cacatoo/docs/PoS_classes.js

Building, exploring, and sharing spatially structured models

class Genome {
    // Genome constructor
    constructor() {
        this.uid = genomeIds.next()
        this.total_num_hk = init_es
        this.total_num_ne = init_ne
    }

    initialise(init_hk, init_ne, init_nc, init_tr, init_transposition_rate) {
        this.generation = 1
        this.chromosome = []

        for (let i = 0; i < init_hk; i++) this.chromosome.push(new Gene("G", i))
        for (let i = 0; i < init_ne; i++) this.chromosome.push(new Gene("g", i))
        for (let i = 0; i < init_nc; i++) this.chromosome.push(new Gene(".", 0))
        for (let i = 0; i < init_tr; i++) this.chromosome.push(new Gene("T", 0, init_transposition_rate))
        shuffle(this.chromosome)
        this.calculate_fitness()
    }

    copy(mutate) {
        let child = new Genome()
        child.chromosome = []
        for (let i = 0; i < this.chromosome.length; i++) child.chromosome.push(this.chromosome[i].copy())
        child.generation = this.generation + 1
        child.fitness = this.fitness
        child.nr_tra = this.nr_tra
        if (mutate) child.mutate()

        return child
    }

    calculate_fitness() {
        this.fitness = 1.0

        let hks = [], nes = []
        this.nr_tra = 0
        hks.length = this.total_num_hk
        nes.length = this.total_num_ne
        for (let i = 0; i < this.chromosome.length; i++) {
            let gene = this.chromosome[i]
            switch (gene.type) {
                case "G":
                    hks[gene.func] = 1
                    break
                case "g":
                    nes[gene.func] = 1
                    break
                case "T":
                    this.nr_tra++
                    break
            }
        }

        let hks_present = 0
        for (let i = 0; i < hks.length; i++) if (hks[i] == 1) hks_present++
        for (let i = 0; i < nes.length; i++) if (nes[i] == 1) this.fitness += 0.1
        this.fitness -= this.nr_tra * transposon_fitness_cost
        if (hks_present < this.total_num_hk) this.fitness = 0.0
        this.fitness = Math.max(0,Math.min(this.fitness,1.0))
    }

    mutate() {
        let mutation = false
        for (let i = 0; i < this.chromosome.length; i++) {
            // Mutations with the javascript "splice" function: splice(pos,num_remove,append_this)
            let randomnr = sim.rng.genrand_real1()
            if (randomnr < gene_deletion_rate) {
                this.chromosome.splice(i, 1)                                                               // Single gene deletion (splice 1 off, starting from i, append nothing)
                mutation = true
            }
            else if (randomnr < gene_deletion_rate + gene_duplication_rate) {
                let newgene = this.chromosome[i].copy()
                this.chromosome.splice(i, 0, newgene)                                            // Single gene duplication (splice 0 off, but append the current pos to the array)
                mutation = true
            }
            else if (randomnr < gene_deletion_rate + gene_duplication_rate + gene_deletion_rate) {
                let size = sim.rng.genrand_real1() * this.chromosome.length / 4
                this.chromosome.splice(i, size)                // Tandem deletion (splice up to a fourth of, plus one to ensure the last can be deleted)
                mutation = true
            }
            else if (randomnr < gene_deletion_rate + gene_duplication_rate + gene_deletion_rate + gene_duplication_rate) {
                if (this.chromosome.length > 1000) break
                let size = Math.floor(1 + sim.rng.genrand_real1() * this.chromosome.length / 4)
                if (size > this.chromosome.length) size = this.chromosome.length
                const strand = [...this.chromosome.slice(i, i + size)]
                this.chromosome.splice(i, 0, ...strand)
                i += size
                mutation = true
            }
            else if (randomnr < gene_deletion_rate + gene_duplication_rate + gene_deletion_rate + gene_duplication_rate + gene_inactivation_rate) {
                this.chromosome[i].type = '.'
                mutation = true
            }
            else if (randomnr < gene_deletion_rate + gene_duplication_rate + gene_deletion_rate + gene_duplication_rate + gene_inactivation_rate + phi_mutation_rate) {
                if (this.chromosome[i].type == 'T') {
                    let step = 0.1 * (2 * sim.rng.genrand_real1() - 1)
                    this.chromosome[i].transposition_rate = Math.min(Math.max(0, this.chromosome[i].transposition_rate + step), 1.0)
                    mutation = true
                }

            }
        }
        if (mutation) this.calculate_fitness()
    }
}

class Gene {
    // Gene constructor
    constructor(type, func, transposition_rate) {
        this.uid = geneIds.next()                       // Just so it has a unique identifier, no biological function
        this.type = type                        // Here assigned a string to a gene, being either "essential", "non-essential", "non-coding", or "transposon"
        this.func = func                // A number indicating the function of that gene (e.g. 1 type of each function is necessary for absolutely essential, while non-essential yields incremental benefits)
        this.transposition_rate = transposition_rate || 0.0
    }

    copy() {
        return new Gene(this.type, this.func, this.transposition_rate)
    }
}


/**
 * Shuffles array in place.
 * @param {Array} a items An array containing the items.
 */
function shuffle(a) {
    var j, x, i;
    for (i = a.length - 1; i > 0; i--) {
        j = Math.floor(sim.rng.genrand_real1() * (i + 1));
        x = a[i];
        a[i] = a[j];
        a[j] = x;
    }
    return a;
}

function* idGenerator() {
    let id = 1;
    while (true) {
        yield id
        id++
    }
}
const genomeIds = idGenerator()
const geneIds = idGenerator()