[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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| 9 | var str="//0\n";
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| 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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| 14 | if (i==number_of_chambers-1)
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| 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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[559] | 18 | }
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| 19 | str+="p:sh=1,sx=%g,sy=%g,sz=%g,vr=%s\n" % effectivesize % effectivesize % effectivesize % rgbstring;
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[557] | 20 | if (i>0)
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| 21 | 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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| 22 | size*=growing;
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| 23 | }
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| 24 | return str;
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| 25 | }
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| 26 |
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[422] | 27 | function init_chambers()
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| 28 | {
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| 29 | colors = ["1.0,1.0,0.0","1.0,0.5,0.0"];
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[552] | 30 | retColors = ["1.0,1.0,1.0", "1.0,1.0,0.0"];
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[496] | 31 | chambers = [ ["p:sh=1, sx=0.2, sy=0.2, sz=0.2, rz=3.14159265358979,",
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| 32 | "p:0.18421219587326, 0.13, sh=1, sx=0.21, sy=0.21, sz=0.21,",
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| 33 | "p:0.323935478925705, 0.195192575454712, -0.0246672090142965, sh=1, sx=0.2205, sy=0.2205, sz=0.2205,",
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| 34 | "p:0.467822402715683, 0.258204102516174, -0.0246672090142965, sh=1, sx=0.231525, sy=0.231525, sz=0.231525,",
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| 35 | "p:0.664101362228394, 0.309014827013016, -0.0246672090142965, sh=1, sx=0.24310125, sy=0.24310125, sz=0.24310125,",
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| 36 | "p:0.860512733459473, 0.274790525436401, -0.0246672090142965, sh=1, sx=0.2552563125, sy=0.2552563125, sz=0.2552563125,",
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| 37 | "p:1.0273220539093, 0.1655353307724, -0.0246672090142965, sh=1, sx=0.268019128125, sy=0.268019128125, sz=0.268019128125,",
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| 38 | "p:1.13825333118439, -0.000509921927005053, -0.0246672090142965, sh=1, sx=0.28142008453125, sy=0.28142008453125, sz=0.28142008453125,",
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| 39 | "p:1.17569863796234, -0.196833491325378, -0.0246672090142965, sh=1, sx=0.295491088757813, sy=0.295491088757813, sz=0.295491088757813,",
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| 40 | "p:1.13369226455688, -0.392314255237579, -0.0246672090142965, sh=1, sx=0.310265643195703, sy=0.310265643195703, sz=0.310265643195703,"],
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| 41 | ["p:sh=1, sx=0.1, sy=0.1, sz=0.1, rz=3.14159265358979,",
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| 42 | "p:0.110527315735817, -0.0167302016913891, sh=1, sx=0.105, sy=0.105, sz=0.105, rx=3.63519277003091e-33,",
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| 43 | "p:0.207026958465576, -0.080698736011982, 1.17627548103266e-17, sh=1, sx=0.11025, sy=0.11025, sz=0.11025,",
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| 44 | "p:0.271191358566284, -0.169948443770409, 1.17627548103266e-17, sh=1, sx=0.1157625, sy=0.1157625, sz=0.1157625,",
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| 45 | "p:0.291628688573837, -0.286643952131271, 1.17627548103266e-17, sh=1, sx=0.121550625, sy=0.121550625, sz=0.121550625,",
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| 46 | "p:0.264833927154541, -0.403534322977066, 1.17627548103266e-17, sh=1, sx=0.12762815625, sy=0.12762815625, sz=0.12762815625,",
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| 47 | "p:0.194418027997017, -0.500668346881866, 1.17627548103266e-17, sh=1, sx=0.1340095640625, sy=0.1340095640625, sz=0.1340095640625,",
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| 48 | "p:0.091719962656498, -0.562735974788666, 1.17627548103266e-17, sh=1, sx=0.140710042265625, sy=0.140710042265625, sz=0.140710042265625,",
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| 49 | "p:-0.0270438715815544, -0.57991486787796, 1.17627548103266e-17, sh=1, sx=0.147745544378906, sy=0.147745544378906, sz=0.147745544378906,",
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| 50 | "p:-0.143122747540474, -0.549489378929138, 1.17627548103266e-17, sh=1, sx=0.155132821597852, sy=0.155132821597852, sz=0.155132821597852,"]];
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[422] | 51 | }
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[401] | 52 |
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[487] | 53 | function createForamMorphology(morphotype, gen, chamber_num)
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[401] | 54 | {
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[496] | 55 | var geno = "//0\nm:Vstyle=foram\n" + chambers[morphotype][0] + "vr=" + colors[gen];
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[401] | 56 |
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[487] | 57 | chamber_num = Math.min(chamber_num, chambers[morphotype].size - 1);
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[422] | 58 |
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| 59 | for (var i = 0; i < chamber_num; i++)
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| 60 | {
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[496] | 61 | geno += "\n" + chambers[morphotype][i+1] + "vr=" + colors[gen];
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[422] | 62 | }
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| 63 |
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| 64 | for (var i = 0; i < chamber_num; i++)
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| 65 | {
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| 66 | geno += "\n" + "j:"+ i +", "+ (i+1) +", sh=1";
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| 67 | }
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[430] | 68 |
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[422] | 69 | return geno;
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| 70 | }
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| 71 |
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| 72 | function setGenotype(mode)
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| 73 | {
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[554] | 74 | if (mode->opt == "growth")
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[422] | 75 | {
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[554] | 76 | mode->cr.data->genes = mode->parent_genes;
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| 77 | mode->cr.data->lifeparams = mode->parent_lifeparams;
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[422] | 78 | }
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[554] | 79 |
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| 80 | else if (mode->opt == "birth")
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[422] | 81 | {
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[554] | 82 | mode->cr.data->genes = String.deserialize(String.serialize(mode->genes));
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| 83 | 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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| 84 |
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[422] | 85 | }
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| 86 | }
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| 87 |
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[479] | 88 | function gametsDivision(parent_energy, energy0)
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| 89 | {
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| 90 | var number = 1;
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| 91 | var result = parent_energy;
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[486] | 92 | while ((result-ExpProperties.divisionCost) >= energy0)
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[479] | 93 | {
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[486] | 94 | result = (result-ExpProperties.divisionCost)/2;
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[479] | 95 | number *= 2;
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| 96 | }
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| 97 | //Simulator.print("parent: " + parent_energy + " result: " + result + " number " + number);
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| 98 | return {"energy" : result, "number" : number};
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| 99 | }
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| 100 |
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[487] | 101 | function getEnergy0(radius)
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| 102 | {
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| 103 | return energyFromVolume(micronsToFrams(radius),1);
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| 104 | }
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| 105 |
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[422] | 106 | function reproduce_haploid(parent, parent2, clone)
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| 107 | {
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[476] | 108 | var number, energy0, new_genes, gen;
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[422] | 109 | if (clone == 1)
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| 110 | {
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[487] | 111 | var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0",0)[0]));
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[479] | 112 | energy0 = offspring->energy;
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| 113 | number = offspring->number;
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[476] | 114 | new_genes = parent.data->genes;
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| 115 | parent.data->lifeparams->gen = 1 - parent.data->lifeparams->gen; //because of reversal of "gen" in createOffspring function
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| 116 | gen = parent.data->lifeparams->gen;
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[422] | 117 | }
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| 118 | else
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| 119 | {
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[487] | 120 | var offspring1 = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[1]));
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| 121 | var offspring2 = gametsDivision(parent2.energy,getEnergy0(getGene(parent2,"energies0", 0)[1]));
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[479] | 122 | energy0 = (offspring1->energy+offspring2->energy);
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[486] | 123 | number = ExpProperties.gametSuccessRate*(offspring1->number+offspring2->number)/2;
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[476] | 124 | new_genes = [parent.data->genes, parent2.data->genes];
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| 125 | gen = 1 - parent.data->lifeparams->gen;
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[493] | 126 |
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| 127 | if (ExpProperties.logging == 1)
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| 128 | {
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| 129 | log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
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| 130 | log(createLogVector(parent2, parent2.energy),ExpProperties.logPref+"repro_energies_log.txt");
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| 131 | log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
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[552] | 132 | log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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| 133 | log(createLogVector(parent2, parent2.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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[493] | 134 | }
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[422] | 135 | }
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| 136 |
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[430] | 137 | Simulator.print("haploid number of offspring: " + number + " energ0: " + energy0);
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[422] | 138 |
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[418] | 139 | for (var j = 0; j < number; j++)
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[401] | 140 | {
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[496] | 141 | createOffspring(createForamMorphology(gen, gen, 0), energy0, new_genes, parent.data->lifeparams);
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[401] | 142 | }
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| 143 | }
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| 144 |
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[418] | 145 | function reproduce_diploid(parent)
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[401] | 146 | {
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[510] | 147 | var offspring = gametsDivision(parent.energy,getEnergy0(getGene(parent,"energies0", 0)[0]));
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| 148 | var energy0 = offspring->energy;
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| 149 | var number = offspring->number;
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[422] | 150 |
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[493] | 151 | if (ExpProperties.logging == 1)
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| 152 | {
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| 153 | log(createLogVector(parent, parent.energy),ExpProperties.logPref+"repro_energies_log.txt");
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| 154 | log(createLogVector(parent, number),ExpProperties.logPref+"repro_num_log.txt");
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[552] | 155 | log(createLogVector(parent, parent.lifespan),ExpProperties.logPref+"lifespan_log.txt");
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[493] | 156 | }
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| 157 |
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[430] | 158 | Simulator.print("diploid number of offspring: " + number+ " energ0: " + energy0);
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[422] | 159 |
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[418] | 160 | for (var j = 0; j < number / 2; j++)
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[401] | 161 | {
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[418] | 162 | var crossed = 0;
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| 163 | //crossover
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[486] | 164 | if (Math.rnd01 < ExpProperties.crossprob)
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[418] | 165 | {
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[422] | 166 | crossover(parent, "min_repro_energies");
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[418] | 167 | crossed = 1;
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| 168 | }
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[401] | 169 |
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[418] | 170 | for (var k = 0; k < 2; k++)
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[404] | 171 | {
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[496] | 172 | 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] | 173 | }
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| 174 |
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[418] | 175 | //reverse of crossover for fossilization
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| 176 | if (crossed == 1)
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[401] | 177 | {
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[422] | 178 | crossover(parent, "min_repro_energies");
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[418] | 179 | crossed = 0;
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[401] | 180 | }
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[418] | 181 |
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[401] | 182 | }
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[404] | 183 | }
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| 184 |
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[422] | 185 | function reproduce_parents(species)
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[404] | 186 | {
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[418] | 187 | var parent1 = null;
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| 188 | var parent2 = null;
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| 189 | var pop = Populations[0];
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| 190 | for (var i = pop.size-1; i >= 0; i--)
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[401] | 191 | {
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[476] | 192 | if (pop[i].data->lifeparams->reproduce == 1 && pop[i].data->lifeparams->species == species)
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[418] | 193 | {
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[486] | 194 | if ((pop[i].data->lifeparams->gen==1) || ((pop[i].data->lifeparams->gen==0) && ExpProperties.stress == 0))
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[401] | 195 | {
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[422] | 196 | continue;
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[401] | 197 | }
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[418] | 198 | else if (parent1 == null)
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[401] | 199 | {
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[418] | 200 | parent1 = pop[i];
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[401] | 201 | }
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[418] | 202 | else if (parent2 == null)
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| 203 | {
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| 204 | parent2 = pop[i];
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| 205 | }
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[430] | 206 | if (parent1 != null && parent2 != null)
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[418] | 207 | {
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[479] | 208 | //when parents are ready for reproduction start gametogenesis
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| 209 | if (parent1.data->lifeparams->division_time == -1 && parent2.data->lifeparams->division_time == -1)
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| 210 | {
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[554] | 211 | var time = int(secToSimSteps(ExpProperties.gametoPeriodSec));
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[479] | 212 | parent1.data->lifeparams->division_time = time;
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| 213 | parent2.data->lifeparams->division_time = time;
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| 214 | parent1.idleen = 0;
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| 215 | parent2.idleen = 0;
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| 216 | //Simulator.print("parents "+parent1.uid + " " + parent2.uid + " ready to repro: "+Simulator.stepNumber);
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| 217 | }
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| 218 | //when gametogenesis is finished fuse gamets
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| 219 | else if (parent1.data->lifeparams->division_time == 0 && parent2.data->lifeparams->division_time == 0)
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| 220 | {
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| 221 | reproduce_haploid(parent1, parent2, 0);
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| 222 | print_repro_info(parent1);
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| 223 | print_repro_info(parent2);
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| 224 | pop.kill(parent1);
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| 225 | pop.kill(parent2);
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| 226 | parent1 = null;
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| 227 | parent2 = null;
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| 228 | }
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[430] | 229 | }
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[418] | 230 | }
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[401] | 231 | }
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[422] | 232 | }
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| 233 |
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| 234 | function readyToRepro(cr)
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| 235 | {
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| 236 | var reproduced = 1;
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| 237 |
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| 238 |
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[476] | 239 | if (cr.data->lifeparams->gen == 1)
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[422] | 240 | {
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| 241 | reproduce_diploid(cr);
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[401] | 242 | }
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| 243 |
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[486] | 244 | else if (ExpProperties.stress == 0)
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[401] | 245 | {
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[422] | 246 | reproduce_haploid(cr, null, 1);
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| 247 | }
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| 248 |
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| 249 | else
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| 250 | {
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| 251 | if (cr.signals.size == 0)
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[401] | 252 | {
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[476] | 253 | cr.signals.add("repro"+cr.data->lifeparams->species);
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[422] | 254 | cr.signals[0].power = 1;
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[401] | 255 | }
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[422] | 256 | reproduced = 0;
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[476] | 257 | cr.data->lifeparams->reproduce = 1;
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[401] | 258 | }
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[422] | 259 |
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| 260 | if (reproduced == 1)
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| 261 | {
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| 262 | print_repro_info(cr);
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| 263 | Populations[0].kill(cr);
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| 264 | }
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| 265 |
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| 266 | return reproduced;
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[401] | 267 | }
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| 268 |
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[422] | 269 | function print_repro_info(cr)
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[421] | 270 | {
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[476] | 271 | Simulator.print("Reproduced " + cr.data->lifeparams->gen + " of species " + cr.data->lifeparams->species + " energy: " + cr.energy);
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[422] | 272 | }
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[421] | 273 |
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[422] | 274 | function foramReproduce(cr)
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| 275 | {
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[488] | 276 | 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] | 277 | var reproduced = 0;
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[422] | 278 |
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| 279 | //if creature has proper energy
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| 280 | if ( properEnergy && cr.signals.size == 0)
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| 281 | {
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| 282 | //reproduce with probability repro_prob
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[486] | 283 | if (Math.rnd01 <= ExpProperties.repro_prob) //TODO env trigger
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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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[476] | 287 | else if (cr.signals.receive("repro"+cr.data->lifeparams->species) > 0)
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[421] | 288 | {
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[422] | 289 | reproduced = readyToRepro(cr);
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[421] | 290 | }
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[422] | 291 | if (reproduced == 1)
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[430] | 292 | return 1;
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[421] | 293 | }
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| 294 |
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[422] | 295 | else if (!properEnergy)
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[421] | 296 | {
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[422] | 297 | cr.signals.clear();
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[476] | 298 | cr.data->lifeparams->reproduce = 0;
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[421] | 299 | }
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[430] | 300 |
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| 301 | return 0;
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[422] | 302 | }
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[421] | 303 |
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[422] | 304 | function crossover(parent, gene)
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| 305 | {
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[476] | 306 | var tmp = parent.data->genes[0][gene];
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| 307 | parent.data->genes[0][gene] = parent.data->genes[1][gene];
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| 308 | parent.data->genes[1][gene] = tmp;
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[422] | 309 | }
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[421] | 310 |
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[476] | 311 | function createOffspring(geno, energy, parent_genes, parent_lifeparams)
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[422] | 312 | {
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[493] | 313 | curColor = retColors[1-parent_lifeparams->gen];
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[422] | 314 | var cr = Populations[0].add(geno);
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| 315 | cr.energy0 = energy;
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| 316 | cr.energy = cr.energy0;
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[554] | 317 | 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] | 318 | placeRandomlyNotColliding(cr);
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[421] | 319 | }
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