private static void runSimulationExecutive(
int sim_duration,
int simulation_time_interval,
List<Cell> cell_population,
int cell_doubling_rate) {
int population_size = cell_population.size();
int next_div_time = cell_doubling_rate;
int[][][] diploid_genome =
new int[haploid_number][2]
[2]; // The genome, chromosome->homologous pair->complementary DNA strands
// Progress through time at selected intervals for a specified duration
for (int current_time = 0;
current_time < sim_duration;
current_time += simulation_time_interval) {
Random rand = new Random();
// Perform division of all cells that can divide as determined by a random number generator
// and the set division threshhold
// As new cells are being added to the list, only go through the cells in the population
// before new cells are added i.e use the previous population size as max number of iterations
for (int counter = 0; counter < population_size; counter++) {
if (cell_population.get(counter).getDivisionStatus()) {
// Random number generator, 0 = divide, 1 = don't divide
double coin_flip = rand.nextDouble();
// printString(Double.toString(coin_flip));
if (coin_flip >= 0.5) {
// Remove one cell from the current generation and add two to the next
// by changing the generation of the dividing cell to current_gen + 1 and
// create a new cell object for the next generation
cell_population.get(counter).setGen(cell_population.get(counter).getGen() + 1);
cell_population.add(
new Cell(
id_of_last_created_cell + 1, newest_generation + 1, -1, true, diploid_genome));
id_of_last_created_cell++;
}
} // if the cell can divide
} // for all items in main population array
population_size =
cell_population.size(); // Update the population size after the round of division
newest_generation++; // Update the value of the most recent generation after the division
// round
next_div_time +=
cell_doubling_rate; // Set the next time of division by adding the doubling rate to the
// current time
printString(current_time + " " + population_size);
} // for
} // runSimulationExecutive
public SNoise3(Random rnd) {
for (int i = 0; i < 256; i++) ptab[i] = (byte) i;
for (int i = 0; i < 256; i++) {
int r = rnd.nextInt(256);
byte t = ptab[i];
ptab[i] = ptab[r];
ptab[r] = t;
}
}