135 lines
4.0 KiB
JavaScript
135 lines
4.0 KiB
JavaScript
const CellStates = require("../Organism/Cell/CellStates");
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const Species = require("./Species");
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const FossilRecord = {
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init: function(){
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this.extant_species = [];
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this.extinct_species = [];
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// if an organism has fewer than this cumulative pop, discard them on extinction
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this.min_discard = 10;
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this.record_size_limit = 500; // store this many data points
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},
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setEnv: function(env) {
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this.env = env;
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this.setData();
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},
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addSpecies: function(org, ancestor) {
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// console.log("Adding Species")
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var new_species = new Species(org.anatomy, ancestor, this.env.total_ticks);
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this.extant_species.push(new_species);
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org.species = new_species;
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return new_species;
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},
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addSpeciesObj: function(species) {
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// console.log("Adding Species")
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this.extant_species.push(species);
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return species;
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},
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fossilize: function(species) {
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// console.log("Extinction")
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species.end_tick = this.env.total_ticks;
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for (i in this.extant_species) {
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var s = this.extant_species[i];
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if (s == species) {
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this.extant_species.splice(i, 1);
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if (species.cumulative_pop < this.min_pop) {
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return false;
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}
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// disabled for now, causes memory problems on long runs
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// this.extinct_species.push(s);
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// console.log("Extant species:", this.extant_species.length)
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// console.log("Extinct species:", this.extinct_species.length)
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return true;
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}
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}
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},
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resurrect: function(species) {
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// console.log("Resurrecting species")
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if (species.extinct) {
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for (i in this.extinct_species) {
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var s = this.extinct_species[i];
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if (s == species) {
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this.extinct_species.splice(i, 1);
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this.extant_species.push(species);
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species.extinct = false;
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}
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}
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}
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},
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setData() {
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// all parallel arrays
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this.tick_record = [0];
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this.pop_counts = [0];
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this.species_counts = [0];
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this.av_mut_rates = [0];
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this.av_cells = [0];
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this.av_cell_counts = [this.calcCellCountAverages()];
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},
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updateData() {
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var tick = this.env.total_ticks;
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this.tick_record.push(tick);
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this.pop_counts.push(this.env.organisms.length);
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this.species_counts.push(this.extant_species.length);
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this.av_mut_rates.push(this.env.averageMutability());
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this.calcCellCountAverages();
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if (this.tick_record.length > this.record_size_limit) {
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this.tick_record.shift();
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this.pop_counts.shift();
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this.species_counts.shift();
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this.av_mut_rates.shift();
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this.av_cells.shift();
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this.av_cell_counts.shift();
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}
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},
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calcCellCountAverages() {
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var total_org = 0;
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var cell_counts = {};
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for (let c of CellStates.living) {
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cell_counts[c.name] = 0;
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}
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var first=true;
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for (let s of this.extant_species) {
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if (s.cumulative_pop < this.min_discard && !first){
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continue;
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}
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for (let name in s.cell_counts) {
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cell_counts[name] += s.cell_counts[name] * s.population;
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}
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total_org += s.population;
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first=false;
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}
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if (total_org == 0)
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return cell_counts;
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var total_cells = 0;
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for (let c in cell_counts) {
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total_cells += cell_counts[c];
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cell_counts[c] /= total_org;
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}
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this.av_cells.push(total_cells / total_org);
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this.av_cell_counts.push(cell_counts);
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},
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clear_record: function() {
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this.extant_species = [];
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this.extinct_species = [];
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this.setData();
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},
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}
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FossilRecord.init();
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module.exports = FossilRecord; |