced = readyToRepro(cr);
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[421] | 282 | }
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[476] | 283 | else if (cr.signals.receive("repro"+cr.data->lifeparams->species) > 0)
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[421] | 284 | {
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[422] | 285 | reproduced = readyToRepro(cr);
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[421] | 286 | }
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[422] | 287 | if (reproduced == 1)
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[430] | 288 | return 1;
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[421] | 289 | }
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| 290 |
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[422] | 291 | else if (!properEnergy)
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[421] | 292 | {
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[422] | 293 | cr.signals.clear();
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[476] | 294 | cr.data->lifeparams->reproduce = 0;
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[421] | 295 | }
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[430] | 296 |
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| 297 | return 0;
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[422] | 298 | }
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[421] | 299 |
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[422] | 300 | function crossover(parent, gene)
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| 301 | {
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[476] | 302 | var tmp = parent.data->genes[0][gene];
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| 303 | parent.data->genes[0][gene] = parent.data->genes[1][gene];
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| 304 | parent.data->genes[1][gene] = tmp;
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[422] | 305 | }
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[421] | 306 |
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[476] | 307 | function createOffspring(geno, energy, parent_genes, parent_lifeparams)
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[422] | 308 | {
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[493] | 309 | curColor = retColors[1-parent_lifeparams->gen];
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[422] | 310 | var cr = Populations[0].add(geno);
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| 311 | cr.energy0 = energy;
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| 312 | cr.energy = cr.energy0;
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[554] | 313 | setGenotype({"opt" : "birth", "cr" : cr, "gen" : 1 - parent_lifeparams->gen, "species" : parent_lifeparams->species, "energy0" : cr.energy0, "genes" : parent_genes});
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[422] | 314 | placeRandomlyNotColliding(cr);
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[421] | 315 | }
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