// This program has been placed into the public domain by its author.

import java.util.Random;

public class GeneRepairPloidity {
  final int pop_size = 100;

  final int mutation_attempts_per_generation = this.pop_size * 6;

  Individual[] population;

  int[] time_at_birth;

  final float mutation_rate = 0.5f;

  final int generation_max = 8000;

  int genome_size = 32;

  int time;

  long total_lifespan;

  long total_expressed_defects_at_birth;

  long total_deaths;

  double[] survival_chance;

  boolean sex;

  int ploidity;


  Random random = new Random();

  private void main() {
    this.survival_chance = new double[32];
    log("Zero epistasis: effects of mutations on mortality are independent");
    for (int i = 0; i < 32; i++) {
      this.survival_chance[i] = Math.pow(0.9f, i);
    }
    metaExperiment();

//    //log("Dysergetic epistasis: mutations have diminishing effect on mortality");
//    for (int i = 0; i < 32; i++) {
//      this.survival_chance[i] = 0.1;
//    }
//    this.survival_chance[0] = 1;
//    this.survival_chance[1] = 0.4;
//    this.survival_chance[2] = 0.2;
//    //metaExperiment();
//
//    //log("Dysergetic epistasis: mutations have diminishing effect on mortality");
//    for (int i = 0; i < 32; i++) {
//      this.survival_chance[i] = 1 / (i + 1);
//    }
//    //metaExperiment();
//
//    //log("Synergetic epistasis: mutations have an increasingly negative effect on mortality");
//    for (int i = 0; i < 32; i++) {
//      this.survival_chance[i] = (i < 16) ? 1.0 : 0.0;
//    }
//    //metaExperiment();
//
//    //log("Synergetic epistasis: mutations have an increasingly negative effect on mortality");
//    for (int i = 0; i < 32; i++) {
//      this.survival_chance[i] = 1.0 - i / 33.0;
//    }
//    //metaExperiment();
  }

  private void metaExperiment() {
    this.sex = true;
    this.ploidity = 1;
    experiment("Haploid");
    this.ploidity = 2;
    experiment("Diploid");
    this.ploidity = 3;
    experiment("Polyploid");

    log("-----");
  }

  private void experiment(String name) {
    log(name + " experiment");

    init();
    do {
      iterate();
    } while (this.time < this.generation_max);

    printStats();
  }

  private void init() {
    this.total_lifespan = 0;
    this.total_expressed_defects_at_birth = 0;
    this.total_deaths = 0;

    this.time = 0;

    this.population = new Individual[this.pop_size];
    for (int idx = this.pop_size; --idx >= 0;) {
      this.population[idx] = new Individual(this.genome_size, this.ploidity);
    }
    this.time_at_birth = new int[this.pop_size];
  }

  private void iterate() {
    mutateAll();
    selectionAll();
    this.time++;
  }

  private void selectionAll() {
    for (int idx = this.pop_size; --idx >= 0;) {
      selection(idx);
    }
  }

  private void selection(int idx) {
    int total_bits = getMember(idx).countExpressedDefects();

    double probability = this.random.nextDouble();

    if (this.survival_chance[total_bits] < probability) {
      deathAndReproduce(idx);
    }
  }

  private void deathAndReproduce(int idx) {
    death(idx);
    reproduction(idx);
  }

  private void reproduction(int idx) {
    this.population[idx] = reproduce();
    this.time_at_birth[idx] = this.time;
    this.total_expressed_defects_at_birth += getMember(idx).countExpressedDefects();
  }

  private Individual reproduce() {
    Individual mother = getMember(chooseIndividualAtRandom());
    if (this.sex) {
      return sexual(mother);
    }

    return mother.asexual();
  }

  private Individual getMember(int parent_1) {
    return this.population[parent_1];
  }

  private Individual sexual(Individual mother) {
    Individual father = getMember(chooseIndividualAtRandom());

    return mother.recombine(father);
  }

  private void death(int idx) {
    this.total_deaths++;
    this.total_lifespan += this.time - this.time_at_birth[idx];
  }

  private int chooseIndividualAtRandom() {
    return (int) (this.random.nextFloat() * this.pop_size);
  }

  private void mutateAll() {
    for (int idx = this.mutation_attempts_per_generation; --idx >= 0;) {
      simulateCosmicRays();
    }
  }

  private void simulateCosmicRays() {
    if (this.random.nextFloat() < this.mutation_rate) {
      getMember(chooseIndividualAtRandom()).mutate();
    }
  }

  private void printStats() {
    log("Total number of deaths: " + this.total_deaths);

    log("Average lifespan:"
      + (this.total_lifespan / (float) this.total_deaths));

    log("Average expressed mutations at birth:"
      + (this.total_expressed_defects_at_birth / (float) this.total_deaths));

    log("Average expressed mutations per individual at end of run:"
      + (getFinalExpressedDefectCount() / (float) this.pop_size));
  }

  private int getFinalExpressedDefectCount() {
    int bits = 0;

    for (int idx = this.pop_size; --idx >= 0;) {
      bits += getMember(idx).countExpressedDefects();
    }
    return bits;
  }

  private void log(String s) {
    System.out.println(s);
  }

  public static void main(String args[]) {
    new GeneRepairPloidity().main();
  }
}

//----------------------------------------------------

class Individual {
  int ploidity;
  int genome_size;
  final float mutation_rate = 0.5f;
  ChromosomeSet[] chromosomes_sets;
  Random random = new Random();

  Individual(int genome_size, int ploidity) {
    this.genome_size = genome_size;
    this.ploidity = ploidity;
    this.chromosomes_sets = new ChromosomeSet[this.ploidity];
    for (int idx = this.ploidity; --idx >= 0;) {
      this.chromosomes_sets[idx] = new ChromosomeSet(this.genome_size);
    }
  }

  int countExpressedDefects() {
    int bit_count = 0;
    for (int idx = this.genome_size; --idx >= 0;) {
      if (allGenesAreDefectiveAtLocus(idx)) {
        bit_count++;
      }
    }

    return bit_count;
  }

  boolean allGenesAreDefectiveAtLocus(int i) {
    for (int idx = this.ploidity; --idx >= 0;) {
      if (!this.chromosomes_sets[idx].genome[i]) {
        return false;
      }
    }
    return true;
  }

  void mutate() {
    for (int idx = this.ploidity; --idx >= 0;) {
      if (this.random.nextFloat() > this.mutation_rate) {
        this.chromosomes_sets[idx].mutate();
      }
    }
  }

  Individual asexual() {
    Individual i = new Individual(this.genome_size, this.ploidity);
    for (int idx = this.ploidity; --idx >= 0;) {
      i.chromosomes_sets[idx] = this.chromosomes_sets[idx].asexual();
    }
    return i;
  }

  Individual recombine(Individual mate) {
    Individual i = new Individual(this.genome_size, this.ploidity);
    for (int idx = this.ploidity; --idx >= 0;) {
      int mc = (int)(this.random.nextFloat() * this.ploidity);
      int fc = (int)(this.random.nextFloat() * this.ploidity);

      ChromosomeSet cs_m = this.chromosomes_sets[mc];
      ChromosomeSet cs_f = mate.chromosomes_sets[fc];
      i.chromosomes_sets[idx] = cs_m.recombine(cs_f);
    }
    return i;
  }

  public String toString() {
    String s = "";
    for (int idx = this.ploidity; --idx >= 0;) {
      s += " >> " + this.chromosomes_sets[idx];
    }

    return s;
  }
}

//----------------------------------------------------

class ChromosomeSet {
  Random random = new Random();

  boolean[] genome;

  ChromosomeSet(int genome_size) {
    this.genome = new boolean[genome_size];
  }

  void mutate() {
    int gene_index = (int) (this.random.nextFloat() * this.genome.length);
    this.genome[gene_index] = !this.genome[gene_index];
  }

  ChromosomeSet recombine(ChromosomeSet mate) {
    ChromosomeSet ni = new ChromosomeSet(this.genome.length);
    for (int idx = this.genome.length; --idx >= 0;) {
      boolean mother = (this.random.nextInt() & 1) == 0;
      ni.genome[idx] = mother ? this.genome[idx] : mate.genome[idx];
    }

    return ni;
  }

  ChromosomeSet asexual() {
    ChromosomeSet ni = new ChromosomeSet(this.genome.length);
    for (int idx = this.genome.length; --idx >= 0;) {
      ni.genome[idx] = this.genome[idx];
    }

    return ni;
  }

  public String toString() {
    String s = "";
    for (int idx = this.genome.length; --idx >= 0;) {
      s += " " + this.genome[idx];
    }

    return s;
  }
}