double* matrix_vector_mult(double mat[5][5], double *vec, int rows, int cols)
{ // in matrix form: result = mat * vec;
int i;
for (i = 0; i < rows; i++) {
mult_result[i] = vectors_dot_prod(mat[i], vec, cols);
}
return mult_result;
}
double* matrix_vector_mult(double mat[5][5], double *vec, int rows, int cols)
{ // in matrix form: result = mat * vec;
int i;
double *result = (double*) malloc (cols* sizeof (double));
for (i = 0; i < rows; i++) {
result[i] = vectors_dot_prod(mat[i], vec, cols);
}
return result;
}
static void mv(void *args)
{
struct work_struct *s = args;
int i;
//printf("[%d]MV size = %d, threads = %d \n", s->id, matrixSize, CPUCORES);
for (i = s->id; i < matrixSize; i += CPUCORES){
cc[i][0] = vectors_dot_prod(aa[i], bb);
}
//printf("%d", s->id);
if (s->id)
job_exit();
}
int main () {
time_t time;
srand ((unsigned) (&time));
lineage lin;
lin.generation = (population*) malloc (100000 * sizeof(population));
int count;
double y[5] = {1, 1, 1, 1, 1};
double optimal_phenotype[5] = {10, 5, 10, 0, 5};
int org;
for (org = 0; org < 1; org++) {
for (count = 0; count < 5; count++) {
// lin.generation[0].organism[org].allele[count].gene_size = 10;
// lin.generation[0].organism[org].allele[count].regulator = malloc (lin.generation[0].organism[org].allele[count].gene_size * sizeof(int));
// lin.generation[0].organism[org].allele[count].protein = malloc (lin.generation[0].organism[org].allele[count].gene_size * sizeof(int));
lin.generation[0].organism[org].allele[count].reg_direction = rand()%2;
lin.generation[0].organism[org].allele[count].pro_direction = rand()%2;
int i;
int p_rand[10];
int r_rand[10];
printf ("GENE %d\n", count);
for (i = 0; i < 10; i++) {
p_rand[i] = rand()%4;
r_rand[i] = rand()%4;
lin.generation[0].organism[org].allele[count].regulator[i] = r_rand[i];
lin.generation[0].organism[org].allele[count].protein[i] = p_rand[i];
printf ("%d\t%d\n", lin.generation[0].organism[org].allele[count].regulator[i], lin.generation[0].organism[org].allele[count].protein[i] );
}
}
int h;
int j;
int k;
for (h = 0; h < 5; h++) {
for (j = 0; j < 5; j++) {
for (k = 0; k < 10; k++) {
if (lin.generation[0].organism[org].allele[h].regulator[k] == lin.generation[0].organism[org].allele[j].protein[k]) {
lin.generation[0].organism[org].GRN[h][j] = (lin.generation[0].organism[org].GRN[h][j] + 1);
/* if (lin.generation[0].organism[org].allele[h].reg_direction == 1) {
lin.generation[0].organism[org].GRN[h][j] = (lin.generation[0].organism[org].GRN[h][j] * (-1));
}
*/ }
}
lin.generation[0].organism[org].GRN[h][j] = ((1/50)* ( exp (lin.generation[0].organism[org].GRN[h][j] - 3)));
if (lin.generation[0].organism[org].allele[h].reg_direction == 1) {
lin.generation[0].organism[org].GRN[h][j] = (lin.generation[0].organism[org].GRN[h][j] * (-1));
}
}
}
int q, r;
for (q = 0; q < 5; q++) {
for (r = 0; r < 5; r++) {
printf ("%f ", lin.generation[0].organism[org].GRN[q][r]);
}
printf ("\n");
}
// double *Mat[] = {lin.generation[0].organism[org].GRN[0], lin.generation[0].organism[org].GRN[1], lin.generation[0].organism[org].GRN[2], lin.generation[0].organism[org].GRN[3], lin.generation[0].organism[org].GRN[4]};
int i;
/* double *ans = matrix_vector_mult (Mat, y, 5, 5);
printf ("\n");
for (i = 0; i < 5; i++) {
printf ("%f\n", ans[i]);
}
*/
printf("\nMatrix iteration:\n");
lin.generation[0].organism[org].phenotype = mat_power(lin.generation[0].organism[org].GRN, y, 5, 5, 100);
for (i = 0; i < 5; i++) {
printf ("%f\n", lin.generation[0].organism[org].phenotype[i]);
}
double euc_dist = sqrt (vectors_dot_prod (lin.generation[0].organism[org].phenotype, lin.generation[0].organism[org].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, lin.generation[0].organism[org].phenotype, 5) ) );
printf ("norm = %f\n", euc_dist);
lin.generation[0].organism[org].fitness = exp ((-1) * (euc_dist));
printf ("fitness-%d = %f\n", org, lin.generation[0].organism[org].fitness);
// free(ans);
}
for (int tst = 1; tst < 100; tst++) {
lin.generation[0].organism[tst] = lin.generation[0].organism[0];
}
for (count = 0; count < 5; count ++){
printf( "copy gene %d\n", count);
for (int i = 0; i < 10; i++) {
printf ("%d\t%d\n", lin.generation[0].organism[1].allele[count].regulator[i], lin.generation[0].organism[org].allele[count].protein[i] );
}
}
/* END OF GEN-0 creation --> Next mutate and recombine to make GEN-1 through GEN-N */
int gen;
int hap;
for (gen = 1; gen < 100000; gen ++) {
double fitnesses[100];
for (org = 0; org < 100; org++) {
fitnesses[org] = lin.generation[gen-1].organism[org].fitness;
}
for (org = 0; org < 100; org++) {
int parent1 = weight_rand(fitnesses);
int parent2 = weight_rand(fitnesses);
// printf ("organism %d has parent 1 = %d and parent 2 = %d\n" , org, parent1, parent2);
for (hap = 0; hap < 5; hap++){
if (hap == 0 || hap == 2 || hap == 3) {
lin.generation[gen].organism[org].allele[hap] = lin.generation[gen-1].organism[parent1].allele[hap];
}
if (hap == 1 || hap == 4) {
lin.generation[gen].organism[org].allele[hap] = lin.generation[gen-1].organism[parent2].allele[hap];
}
for (int nuc = 0; nuc < 10; nuc++) {
int mut_reg1 = rand()%1000;
int mut_reg2 = rand()%4;
int mut_pro1 = rand()%1000;
int mut_pro2 = rand()%4;
if (mut_reg1 == 1 && mut_reg2 == 0) {
lin.generation[gen].organism[org].allele[hap].regulator[nuc] = 0;
}
if (mut_reg1 == 1 && mut_reg2 == 1) {
lin.generation[gen].organism[org].allele[hap].regulator[nuc] = 1;
}
if (mut_reg1 == 1 && mut_reg2 == 2) {
lin.generation[gen].organism[org].allele[hap].regulator[nuc] = 2;
}
if (mut_reg1 == 1 && mut_reg2 == 3) {
lin.generation[gen].organism[org].allele[hap].regulator[nuc] = 3;
}
if (mut_pro1 == 1 && mut_pro2 == 0) {
lin.generation[gen].organism[org].allele[hap].protein[nuc] = 0;
}
if (mut_pro1 == 1 && mut_pro2 == 1) {
lin.generation[gen].organism[org].allele[hap].protein[nuc] = 1;
}
if (mut_pro1 == 1 && mut_pro2 == 2) {
lin.generation[gen].organism[org].allele[hap].protein[nuc] = 2;
}
if (mut_pro1 == 1 && mut_pro2 == 3) {
lin.generation[gen].organism[org].allele[hap].protein[nuc] = 3;
}
// printf ("%d\t%d\n", lin.generation[0].organism[0].allele[hap].protein[nuc], lin.generation[gen].organism[org].allele[hap].protein[nuc] );
}
// printf ("\n");
int mut_dir = rand()%1000;
// int mut_dir2 = rand()%10000;
if (mut_dir == 1 && lin.generation[gen].organism[org].allele[hap].reg_direction == 1) {
lin.generation[gen].organism[org].allele[hap].reg_direction = 0;
}
if (mut_dir == 1 && lin.generation[gen].organism[org].allele[hap].reg_direction == 0) {
lin.generation[gen].organism[org].allele[hap].reg_direction = 1;
}
/* if (mut_dir2 == 1 && lin.generation[gen].organism[org].allele[hap].pro_direction %2 == 1) {
lin.generation[gen].organism[org].allele[hap].reg_direction = 0;
}
if (mut_dir2 == 1 && lin.generation[gen].organism[org].allele[hap].pro_direction %2 == 0) {
lin.generation[gen].organism[org].allele[hap].reg_direction = 1;
}
*/
}
int h, j, k;
for (h = 0; h < 5; h++) {
for (j = 0; j < 5; j++) {
for (k = 0; k < 10; k++) {
if (lin.generation[gen].organism[org].allele[h].regulator[k] == lin.generation[gen].organism[org].allele[j].protein[k]) {
lin.generation[gen].organism[org].GRN[h][j] = (lin.generation[gen].organism[org].GRN[h][j] + 1);
/* if (lin.generation[gen].organism[org].allele[h].reg_direction == 1) {
lin.generation[gen].organism[org].GRN[h][j] = (abs (lin.generation[gen].organism[org].GRN[h][j]) * (-1));
}
*/ }
}
// lin.generation[gen].organism[org].GRN[h][j] = ((1/50) * ( exp (lin.generation[gen].organism[org].GRN[h][j] - 3)));
if (lin.generation[gen].organism[org].allele[h].reg_direction == 0) {
lin.generation[gen].organism[org].GRN[h][j] = (lin.generation[gen].organism[org].GRN[h][j] * (-1));
}
}
}
/* don't need pmat now that matrix_vec_mult has mat[5][5] instead **mat now */
// double *pmat[] = {lin.generation[gen].organism[org].GRN[0], lin.generation[gen].organism[org].GRN[1], lin.generation[gen].organism[org].GRN[2], lin.generation[gen].organism[org].GRN[3], lin.generation[gen].organism[org].GRN[4]};
lin.generation[gen].organism[org].phenotype = mat_power (lin.generation[gen].organism[org].GRN, y, 5, 5, 100);
double euc_dist = sqrt (vectors_dot_prod (lin.generation[gen].organism[org].phenotype, lin.generation[gen].organism[org].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, lin.generation[gen].organism[org].phenotype, 5) ) );
// printf ("norm = %f\n", euc_dist);
lin.generation[gen].organism[org].fitness = exp ((-1) * pow ((euc_dist), 1));
if ( gen % 100 == 0 && org == 0 ){
printf ("GENERATION %d fitness-%d = %f\n", gen, org, lin.generation[gen].organism[org].fitness);
int q, r;
for (q = 0; q < 5; q++) {
for (r = 0; r < 5; r++) {
printf ("%f ", lin.generation[gen].organism[org].GRN[q][r]);
}
printf ("\n");
}
/* for (hap = 0; hap < 5; hap++) {
printf ("Gene %d\n", hap);
for (int i = 0; i < 10; i++) {
printf ("%d\t%d\n", lin.generation[gen].organism[org].allele[hap].regulator[i], lin.generation[gen].organism[org].allele[hap].protein[i] );
}
} */
}
}
}
FILE *f;
f = fopen ("long-run-lin1.dat", "wb");
fwrite (lin.generation, sizeof(population), 10000000, f);
fclose(f);
free (lin.generation);
}
int main () {
time_t time;
srand ((unsigned) (&time));
// population pop;
lineage lin;
lin.generation = (population*) malloc (1000000 * sizeof(population));
int count;
double y[5] = {1, 1, 1, 1, 1};
double optimal_phenotype[5] = {1, 1, 1, 1, 1};
int org;
for (org = 0; org < 1; org++) {
int i;
printf ("GENE %d\n", count);
lin.generation[0].organism[org].allele[0].regulator[1] ;
lin.generation[0].organism[org].allele[0].regulator[2] ;
lin.generation[0].organism[org].allele[0].regulator[2] ;
lin.generation[0].organism[org].allele[0].regulator[1] ;
lin.generation[0].organism[org].allele[0].regulator[2] ;
lin.generation[0].organism[org].allele[0].regulator[2] ;
lin.generation[0].organism[org].allele[0].regulator[2] ;
lin.generation[0].organism[org].allele[0].regulator[0] ;
lin.generation[0].organism[org].allele[0].regulator[0] ;
lin.generation[0].organism[org].allele[0].regulator[0] ;
lin.generation[0].organism[org].allele[1].regulator[1] ;
lin.generation[0].organism[org].allele[1].regulator[2] ;
lin.generation[0].organism[org].allele[1].regulator[1] ;
lin.generation[0].organism[org].allele[1].regulator[1] ;
lin.generation[0].organism[org].allele[1].regulator[3] ;
lin.generation[0].organism[org].allele[1].regulator[1] ;
lin.generation[0].organism[org].allele[1].regulator[1] ;
lin.generation[0].organism[org].allele[1].regulator[0] ;
lin.generation[0].organism[org].allele[1].regulator[1] ;
lin.generation[0].organism[org].allele[1].regulator[0] ;
lin.generation[0].organism[org].allele[2].regulator[0] ;
lin.generation[0].organism[org].allele[2].regulator[0] ;
lin.generation[0].organism[org].allele[2].regulator[2] ;
lin.generation[0].organism[org].allele[2].regulator[3] ;
lin.generation[0].organism[org].allele[2].regulator[3] ;
lin.generation[0].organism[org].allele[2].regulator[1] ;
lin.generation[0].organism[org].allele[2].regulator[2] ;
lin.generation[0].organism[org].allele[2].regulator[0] ;
lin.generation[0].organism[org].allele[2].regulator[0] ;
lin.generation[0].organism[org].allele[2].regulator[0] ;
lin.generation[0].organism[org].allele[3].regulator[1] ;
lin.generation[0].organism[org].allele[3].regulator[0] ;
lin.generation[0].organism[org].allele[3].regulator[2] ;
lin.generation[0].organism[org].allele[3].regulator[1] ;
lin.generation[0].organism[org].allele[3].regulator[3] ;
lin.generation[0].organism[org].allele[3].regulator[2] ;
lin.generation[0].organism[org].allele[3].regulator[2] ;
lin.generation[0].organism[org].allele[3].regulator[1] ;
lin.generation[0].organism[org].allele[3].regulator[1] ;
lin.generation[0].organism[org].allele[3].regulator[0] ;
lin.generation[0].organism[org].allele[4].regulator[1] ;
lin.generation[0].organism[org].allele[4].regulator[0] ;
lin.generation[0].organism[org].allele[4].regulator[1] ;
lin.generation[0].organism[org].allele[4].regulator[1] ;
lin.generation[0].organism[org].allele[4].regulator[2] ;
lin.generation[0].organism[org].allele[4].regulator[2] ;
lin.generation[0].organism[org].allele[4].regulator[2] ;
lin.generation[0].organism[org].allele[4].regulator[0] ;
lin.generation[0].organism[org].allele[4].regulator[0] ;
lin.generation[0].organism[org].allele[4].regulator[0] ;
lin.generation[0].organism[org].allele[0].protein[2] ;
lin.generation[0].organism[org].allele[0].protein[1] ;
lin.generation[0].organism[org].allele[0].protein[3] ;
lin.generation[0].organism[org].allele[0].protein[2] ;
lin.generation[0].organism[org].allele[0].protein[1] ;
lin.generation[0].organism[org].allele[0].protein[3] ;
lin.generation[0].organism[org].allele[0].protein[1] ;
lin.generation[0].organism[org].allele[0].protein[2] ;
lin.generation[0].organism[org].allele[0].protein[2] ;
lin.generation[0].organism[org].allele[0].protein[3] ;
lin.generation[0].organism[org].allele[1].protein[2] ;
lin.generation[0].organism[org].allele[1].protein[1] ;
lin.generation[0].organism[org].allele[1].protein[0] ;
lin.generation[0].organism[org].allele[1].protein[2] ;
lin.generation[0].organism[org].allele[1].protein[0] ;
lin.generation[0].organism[org].allele[1].protein[3] ;
lin.generation[0].organism[org].allele[1].protein[3] ;
lin.generation[0].organism[org].allele[1].protein[3] ;
lin.generation[0].organism[org].allele[1].protein[3] ;
lin.generation[0].organism[org].allele[1].protein[3] ;
lin.generation[0].organism[org].allele[2].protein[0] ;
lin.generation[0].organism[org].allele[2].protein[1] ;
lin.generation[0].organism[org].allele[2].protein[0] ;
lin.generation[0].organism[org].allele[2].protein[2] ;
lin.generation[0].organism[org].allele[2].protein[1] ;
lin.generation[0].organism[org].allele[2].protein[3] ;
lin.generation[0].organism[org].allele[2].protein[0] ;
lin.generation[0].organism[org].allele[2].protein[1] ;
lin.generation[0].organism[org].allele[2].protein[3] ;
lin.generation[0].organism[org].allele[2].protein[2] ;
lin.generation[0].organism[org].allele[3].protein[3] ;
lin.generation[0].organism[org].allele[3].protein[1] ;
lin.generation[0].organism[org].allele[3].protein[3] ;
lin.generation[0].organism[org].allele[3].protein[2] ;
lin.generation[0].organism[org].allele[3].protein[2] ;
lin.generation[0].organism[org].allele[3].protein[0] ;
lin.generation[0].organism[org].allele[3].protein[0] ;
lin.generation[0].organism[org].allele[3].protein[3] ;
lin.generation[0].organism[org].allele[3].protein[2] ;
lin.generation[0].organism[org].allele[3].protein[2] ;
lin.generation[0].organism[org].allele[4].protein[2] ;
lin.generation[0].organism[org].allele[4].protein[1] ;
lin.generation[0].organism[org].allele[4].protein[0] ;
lin.generation[0].organism[org].allele[4].protein[0] ;
lin.generation[0].organism[org].allele[4].protein[0] ;
lin.generation[0].organism[org].allele[4].protein[0] ;
lin.generation[0].organism[org].allele[4].protein[3] ;
lin.generation[0].organism[org].allele[4].protein[3] ;
lin.generation[0].organism[org].allele[4].protein[2] ;
lin.generation[0].organism[org].allele[4].protein[1] ;
printf ("%d\t%d\n", lin.generation[0].organism[org].allele[count].regulator[i], lin.generation[0].organism[org].allele[count].protein[i] );
int h;
int j;
int k;
for (h = 0; h < 5; h++) {
for (j = 0; j < 5; j++) {
for (k = 0; k < 10; k++) {
if (lin.generation[0].organism[org].allele[h].regulator[k] == lin.generation[0].organism[org].allele[j].protein[k]) {
lin.generation[0].organism[org].GRN[h][j] = (lin.generation[0].organism[org].GRN[h][j] + 1);
/* if (lin.generation[0].organism[org].allele[h].reg_direction == 1) {
lin.generation[0].organism[org].GRN[h][j] = (lin.generation[0].organism[org].GRN[h][j] * (-1));
}
*/ }
}
/* if ((lin.generation[0].organism[org].allele[h].reg_direction % 2) == (lin.generation[0].organism[org].allele[j].pro_direction % 2)) {
lin.generation[0].organism[org].GRN[h][j] = (lin.generation[0].organism[org].GRN[h][j] * (-1));
}
*/ }
}
int q, r;
for (q = 0; q < 5; q++) {
for (r = 0; r < 5; r++) {
printf ("%f ", lin.generation[0].organism[org].GRN[q][r]);
}
printf ("\n");
}
// double *Mat[] = {lin.generation[0].organism[org].GRN[0], lin.generation[0].organism[org].GRN[1], lin.generation[0].organism[org].GRN[2], lin.generation[0].organism[org].GRN[3], lin.generation[0].organism[org].GRN[4]};
int i;
/* double *ans = matrix_vector_mult (Mat, y, 5, 5);
printf ("\n");
for (i = 0; i < 5; i++) {
printf ("%f\n", ans[i]);
}
*/
printf("\nMatrix iteration:\n");
lin.generation[0].organism[org].phenotype = mat_power(lin.generation[0].organism[org].GRN, y, 5, 5, 2);
for (i = 0; i < 5; i++) {
printf ("%f\n", lin.generation[0].organism[org].phenotype[i]);
}
double euc_dist = sqrt (vectors_dot_prod (lin.generation[0].organism[org].phenotype, lin.generation[0].organism[org].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, lin.generation[0].organism[org].phenotype, 5) ) );
printf ("norm = %f\n", euc_dist);
lin.generation[0].organism[org].fitness = exp ((-1) * (euc_dist));
printf ("fitness-%d = %f\n", org, lin.generation[0].organism[org].fitness);
// free(ans);
}
for (int tst = 1; tst < 100; tst++) {
lin.generation[0].organism[tst] = lin.generation[0].organism[0];
}
/* END OF GEN-0 creation --> Next mutate and recombine to make GEN-1 through GEN-N */
// float sum_of_weight = 0;
// for (int i = 0; i < 10; i++) {
// sum_of_weight += lin.generation[0].organism[i].fitness;
// printf ("sum of weight = %f\n" , sum_of_weight);
// }
// float rnd = fmod((double)rand()/((double)RAND_MAX), sum_of_weight);
// printf ("rnd = %f\n", rnd);
// for (int i = 0; i < 10; i++) {
// if (rnd < lin.generation[0].organism[i].fitness){
// printf ("%d is fit to reproduce\n", i);
// return i;
// break;
// }
// rnd -= lin.generation[0].organism[i].fitness;
// }
int gen;
int hap;
for (gen = 1; gen < 150000; gen ++) {
float fitnesses[100];
for (org = 0; org < 100; org++) {
fitnesses[org] = lin.generation[gen-1].organism[org].fitness;
}
for (org = 0; org < 100; org++) {
int parent1 = weight_rand(fitnesses);
int parent2 = weight_rand(fitnesses);
// printf ("organism %d has parent 1 = %d and parent 2 = %d\n" , org, parent1, parent2);
for (hap = 0; hap < 5; hap++){
if (hap == 0 || hap == 2 || hap == 3) {
lin.generation[gen].organism[org].allele[hap] = lin.generation[gen-1].organism[parent1].allele[hap];
}
if (hap == 1 || hap == 4) {
lin.generation[gen].organism[org].allele[hap] = lin.generation[gen-1].organism[parent2].allele[hap];
}
for (int nuc = 0; nuc < 10; nuc++) {
int mut_reg1 = rand()%10000;
int mut_reg2 = rand()%4;
int mut_pro1 = rand()%10000;
int mut_pro2 = rand()%4;
if (mut_reg1 == 1 && mut_reg2 == 0) {
lin.generation[gen].organism[org].allele[hap].regulator[nuc] = 0;
}
if (mut_reg1 == 1 && mut_reg2 == 1) {
lin.generation[gen].organism[org].allele[hap].regulator[nuc] = 1;
}
if (mut_reg1 == 1 && mut_reg2 == 2) {
lin.generation[gen].organism[org].allele[hap].regulator[nuc] = 2;
}
if (mut_reg1 == 1 && mut_reg2 == 3) {
lin.generation[gen].organism[org].allele[hap].regulator[nuc] = 3;
}
if (mut_pro1 == 1 && mut_pro2 == 0) {
lin.generation[gen].organism[org].allele[hap].protein[nuc] = 0;
}
if (mut_pro1 == 1 && mut_pro2 == 1) {
lin.generation[gen].organism[org].allele[hap].protein[nuc] = 1;
}
if (mut_pro1 == 1 && mut_pro2 == 2) {
lin.generation[gen].organism[org].allele[hap].protein[nuc] = 2;
}
if (mut_pro1 == 1 && mut_pro2 == 3) {
lin.generation[gen].organism[org].allele[hap].protein[nuc] = 3;
}
// printf ("%d\t%d\n", lin.generation[0].organism[0].allele[hap].protein[nuc], lin.generation[gen].organism[org].allele[hap].protein[nuc] );
}
// printf ("\n");
/* int mut_dir = rand()%10000;
int mut_dir2 = rand()%10000;
if (mut_dir == 1 && lin.generation[gen].organism[org].allele[hap].reg_direction %2 == 1) {
lin.generation[gen].organism[org].allele[hap].reg_direction = 0;
}
if (mut_dir == 1 && lin.generation[gen].organism[org].allele[hap].reg_direction %2 == 0) {
lin.generation[gen].organism[org].allele[hap].reg_direction = 1;
}
if (mut_dir2 == 1 && lin.generation[gen].organism[org].allele[hap].pro_direction %2 == 1) {
lin.generation[gen].organism[org].allele[hap].reg_direction = 0;
}
if (mut_dir2 == 1 && lin.generation[gen].organism[org].allele[hap].pro_direction %2 == 0) {
lin.generation[gen].organism[org].allele[hap].reg_direction = 1;
}
*/
}
int h, j, k;
for (h = 0; h < 5; h++) {
for (j = 0; j < 5; j++) {
for (k = 0; k < 10; k++) {
if (lin.generation[gen].organism[org].allele[h].regulator[k] == lin.generation[gen].organism[org].allele[j].protein[k]) {
lin.generation[gen].organism[org].GRN[h][j] = (lin.generation[gen].organism[org].GRN[h][j] + 1);
/* if (lin.generation[gen].organism[org].allele[h].reg_direction == 1) {
lin.generation[gen].organism[org].GRN[h][j] = (abs (lin.generation[gen].organism[org].GRN[h][j]) * (-1));
}
*/ }
}
/* if ((lin.generation[gen].organism[org].allele[h].reg_direction) != (lin.generation[gen].organism[org].allele[j].pro_direction)) {
lin.generation[gen].organism[org].GRN[h][j] = (lin.generation[gen].organism[org].GRN[h][j] * (-1));
}
*/ }
}
/* don't need pmat now that matrix_vec_mult has mat[5][5] instead **mat now */
// double *pmat[] = {lin.generation[gen].organism[org].GRN[0], lin.generation[gen].organism[org].GRN[1], lin.generation[gen].organism[org].GRN[2], lin.generation[gen].organism[org].GRN[3], lin.generation[gen].organism[org].GRN[4]};
lin.generation[gen].organism[org].phenotype = mat_power (lin.generation[gen].organism[org].GRN, y, 5, 5, 2);
double euc_dist = sqrt (vectors_dot_prod (lin.generation[gen].organism[org].phenotype, lin.generation[gen].organism[org].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, lin.generation[gen].organism[org].phenotype, 5) ) );
// printf ("norm = %f\n", euc_dist);
lin.generation[gen].organism[org].fitness = exp ((-1) * (euc_dist));
if ( gen % 1000 == 0 ){
printf ("GENERATION %d fitness-%d = %f\n", gen, org, lin.generation[gen].organism[org].fitness);
int q, r;
for (q = 0; q < 5; q++) {
for (r = 0; r < 5; r++) {
printf ("%f ", lin.generation[gen].organism[org].GRN[q][r]);
}
printf ("\n");
}
}
}
}
free (lin.generation);
}
int main (int argc, char * argv[]) {
time_t time;
srand ((unsigned) (&time));
double y[5] = {1, 1, 1, 1, 1};
double optimal_phenotype[5] = {10, 5, 10, 0, 5};
lineage ancestral_lin;
lineage lin1;
ancestral_lin.generation = (population*) malloc (10000 * sizeof(population));
lin1.generation = (population*) malloc (10000 * sizeof(population));
FILE *op = fopen ("lineage1.dat", "rb");
fread (ancestral_lin.generation, sizeof (population), 10000, op);
lin1.generation[0] = ancestral_lin.generation[9999];
/* END OF GEN-0 creation --> Next mutate and recombine to make GEN-1 through GEN-N */
int gen;
int hap;
for (gen = 1; gen < 10000; gen ++) {
double fitnesses[100];
for (int org = 0; org < 100; org++) {
fitnesses[org] = lin1.generation[gen-1].organism[org].fitness;
}
for (int org = 0; org < 100; org++) {
int parent1 = weight_rand(fitnesses);
int parent2 = weight_rand(fitnesses);
// printf ("organism %d has parent 1 = %d and parent 2 = %d\n" , org, parent1, parent2);
for (hap = 0; hap < 5; hap++){
if (hap == 0 || hap == 2 || hap == 3) {
lin1.generation[gen].organism[org].allele[hap] = lin1.generation[gen-1].organism[parent1].allele[hap];
}
if (hap == 1 || hap == 4) {
lin1.generation[gen].organism[org].allele[hap] = lin1.generation[gen-1].organism[parent2].allele[hap];
}
for (int nuc = 0; nuc < 10; nuc++) {
int mut_reg1 = rand()%10000;
int mut_reg2 = rand()%4;
int mut_pro1 = rand()%10000;
int mut_pro2 = rand()%4;
if (mut_reg1 == 1 && mut_reg2 == 0) {
lin1.generation[gen].organism[org].allele[hap].regulator[nuc] = 0;
}
if (mut_reg1 == 1 && mut_reg2 == 1) {
lin1.generation[gen].organism[org].allele[hap].regulator[nuc] = 1;
}
if (mut_reg1 == 1 && mut_reg2 == 2) {
lin1.generation[gen].organism[org].allele[hap].regulator[nuc] = 2;
}
if (mut_reg1 == 1 && mut_reg2 == 3) {
lin1.generation[gen].organism[org].allele[hap].regulator[nuc] = 3;
}
if (mut_pro1 == 1 && mut_pro2 == 0) {
lin1.generation[gen].organism[org].allele[hap].protein[nuc] = 0;
}
if (mut_pro1 == 1 && mut_pro2 == 1) {
lin1.generation[gen].organism[org].allele[hap].protein[nuc] = 1;
}
if (mut_pro1 == 1 && mut_pro2 == 2) {
lin1.generation[gen].organism[org].allele[hap].protein[nuc] = 2;
}
if (mut_pro1 == 1 && mut_pro2 == 3) {
lin1.generation[gen].organism[org].allele[hap].protein[nuc] = 3;
}
// printf ("%d\t%d\n", lin1.generation[0].organism[0].allele[hap].protein[nuc], lin1.generation[gen].organism[org].allele[hap].protein[nuc] );
}
// printf ("\n");
int mut_dir = rand()%10000;
// int mut_dir2 = rand()%10000;
if (mut_dir == 1 && lin1.generation[gen].organism[org].allele[hap].reg_direction == 1) {
lin1.generation[gen].organism[org].allele[hap].reg_direction = 0;
}
if (mut_dir == 1 && lin1.generation[gen].organism[org].allele[hap].reg_direction == 0) {
lin1.generation[gen].organism[org].allele[hap].reg_direction = 1;
}
/* if (mut_dir2 == 1 && lin1.generation[gen].organism[org].allele[hap].pro_direction %2 == 1) {
lin1.generation[gen].organism[org].allele[hap].reg_direction = 0;
}
if (mut_dir2 == 1 && lin1.generation[gen].organism[org].allele[hap].pro_direction %2 == 0) {
lin1.generation[gen].organism[org].allele[hap].reg_direction = 1;
}
*/
}
int h, j, k;
for (h = 0; h < 5; h++) {
for (j = 0; j < 5; j++) {
lin1.generation[gen].organism[org].GRN[h][j] = 0;
for (k = 0; k < 10; k++) {
if (lin1.generation[gen].organism[org].allele[h].regulator[k] == lin1.generation[gen].organism[org].allele[j].protein[k]) {
lin1.generation[gen].organism[org].GRN[h][j] = (lin1.generation[gen].organism[org].GRN[h][j] + 1);
/* if (lin1.generation[gen].organism[org].allele[h].reg_direction == 1) {
lin1.generation[gen].organism[org].GRN[h][j] = (abs (lin1.generation[gen].organism[org].GRN[h][j]) * (-1));
}
*/ }
}
// lin1.generation[gen].organism[org].GRN[h][j] = ((1/50) * ( exp (lin1.generation[gen].organism[org].GRN[h][j] - 3)));
if (lin1.generation[gen].organism[org].allele[h].reg_direction == 0) {
lin1.generation[gen].organism[org].GRN[h][j] = (lin1.generation[gen].organism[org].GRN[h][j] * (-1));
}
}
}
lin1.generation[gen].organism[org].phenotype = mat_power (lin1.generation[gen].organism[org].GRN, y, 5, 5, 100);
double euc_dist = sqrt (vectors_dot_prod (lin1.generation[gen].organism[org].phenotype, lin1.generation[gen].organism[org].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, lin1.generation[gen].organism[org].phenotype, 5) ) );
// printf ("norm = %f\n", euc_dist);
lin1.generation[gen].organism[org].fitness = exp ((-1) * pow ((euc_dist), 2));
if ( gen % 100 == 0 && org == 0 ){
printf ("GENERATION %d fitness-%d = %f\n", gen, org, lin1.generation[gen].organism[org].fitness);
int q, r;
for (q = 0; q < 5; q++) {
for (r = 0; r < 5; r++) {
printf ("%f ", lin1.generation[gen].organism[org].GRN[q][r]);
}
printf ("\n");
}
/* for (hap = 0; hap < 5; hap++) {
printf ("Gene %d\n", hap);
for (int i = 0; i < 10; i++) {
printf ("%d\t%d\n", lin1.generation[gen].organism[org].allele[hap].regulator[i], lin1.generation[gen].organism[org].allele[hap].protein[i] );
}
} */
}
}
}
FILE *f;
f = fopen (argv[1], "wb");
fwrite (lin1.generation, sizeof(population), 10000, f);
fclose(f);
free (lin1.generation);
}
int main () {
double meanfit;
double meanfit1;
double meanfit2;
FILE *fit;
fit = fopen ("fitness.dat", "w");
FILE *flocation;
flocation = fopen("location.dat", "w");
FILE *hybridfit;
hybridfit = fopen ("Hybrid_Fitnesses.txt", "w");
FILE *allo1fit;
allo1fit = fopen("Allo1_Fitness.txt", "w");
FILE *allo2fit;
allo2fit = fopen("Allo2_Fitness.txt", "w");
time_t time;
srand ((unsigned) (&time));
/* "time_t" above ensures better random number generation since it uses time.
*/
//lineage lin;
//lin.generation = (population*) malloc (N * sizeof(population));
/* Assigning a lineage struct to to "lin"
* lin.generation is an array of 1,000,000 populations.
*/
population currpop;
population prevpop;
population allo1curr;
population allo1prev;
population allo2curr;
population allo2prev;
int count;
double y[5]; // = {1, 1, 1, 1, 1};
double optimal_phenotype[5]; // = {2, 2, 2, 2, 2};
for (int ph = 0; ph < 5; ph++)
{
y[ph] = ((double) rand()/(double) RAND_MAX)*(rand()%10);
optimal_phenotype[ph] = ((double) rand()/(double) RAND_MAX)*(rand()%10);
}
/* y[5] is a 5 dimensional initial vector.
* Interpreted as the "environment."
*/
/* the below for loop generates ONLY the first generation (currpop) of the simulation.
* All individuals in this generation are identical and random.
*/
currpop.organism[0].location = 0;
for (count = 0; count < 5; count++) {
currpop.organism[0].allele[count].reg_direction = rand()%2;
currpop.organism[0].allele[count].pro_direction = rand()%2;
int i;
int p_rand[g];
int r_rand[g];
printf ("GENE %d\n", count);
for (i = 0; i < g; i++) {
p_rand[i] = rand()%4;
r_rand[i] = rand()%4;
currpop.organism[0].allele[count].regulator[i] = r_rand[i];
currpop.organism[0].allele[count].protein[i] = p_rand[i];
printf ("%d\t%d\n", currpop.organism[0].allele[count].regulator[i], currpop.organism[0].allele[count].protein[i] );
}
}
int h;
int j;
int k;
for (h = 0; h < 5; h++) {
for (j = 0; j < 5; j++) {
for (k = 0; k < g; k++) {
if (currpop.organism[0].allele[h].regulator[k] == currpop.organism[0].allele[j].protein[k]) {
currpop.organism[0].GRN[h][j] = (currpop.organism[0].GRN[h][j]) + 1;
/* if (currpop.organism[org].allele[h].reg_direction == 1) {
currpop.organism[org].GRN[h][j] = (currpop.organism[org].GRN[h][j] * (-1));
}
*/ }
}
if (currpop.organism[0].allele[h].reg_direction == currpop.organism[0].allele[j].pro_direction) {
currpop.organism[0].GRN[h][j] = (currpop.organism[0].GRN[h][j] * (-1));
}
}
}
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
// currpop.organism[org].GRN[h][j] = pow(0.5 + (exp(6 - currpop.organism[org].GRN[h][j]))/5, -1);
if (currpop.organism[0].allele[h].reg_direction == 1)
{
currpop.organism[0].GRN[h][j] = (currpop.organism[0].GRN[h][j] * (-1));
}
}
}
int q, r;
for (q = 0; q < 5; q++) {
for (r = 0; r < 5; r++) {
printf ("%f ", currpop.organism[0].GRN[q][r]);
}
printf ("\n");
}
// double *Mat[] = {currpop.organism[org].GRN[0], currpop.organism[org].GRN[1], currpop.organism[org].GRN[2], currpop.organism[org].GRN[3], currpop.organism[org].GRN[4]};
int i;
/* double *ans = matrix_vector_mult (Mat, y, 5, 5);
printf ("\n");
for (i = 0; i < 5; i++) {
printf ("%f\n", ans[i]);
}
*/
printf("\nMatrix iteration:\n");
currpop.organism[0].phenotype = mat_power(currpop.organism[0].GRN, y, 5, 5, 10);
for (i = 0; i < 5; i++) {
printf ("%f\n", currpop.organism[0].phenotype[i]);
}
double euc_dist = sqrt (vectors_dot_prod (currpop.organism[0].phenotype, currpop.organism[0].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, currpop.organism[0].phenotype, 5) ) );
printf ("norm = %f\n", euc_dist);
currpop.organism[0].fitness = exp ((-1) * (pow(euc_dist, 2)));
printf ("fitness-%d = %f\n", 0, currpop.organism[0].fitness);
// free(ans);
for (int tst = 1; tst < pop; tst++) {
currpop.organism[tst] = currpop.organism[0];
}
for (count = 0; count < 5; count ++){
printf( "copy gene %d\n", count);
for (int i = 0; i < g; i++) {
printf ("%d\t%d\n", currpop.organism[1].allele[count].regulator[i], currpop.organism[0].allele[count].protein[i] );
}
}
/***************************** Simulation after initial (0th) generation *************************
*
* Generations gen = 1 through gen = 100,000.
*/
int gen;
int hap;
for (gen = 1; gen < N; gen ++) {
prevpop = currpop;
int org;
meanfit = 0;
double fitnesses[pop];
// if (gen % 20000 == 0)
// {
// for (int ph = 0; ph < 5; ph++)
// {
// optimal_phenotype[ph] = ((double) rand()/(double) RAND_MAX) * (rand()%10);
// }
// }
for (org = 0; org < pop; org++) {
fitnesses[org] = prevpop.organism[org].fitness;
// printf ("org %d fitness - %f\n ", org, fitnesses[org]);
}
for (org = 0; org < pop; org++) {
int parent1 = weight_rand(fitnesses);
//printf("gen-%d org-%d parent-%d\n", gen, org, parent1);
// int geog[pop];
// for (int loc = 0; loc < pop; loc++)
// {
// geog[loc] = abs(prevpop.organism[parent1].location - prevpop.organism[loc].location);
// }
// int parent2 = geography_rand(fitnesses, geog);
int parent2 = weight_rand(fitnesses);
// printf ("organism %d has parent 1 = %d and parent 2 = %d\n" , org, parent1, parent2);
for (hap = 0; hap < 5; hap++){
int rec = rand()%2;
// if (org < (pop/2))
// {
// currpop.organism[org].allele[hap] = prevpop.organism[parent1].allele[hap];
// }
if (/* org > (pop/2) && */rec == 0) {
currpop.organism[org].allele[hap] = prevpop.organism[parent1].allele[hap];
currpop.organism[org].allele[hap].reg_direction = prevpop.organism[parent1].allele[hap].reg_direction;
currpop.organism[org].allele[hap].pro_direction = prevpop.organism[parent1].allele[hap].pro_direction;
}
if (/* org > (pop/2) && */rec == 1) {
currpop.organism[org].allele[hap] = prevpop.organism[parent2].allele[hap];
currpop.organism[org].allele[hap].reg_direction = prevpop.organism[parent2].allele[hap].reg_direction;
currpop.organism[org].allele[hap].pro_direction = prevpop.organism[parent2].allele[hap].pro_direction;
}
for (int nuc = 0; nuc < g; nuc++) {
int mut_reg1 = rand()%mutate;
int mut_reg2 = rand()%4;
int mut_pro1 = rand()%mutate;
int mut_pro2 = rand()%4;
if (mut_reg1 == 1 && mut_reg2 == 0) {
currpop.organism[org].allele[hap].regulator[nuc] = 0;
}
if (mut_reg1 == 1 && mut_reg2 == 1) {
currpop.organism[org].allele[hap].regulator[nuc] = 1;
}
if (mut_reg1 == 1 && mut_reg2 == 2) {
currpop.organism[org].allele[hap].regulator[nuc] = 2;
}
if (mut_reg1 == 1 && mut_reg2 == 3) {
currpop.organism[org].allele[hap].regulator[nuc] = 3;
}
if (mut_pro1 == 1 && mut_pro2 == 0) {
currpop.organism[org].allele[hap].protein[nuc] = 0;
}
if (mut_pro1 == 1 && mut_pro2 == 1) {
currpop.organism[org].allele[hap].protein[nuc] = 1;
}
if (mut_pro1 == 1 && mut_pro2 == 2) {
currpop.organism[org].allele[hap].protein[nuc] = 2;
}
if (mut_pro1 == 1 && mut_pro2 == 3) {
currpop.organism[org].allele[hap].protein[nuc] = 3;
}
// printf ("%d\t%d\n", currpop.organism[0].allele[hap].protein[nuc], currpop.organism[org].allele[hap].protein[nuc] );
}
// printf ("\n");
int mut_dir = rand()%mutate;
int mut_dir2 = rand()%mutate;
if (mut_dir == 1 && currpop.organism[org].allele[hap].reg_direction == 1) {
currpop.organism[org].allele[hap].reg_direction = 0;
}
else if (mut_dir == 1 && currpop.organism[org].allele[hap].reg_direction == 0) {
currpop.organism[org].allele[hap].reg_direction = 1;
}
if (mut_dir2 == 1 && currpop.organism[org].allele[hap].pro_direction == 1) {
currpop.organism[org].allele[hap].pro_direction = 0;
}
else if (mut_dir2 == 1 && currpop.organism[org].allele[hap].pro_direction == 0) {
currpop.organism[org].allele[hap].pro_direction = 1;
}
}
// int mig_rand = rand()%3;
// int mig_dist;
// if (mig_rand == 0)
// {
// mig_dist = 0;
// }
// if (mig_rand == 1)
// {
// mig_dist = 1;
// }
// if (mig_rand == 2)
// {
// mig_dist = -1;
// }
// currpop.organism[org].location = prevpop.organism[parent1].location + mig_dist;
// if (gen % 100 == 0)
// {
// fprintf (flocation, "%d,", currpop.organism[org].location);
// if (org == (pop-1))
// {
// fprintf(flocation, "\n");
// }
// }
int h, j, k;
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
currpop.organism[org].GRN[h][j] = 0;
}
}
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
for (k = 0; k < g; k++)
{
if (currpop.organism[org].allele[h].regulator[k] == currpop.organism[org].allele[j].protein[k])
{
currpop.organism[org].GRN[h][j] = (currpop.organism[org].GRN[h][j] + 0.001);
}
}
// if (currpop.organism[org].allele[h].reg_direction == 0)
// {
// currpop.organism[org].GRN[h][j] = (currpop.organism[org].GRN[h][j] * (-1));
// }
}
}
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
// currpop.organism[org].GRN[h][j] = pow(0.5 + (exp(6 - currpop.organism[org].GRN[h][j]))/5, -1);
if (currpop.organism[org].allele[h].reg_direction != currpop.organism[org].allele[j].pro_direction)
{
currpop.organism[org].GRN[h][j] = (currpop.organism[org].GRN[h][j] * (-1));
}
}
}
/* don't need pmat now that matrix_vec_mult has mat[5][5] instead **mat now */
// double *pmat[] = {currpop.organism[org].GRN[0], currpop.organism[org].GRN[1], currpop.organism[org].GRN[2], currpop.organism[org].GRN[3], currpop.organism[org].GRN[4]};
currpop.organism[org].phenotype = mat_power (currpop.organism[org].GRN, y, 5, 5, 100);
double euc_dist = sqrt (vectors_dot_prod (currpop.organism[org].phenotype, currpop.organism[org].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, currpop.organism[org].phenotype, 5) ) );
// printf ("norm = %f\n", euc_dist);
currpop.organism[org].fitness = exp (((-1) * (pow ((euc_dist), 2))));
if (currpop.organism[org].fitness <= 0.0000001)
{
currpop.organism[org].fitness = 0.0000001;
}
/* if (currpop.organism[org].fitness <= 0.000001)
{
currpop.organism[org].fitness = 0.000001;
}*/
if ( (gen == 1 || gen % 1000 == 0) && org == 1 ){
printf ("GENERATION %d fitness-%d = %f\n", gen, org, currpop.organism[org].fitness);
int q, r;
for (q = 0; q < 5; q++) {
for (r = 0; r < 5; r++) {
printf ("%f ", currpop.organism[org].GRN[q][r]);
}
printf ("\n");
}
/* for (hap = 0; hap < 5; hap++) {
printf ("Gene %d\n", hap);
for (int i = 0; i < g; i++) {
printf ("%d\t%d\n", currpop.organism[org].allele[hap].regulator[i], currpop.organism[org].allele[hap].protein[i] );
}
} */
}
meanfit += currpop.organism[org].fitness*0.01;
if (gen % 1 == 0)
{
if (org == (pop - 1))
{
fprintf (fit, "%f\n,", meanfit);
}
}
}
}
lineage allo1;
lineage allo2;
allo1.generation = malloc (isolate * sizeof(population));
allo2.generation = malloc (isolate * sizeof(population));
allo1curr = currpop;
allo2curr = currpop;
for (int gee = 0; gee < isolate; gee ++) {
meanfit1 = 0;
allo1prev = allo1curr;
int org;
double fitnesses[pop];
for (int org = 0; org < pop; org++) {
fitnesses[org] = allo1prev.organism[org].fitness;
// printf ("org %d fitness - %f\n ", org, fitnesses[org]);
}
for (org = 0; org < pop; org++) {
int parent1 = weight_rand(fitnesses);
int parent2 = weight_rand(fitnesses);
for (hap = 0; hap < 5; hap++){
int rec = rand()%2;
if (/* org > (pop/2) && */rec == 0) {
allo1curr.organism[org].allele[hap] = allo1prev.organism[parent1].allele[hap];
}
if (/* org > (pop/2) && */rec == 1) {
allo1curr.organism[org].allele[hap] = allo1prev.organism[parent2].allele[hap];
}
for (int nuc = 0; nuc < g; nuc++) {
int mut_reg1 = rand()%mutate;
int mut_reg2 = rand()%4;
int mut_pro1 = rand()%mutate;
int mut_pro2 = rand()%4;
if (mut_reg1 == 1 && mut_reg2 == 0) {
allo1curr.organism[org].allele[hap].regulator[nuc] = 0;
}
if (mut_reg1 == 1 && mut_reg2 == 1) {
allo1curr.organism[org].allele[hap].regulator[nuc] = 1;
}
if (mut_reg1 == 1 && mut_reg2 == 2) {
allo1curr.organism[org].allele[hap].regulator[nuc] = 2;
}
if (mut_reg1 == 1 && mut_reg2 == 3) {
allo1curr.organism[org].allele[hap].regulator[nuc] = 3;
}
if (mut_pro1 == 1 && mut_pro2 == 0) {
allo1curr.organism[org].allele[hap].protein[nuc] = 0;
}
if (mut_pro1 == 1 && mut_pro2 == 1) {
allo1curr.organism[org].allele[hap].protein[nuc] = 1;
}
if (mut_pro1 == 1 && mut_pro2 == 2) {
allo1curr.organism[org].allele[hap].protein[nuc] = 2;
}
if (mut_pro1 == 1 && mut_pro2 == 3) {
allo1curr.organism[org].allele[hap].protein[nuc] = 3;
}
// printf ("%d\t%d\n", allo1curr.organism[0].allele[hap].protein[nuc], allo1curr.organism[org].allele[hap].protein[nuc] );
}
// printf ("\n");
int mut_dir = rand()%mutate;
int mut_dir2 = rand()%mutate;
if (mut_dir == 1 && allo1curr.organism[org].allele[hap].reg_direction == 1) {
allo1curr.organism[org].allele[hap].reg_direction = 0;
}
else if (mut_dir == 1 && allo1curr.organism[org].allele[hap].reg_direction == 0) {
allo1curr.organism[org].allele[hap].reg_direction = 1;
}
if (mut_dir2 == 1 && allo1curr.organism[org].allele[hap].pro_direction == 1) {
allo1curr.organism[org].allele[hap].pro_direction = 0;
}
else if (mut_dir2 == 1 && allo1curr.organism[org].allele[hap].pro_direction == 0) {
allo1curr.organism[org].allele[hap].pro_direction = 1;
}
}
int h, j, k;
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
allo1curr.organism[org].GRN[h][j] = 0;
}
}
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
for (k = 0; k < g; k++)
{
if (allo1curr.organism[org].allele[h].regulator[k] == allo1curr.organism[org].allele[j].protein[k])
{
allo1curr.organism[org].GRN[h][j] = (allo1curr.organism[org].GRN[h][j] + 0.001);
}
}
// if (allo1curr.organism[org].allele[h].reg_direction == 0)
// {
// allo1curr.organism[org].GRN[h][j] = (allo1curr.organism[org].GRN[h][j] * (-1));
// }
}
}
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
// allo1curr.organism[org].GRN[h][j] = pow(0.5 + (exp(6 - allo1curr.organism[org].GRN[h][j]))/5, -1);
if (allo1curr.organism[org].allele[h].reg_direction != allo1curr.organism[org].allele[j].pro_direction)
{
allo1curr.organism[org].GRN[h][j] = (allo1curr.organism[org].GRN[h][j] * (-1));
}
}
}
/* don't need pmat now that matrix_vec_mult has mat[5][5] instead **mat now */
// double *pmat[] = {allo1curr.organism[org].GRN[0], allo1curr.organism[org].GRN[1], allo1curr.organism[org].GRN[2], allo1curr.organism[org].GRN[3], allo1curr.organism[org].GRN[4]};
allo1curr.organism[org].phenotype = mat_power (allo1curr.organism[org].GRN, y, 5, 5, 100);
double euc_dist = sqrt (vectors_dot_prod (allo1curr.organism[org].phenotype, allo1curr.organism[org].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, allo1curr.organism[org].phenotype, 5) ) );
allo1curr.organism[org].fitness = exp (((-1) * (pow ((euc_dist), 2))));
if (allo1curr.organism[org].fitness <= 0.0000001)
{
allo1curr.organism[org].fitness = 0.0000001;
}
meanfit1 += allo1curr.organism[org].fitness*0.01;
if (gee % 1 == 0)
{
if (org == (pop - 1))
{
fprintf (allo1fit, "%f\n,", meanfit1);
}
}
if ( (gee == 1 || gee % 1000 == 0) && org == 1 ){
printf ("geeERATION %d fitness-%d = %f\n", gee, org, allo1curr.organism[org].fitness);
int q, r;
for (q = 0; q < 5; q++) {
for (r = 0; r < 5; r++) {
printf ("%f ", allo1curr.organism[org].GRN[q][r]);
}
printf ("\n");
}
}
}
allo1.generation[gee].organism[0] = allo1curr.organism[0];
}
for (int eeg = 0; eeg < isolate; eeg ++) {
meanfit2=0;
allo2prev = allo2curr;
int org;
meanfit = 0;
double fitnesses[pop];
for (org = 0; org < pop; org++) {
fitnesses[org] = allo2prev.organism[org].fitness;
}
for (org = 0; org < pop; org++) {
int parent1 = weight_rand(fitnesses);
int parent2 = weight_rand(fitnesses);
for (hap = 0; hap < 5; hap++){
int rec = rand()%2;
if (rec == 0) {
allo2curr.organism[org].allele[hap] = allo2prev.organism[parent1].allele[hap];
allo2curr.organism[org].allele[hap].reg_direction = allo2prev.organism[parent1].allele[hap].reg_direction;
allo2curr.organism[org].allele[hap].pro_direction = allo2prev.organism[parent1].allele[hap].pro_direction;
}
if (rec == 1) {
allo2curr.organism[org].allele[hap] = allo2prev.organism[parent2].allele[hap];
allo2curr.organism[org].allele[hap].reg_direction = allo2prev.organism[parent2].allele[hap].reg_direction;
allo2curr.organism[org].allele[hap].pro_direction = allo2prev.organism[parent2].allele[hap].pro_direction;
}
for (int nuc = 0; nuc < g; nuc++) {
int mut_reg1 = rand()%mutate;
int mut_reg2 = rand()%4;
int mut_pro1 = rand()%mutate;
int mut_pro2 = rand()%4;
if (mut_reg1 == 1 && mut_reg2 == 0) {
allo2curr.organism[org].allele[hap].regulator[nuc] = 0;
}
if (mut_reg1 == 1 && mut_reg2 == 1) {
allo2curr.organism[org].allele[hap].regulator[nuc] = 1;
}
if (mut_reg1 == 1 && mut_reg2 == 2) {
allo2curr.organism[org].allele[hap].regulator[nuc] = 2;
}
if (mut_reg1 == 1 && mut_reg2 == 3) {
allo2curr.organism[org].allele[hap].regulator[nuc] = 3;
}
if (mut_pro1 == 1 && mut_pro2 == 0) {
allo2curr.organism[org].allele[hap].protein[nuc] = 0;
}
if (mut_pro1 == 1 && mut_pro2 == 1) {
allo2curr.organism[org].allele[hap].protein[nuc] = 1;
}
if (mut_pro1 == 1 && mut_pro2 == 2) {
allo2curr.organism[org].allele[hap].protein[nuc] = 2;
}
if (mut_pro1 == 1 && mut_pro2 == 3) {
allo2curr.organism[org].allele[hap].protein[nuc] = 3;
}
}
int mut_dir = rand()%mutate;
int mut_dir2 = rand()%mutate;
if (mut_dir == 1 && allo2curr.organism[org].allele[hap].reg_direction == 1) {
allo2curr.organism[org].allele[hap].reg_direction = 0;
}
else if (mut_dir == 1 && allo2curr.organism[org].allele[hap].reg_direction == 0) {
allo2curr.organism[org].allele[hap].reg_direction = 1;
}
if (mut_dir2 == 1 && allo2curr.organism[org].allele[hap].pro_direction == 1) {
allo2curr.organism[org].allele[hap].pro_direction = 0;
}
else if (mut_dir2 == 1 && allo2curr.organism[org].allele[hap].pro_direction == 0) {
allo2curr.organism[org].allele[hap].pro_direction = 1;
}
}
int h, j, k;
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
allo2curr.organism[org].GRN[h][j] = 0;
}
}
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
for (k = 0; k < g; k++)
{
if (allo2curr.organism[org].allele[h].regulator[k] == allo2curr.organism[org].allele[j].protein[k])
{
allo2curr.organism[org].GRN[h][j] = (allo2curr.organism[org].GRN[h][j] + 0.001);
}
}
}
}
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
if (allo2curr.organism[org].allele[h].reg_direction != allo2curr.organism[org].allele[j].pro_direction)
{
allo2curr.organism[org].GRN[h][j] = (allo2curr.organism[org].GRN[h][j] * (-1));
}
}
}
allo2curr.organism[org].phenotype = mat_power (allo2curr.organism[org].GRN, y, 5, 5, 100);
double euc_dist = sqrt (vectors_dot_prod (allo2curr.organism[org].phenotype, allo2curr.organism[org].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, allo2curr.organism[org].phenotype, 5) ) );
allo2curr.organism[org].fitness = exp (((-1) * (pow ((euc_dist), 2))));
if (allo2curr.organism[org].fitness <= 0.0000001)
{
allo2curr.organism[org].fitness = 0.0000001;
}
meanfit2 += allo2curr.organism[org].fitness*0.01;
if (eeg % 1 == 0)
{
if (org == (pop - 1))
{
fprintf (allo2fit, "%f\n,", meanfit2);
}
}
if ( (eeg == 1 || eeg % 1000 == 0) && org == 1 ){
printf ("eegERATION %d fitness-%d = %f\n", eeg, org, allo2curr.organism[org].fitness);
int q, r;
for (q = 0; q < 5; q++) {
for (r = 0; r < 5; r++) {
printf ("%f ", allo2curr.organism[org].GRN[q][r]);
}
printf ("\n");
}
}
}
allo2.generation[eeg].organism[0] = allo2curr.organism[0];
}
lineage hybrid;
hybrid.generation = malloc (isolate * sizeof(population));
for (int hy = 0; hy < isolate; hy++)
{
for (int a = 0; a < 5; a++)
{
int mate = rand()%2;
if (mate == 0)
{
hybrid.generation[hy].organism[0].allele[a] = allo1.generation[hy].organism[0].allele[a];
}
if (mate == 1)
{
hybrid.generation[hy].organism[0].allele[a] = allo2.generation[hy].organism[0].allele[a];
}
}
int h, j, k;
//
// for (h = 0; h < 5; h++)
// {
// for (j = 0; j < 5; j++)
// {
// hybrid.generation[hy].organism[0].GRN[h][j] = 0;
// }
// }
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
for (k = 0; k < g; k++)
{
if (hybrid.generation[hy].organism[0].allele[h].regulator[k] == hybrid.generation[hy].organism[0].allele[j].protein[k])
{
hybrid.generation[hy].organism[0].GRN[h][j] = (hybrid.generation[hy].organism[0].GRN[h][j] + 0.001);
}
}
}
}
for (h = 0; h < 5; h++)
{
for (j = 0; j < 5; j++)
{
if (hybrid.generation[hy].organism[0].allele[h].reg_direction != hybrid.generation[hy].organism[0].allele[j].pro_direction)
{
hybrid.generation[hy].organism[0].GRN[h][j] = (hybrid.generation[hy].organism[0].GRN[h][j] * (-1));
}
}
}
hybrid.generation[hy].organism[0].phenotype = mat_power (hybrid.generation[hy].organism[0].GRN, y, 5, 5, 100);
double euc_dist = sqrt (vectors_dot_prod (hybrid.generation[hy].organism[0].phenotype, hybrid.generation[hy].organism[0].phenotype, 5) + vectors_dot_prod (optimal_phenotype, optimal_phenotype, 5) - (2 * vectors_dot_prod (optimal_phenotype, hybrid.generation[hy].organism[0].phenotype, 5) ) );
hybrid.generation[hy].organism[0].fitness = exp (((-1) * (pow ((euc_dist), 2))));
fprintf (hybridfit, "%f\n", hybrid.generation[hy].organism[0].fitness);
}
fclose(fit);
fclose(flocation);
fclose(hybridfit);
fclose(allo1fit);
fclose(allo2fit);
free(allo1.generation);
free(allo2.generation);
free(hybrid.generation);
/* FILE *f;
* f = fopen ("long-run-lin1.dat", "wb");
* fwrite (lin.generation, sizeof(population), 10000000, f);
* fclose(f);
*/ // free (lin.generation);
}