/**
* main program
*/
int
main (void)
{
float cpu1,cpu2;
cpu1 = ((float) clock())/CLOCKS_PER_SEC;
srand (time (NULL));
ga_struct *population = malloc (sizeof (ga_struct) * POPSIZE);
ga_struct *beta_population = malloc (sizeof (ga_struct) * POPSIZE);
init_population (population, beta_population);
char *gen_str = population[0].gen;
char element[5] = "\0";
strncpy (element, gen_str, 4);
//if (strcmp ("0000", element) == 0)
int index = 0;
for (; index < POPSIZE; index++)
{
cal_fitness (population);
sort_by_fitness (population);
// print current best individual
printf ("binary string: %s - fitness: %d\n", population[0].gen,
population[0].fitness);
if (population[0].fitness == 0)
{
//~ print equation
decode_gen (&population[0]);
break;
}
mate (population, beta_population);
swap (&population, &beta_population);
}
free_population (population);
free_population (beta_population);
cpu2 = ((float) clock())/CLOCKS_PER_SEC;
printf("Execution time (s) = %le\n",cpu2-cpu1);
return 0;
}
int main()
{
int x, y;
int check = 0;
int pop_size = 1;
int bit_count = 2;
int data_count = 2;
population *pop = create_population(pop_size, bit_count, data_count);
while(1)
{
printf("x : ");
scanf("%d", &x);
printf("y : ");
scanf("%d", &y);
if(x<0 || x>14)// 오목판을 넘어가는 숫자를 입력시 다시 입력
{
check = 1;
}
else if(y<0 || y>14)
{
check = 1;
}
if(check == 1)
{
printf("다시 입력 하세요\n");
check = 0;
continue;
}
if(board[x][y] == 1)// 중복을막음
{
printf("중복된 곳입니다.\n");
continue;
}
board[x][y] = 1;
rand_population(pop);//랜덤수 추출
for(int i = 0; i < pop->pop_size; i++){
printf("컴퓨터의 출력\n");
for(int j = 0; j < bit_count; j++){
printf("%d ", pop->ivd[i].crms[j]);//랜덤한 좌표출력
}
printf("\n");
}
}
free_population(pop);
printf("아무키나 누르십시오...");getchar();
return 0;
}
/* Free metapopulation */
void free_metapopulation(struct metapopulation *in){
int i, npat=get_maxnpat(in), npop=get_npop(in);
for(i=0;i<npat;i++){
if(in->pathogens[i] != NULL) free_pathogen((in->pathogens)[i]);
}
for(i=0;i<npop;i++){
if(in->populations[i] != NULL) free_population(in->populations[i]);
}
free(in->pathogens);
free(in->populations);
free(in);
}
void reduce_population_through_ranking(GeneWrapper * population_after, int population_size_after,
GeneWrapper * population_before, int population_size_before,
GeneWrapper * base_population, int base_population_size)
{
char buffer[51];
int i = population_size_after - 1;
int j = population_size_before - 1;
GeneWrapper * population_before_copy = NULL;
copy_population(&population_before_copy, population_before, population_size_before);
rank_compete(population_before_copy, population_size_before, base_population, base_population_size);
while (i >= 0) {
NewStringFromGene(population_before_copy[j].gene, buffer);
SetGeneFromString(buffer, population_after[i].gene);
i--;
j--;
}
free_population(population_before_copy, population_size_before);
}
void reduce_population_through_competition(GeneWrapper * initial_population, GeneWrapper * new_population,
int initial_population_size, int new_population_size) {
char buffer[51];
int i = initial_population_size - 1;
int j = new_population_size - 1;
GeneWrapper * new_population_copy = NULL;
copy_population(&new_population_copy, new_population, new_population_size);
mutual_compete(new_population_size, new_population_copy);
while (i >= 0) {
NewStringFromGene(new_population_copy[j].gene, buffer);
SetGeneFromString(buffer, initial_population[i].gene);
i--;
j--;
}
free_population(new_population_copy, new_population_size);
}
int main(int argc, char **argv)
{
extern char *optarg;
int optchar;
char *treefile_name = NULL, *genomefile_name = NULL, *outfile_name = NULL, *corrfile_name = NULL;
FILE *treefile, *genomefile, *outfile, *corrfile;
long genome_generation, tree_generation, i, j, num_trees;
double tree_d, gen_d, change_rate, m1, m_a, mutation_rate;
double *tree_dist = NULL, *m_app = NULL;
double grade, y0, r;
long num_data;
PHYLTREE phyltree;
POPULATION population;
int ret_code;
phyl_init_tree(&phyltree);
while ((optchar = getopt(argc, argv, "hg:t:o:c:m:")) != -1)
{
switch (optchar)
{
case 'g':
genomefile_name = optarg;
break;
case 't':
treefile_name = optarg;
break;
case 'c':
corrfile_name = optarg;
break;
case 'o':
outfile_name = optarg;
break;
case 'h':
printf("mutcheck -- analyze apparent mutation rates\n");
printf("\n");
printf("Command line usage:\n");
printf("-g <filename>: Specify genome file (mandatory)\n");
printf("-t <filename>: Specify tree file (mandatory)\n");
printf("-o <filename>: Specify name for individual generation's output file\n");
printf("-c <filename>: Specify file for treedist vs reconstructed dist correlations\n");
printf("-h: Print this help and exit\n");
exit (EXIT_SUCCESS);
}
}
if (treefile_name == NULL)
{
fprintf(stderr, "no tree file specified -- exit\n");
exit (EXIT_FAILURE);
}
if ((treefile = fopen(treefile_name, "r")) == NULL)
{
fprintf(stderr, "failed to open tree file \"%s\" -- exit\n", treefile_name);
exit (EXIT_FAILURE);
}
if (genomefile_name == NULL)
{
fprintf(stderr, "No genome file specified -- exit\n");
fclose(treefile);
exit (EXIT_FAILURE);
}
if ((genomefile = fopen(genomefile_name, "r")) == NULL)
{
fprintf(stderr, "Failed to open genome file \"%s\" -- exit\n", genomefile_name);
fclose(treefile);
exit (EXIT_FAILURE);
}
if (corrfile_name)
{
if ((corrfile = fopen(corrfile_name, "w")) == NULL)
{
fprintf(stderr, "Failed to open \"%s\" for correlation output -- exit\n", corrfile_name);
fclose(treefile);
fclose(genomefile);
exit (EXIT_FAILURE);
}
}
else
{
corrfile = stdout;
corrfile_name = "stdout";
}
if (outfile_name)
{
if ((outfile = fopen(outfile_name, "w")) == NULL)
{
fprintf(stderr, "mutcheck: Failed to open %s for output -- exit\n", outfile_name);
fclose(treefile);
fclose(genomefile);
if (corrfile_name)
fclose(corrfile);
exit (EXIT_FAILURE);
}
}
else
outfile = NULL;
while (!feof(genomefile) && !ferror(genomefile) && !feof(treefile) && !ferror(treefile))
{
fgets(buf, 256, treefile);
if ((buf[0] != 'g') || (buf[1] != ' '))
{
fprintf(stderr, "Treefile corrupt after generation %ld\n", tree_generation);
break;
}
tree_generation = strtol(buf + 2, NULL, 10);
fgets(buf, 256, genomefile);
if ((buf[0] != 'g') || (buf[1] != ' '))
{
fprintf(stderr, "Genome file corrupt after generation %ld\n", genome_generation);
break;
}
genome_generation = strtol(buf + 2, NULL, 10);
fgets(buf, 256, treefile);
num_trees = strtol(buf, (char **) NULL, 10);
if (num_trees != 1)
{
fprintf(stderr, "%ld trees in generation %ld -- skipping\n", num_trees, tree_generation);
for (i = 0; i < num_trees; i++)
{
phyl_read_tree(treefile, &phyltree);
phyl_free_tree(&phyltree);
}
}
else
phyl_read_tree(treefile, &phyltree);
read_genomes(genomefile, &population);
if ((num_trees == 1) && (tree_generation == genome_generation))
{
if ((tree_dist = (double *) malloc((population.size * population.size - 1) / 2 * sizeof(double))) == NULL)
fprintf(stderr, "Failed to allocate array of tree distances\n");
else
{
if ((m_app = (double *) malloc(population.size * (population.size - 1) / 2 * sizeof(double))) == NULL)
fprintf(stderr, "Failed to allocate array of reconstructed distances\n");
else
{
num_data = 0;
for (i = 0; i < population.size; i++)
{
for (j = 0; j < i; j++)
{
tree_d = phyl_leafdistance(&phyltree, population.seq[i].name, population.seq[j].name);
if (tree_d < 0)
{
fprintf(stderr, "Generation %ld: Trees and genomes inconsistent: error #%f\n", tree_generation, tree_d);
break;
}
gen_d = diffchar_distance(population.seq[i].genome.length,
population.seq[i].genome.g,
population.seq[j].genome.length, population.seq[j].genome.g);
change_rate = gen_d / (population.seq[i].genome.length);
m1 = 1.0 - 256.0 / 255.0 * change_rate;
if (m1 > 0.0)
{
errno = 0;
m_a = 1.0 - pow(m1, 1.0 / 2.0 / tree_d);
if (errno)
perror("mutcheck: error in pow()");
else
{
tree_dist[num_data] = tree_d;
m_app[num_data] = m_a;
num_data++;
if (outfile)
fprintf(outfile, "%f %f\n", tree_d, m_a);
}
}
else if (outfile)
fprintf(outfile, "# Negative base operand to exponentiation: %f)\n", m1);
}
if (j < i)
break;
}
if ((ret_code = linear_regression(num_data, tree_dist, m_app, &grade, &y0, &r)) < 0)
{
fprintf(stderr, "Error #%d in linear regression\n", ret_code);
}
else
{
mutation_rate = 1.0 - exp(grade);
if (corrfile)
fprintf(corrfile, "%ld %f %f\n", tree_generation, grade, r);
}
free(m_app);
}
free(tree_dist);
}
}
phyl_free_tree(&phyltree);
free_population(&population);
#ifdef MEMDEBUG
print_MemdebugStatistics();
#endif
}
if (corrfile != stdout)
fclose(corrfile);
if (outfile)
fclose(outfile);
fclose(treefile);
fclose(genomefile);
return (EXIT_SUCCESS);
}
//HJJA
population *change_population ( population *oldpop, breedphase *bp )
{
population *newpop;
int i, j;
int numphases;
double totalrate = 0.0;
double r, r2;
int prob_oper = atoi ( get_parameter ( "probabilistic_operators" ) );
/* allocate the new population. */
newpop = allocate_population ( oldpop->size );
globaldata* g = get_globaldata();//get the lists
if(g->bUseHFC){
if( IsHighestActiveLevel(g->current_population)){
/*reproduce best guys into the new population. */
for(i=0;i<run_stats[0].bestn;i++){
//printf("best %d ind\n", i);
duplicate_individual ( (newpop->ind)+newpop->next, run_stats[0].best[i]->ind);
newpop->ind[newpop->next].flags = FLAG_NONE;
++(newpop->next);
//HJJS structure niching: mutation
//Assumption: we think any structure mutation will create a new structure
//for numeric mutation, we won't change the structure
CStruct* pSt;
int structID = newpop->ind[newpop->next].structID;
pSt = g->pStructHash->find(structID);
if(pSt==NULL){ //make sure,though redudency code
pSt = new CStruct();
pSt->structID = ++(g->currMaxStructID);
pSt->age=1;
pSt->lastGen=g->current_generation+1;
pSt->nIndividuals=0;
pSt->nIndNextGen=1;
newpop->ind[newpop->next].structID=pSt->structID;
g->pStructHash->insert(pSt);
}
else{
if(pSt->lastGen != g->current_generation+1){//the first individual in this generation
pSt->age++;
pSt->lastGen = g->current_generation+1;
}
pSt->nIndNextGen++;//increase the ind no of this population
}
//HJJS end
}
}
//End HJJ_ELITISM
}//End useHFC
/* the first element of the breedphase table is a dummy -- its
operator field stores the number of phases. */
numphases = bp[0].operatorID;
/* call the start method for each phase. */
for ( i = 1; i <= numphases; ++i )
{
totalrate += bp[i].rate;
if ( bp[i].operator_start )
bp[i].operator_start ( oldpop, bp[i].data );
}
/* now fill the new population. */
while ( newpop->next < newpop->size )
{
/** select an operator, either stochastically or not depending on
the probabilistic_operators parameter. **/
if ( prob_oper )
r = totalrate * random_double();
else
r = totalrate * ((double)newpop->next/(double)newpop->size);
r2 = bp[1].rate;
for ( i = 1; r2 < r; )
r2 += bp[++i].rate;
#ifdef DEBUG
fprintf ( stderr, "picked %10.3lf; operator %d\n", r, i );
#endif
/* call the phase's method to do the operation. */
if ( bp[i].operator_operate ){
bp[i].operator_operate ( oldpop, newpop, bp[i].data );
}
}
/* call each phase's method to do cleanup. */
for ( i = 1; i <= numphases; ++i )
{
if ( bp[i].operator_end )
bp[i].operator_end ( bp[i].data );
}
/* mark all the ERCs referenced in the new population. */
for ( i = 0; i < newpop->size; ++i )
for ( j = 0; j < tree_count; ++j )
reference_ephem_constants ( newpop->ind[i].tr[j].data, 1 );
/* free the old population. */
free_population ( oldpop ); //Bug when do reproduction ?
return ( newpop );
}
int main(int argc, char *argv[])
{
// Need to change to 3. need to remove the logging.
if (argc != 4)
{
printf("Usage: ./maxcut <input data path> <output data path> <log file>\n");
exit(-1);
}
// Need to remove when submitting.
log_file = fopen(argv[3], "w");
fprintf(log_file, "rate, elasped time (s), max val, avg val\n");
start_time = get_seconds();
in = fopen(argv[1], "r");
out = fopen(argv[2], "w");
int i, j, v1, v2, w; // (v1, v2) is the vertex and w is the weight
fscanf(in, "%d %d\n", &num_of_vertex, &num_of_edge);
int edge[num_of_vertex+1][num_of_vertex+1];
for (i=0; i<=SIZE; i++)
for (j=0; j<=SIZE; j++)
edge[i][j] = 0;
while (fscanf(in, "%d %d %d\n", &v1, &v2, &w) != EOF)
{
edge[v1][v2] = w;
edge[v2][v1] = w;
}
init_population();
init_offsprings();
init_cost(edge);
sort_population();
init_crossover();
int p1, p2;
while (!(stop_condition()))
{
generation++;
for (i=1; i<=K; i++)
{
selection(&p1, &p2);
crossover(i, p1, p2);
mutation(i);
local_optimization(i, edge);
}
replacement(edge);
sort_population();
}
for (i=1; i<=SIZE; i++)
{
if (population[N]->ch[i] == 1)
fprintf(out, "%d ", i);
}
free_population();
fclose(in);
fclose(out);
printf("N: %d, K: %d, S_RATE: %lf, M_THRE: %lf, P0: %lf, POINTS: %d, K_FIT: %d, T: %lf\n", N, K, S_RATE, M_THRE, P0, POINTS, K_FIT, T);
return 0;
}
int main(int argc, char **argv)
{
extern char *optarg;
int optchar;
char *treefile_name = NULL, *genomefile_name = NULL, *outfile_name = NULL, *corrfile_name = NULL, *mutfile_name = NULL;
FILE *treefile, *genomefile, *outfile, *corrfile, *mutfile;
long genome_generation, tree_generation, i, j, num_trees;
double tree_d, rec_d, rec_d1, change_rate, mutation_rate;
double *tree_dist = NULL, *reconst_dist = NULL;
double lambda, y0, r;
long num_data;
PHYLTREE phyltree;
POPULATION population;
int ret_code;
phyl_init_tree(&phyltree);
while ((optchar = getopt(argc, argv, "hg:t:o:c:m:")) != -1)
{
switch (optchar)
{
case 'g':
genomefile_name = optarg;
break;
case 't':
treefile_name = optarg;
break;
case 'c':
corrfile_name = optarg;
break;
case 'm':
mutfile_name = optarg;
break;
case 'o':
outfile_name = optarg;
break;
case 'h':
printf("treecorr -- check correlation between corrected\n");
printf(" edit or hamming diatance and true tree distance\n");
printf("\n");
printf("Command line usage:\n");
printf("-g <filename>: Specify genome file (mandatory)\n");
printf("-t <filename>: Specify tree file (mandatory)\n");
printf("-o <filename>: Specify base name for individual generation's output file\n");
printf("-c <filename>: Specify file for treedist vs reconstructed dist correlations\n");
printf("-m <filename>: Specify file for reconstructed mutation rates\n");
printf("-h: Print this help and exit\n");
exit (EXIT_SUCCESS);
}
}
if (treefile_name == NULL)
{
fprintf(stderr, "no tree file specified -- exit\n");
exit (EXIT_FAILURE);
}
if ((treefile = fopen(treefile_name, "r")) == NULL)
{
fprintf(stderr, "failed to open tree file \"%s\" -- exit\n", treefile_name);
exit (EXIT_FAILURE);
}
if (genomefile_name == NULL)
{
fprintf(stderr, "No genome file specified -- exit\n");
fclose(treefile);
exit (EXIT_FAILURE);
}
if ((genomefile = fopen(genomefile_name, "r")) == NULL)
{
fprintf(stderr, "Failed to open genome file \"%s\" -- exit\n", genomefile_name);
fclose(treefile);
exit (EXIT_FAILURE);
}
if (corrfile_name)
{
if ((corrfile = fopen(corrfile_name, "w")) == NULL)
{
fprintf(stderr, "Failed to open \"%s\" for correlation output -- exit\n", corrfile_name);
fclose(treefile);
fclose(genomefile);
exit (EXIT_FAILURE);
}
}
else
{
corrfile = stdout;
corrfile_name = "stdout";
}
if (mutfile_name)
{
if ((mutfile = fopen(mutfile_name, "w")) == NULL)
{
fprintf(stderr, "Failed to open \"%s\" for mutation output -- exit\n", mutfile_name);
fclose(treefile);
fclose(genomefile);
if (corrfile != stdout)
fclose(corrfile);
exit (EXIT_FAILURE);
}
}
else
mutfile = NULL;
while (!feof(genomefile) && !ferror(genomefile) && !feof(treefile) && !ferror(treefile))
{
fgets(buf, 256, treefile);
if ((buf[0] != 'g') || (buf[1] != ' '))
{
fprintf(stderr, "Treefile corrupt after generation %ld\n", tree_generation);
break;
}
tree_generation = strtol(buf + 2, NULL, 10);
fgets(buf, 256, genomefile);
if ((buf[0] != 'g') || (buf[1] != ' '))
{
fprintf(stderr, "Genome file corrupt after generation %ld\n", genome_generation);
break;
}
genome_generation = strtol(buf + 2, NULL, 10);
fgets(buf, 256, treefile);
num_trees = strtol(buf, (char **) NULL, 10);
if (num_trees != 1)
{
fprintf(stderr, "%ld trees in generation %ld -- skipping\n", num_trees, tree_generation);
for (i = 0; i < num_trees; i++)
{
phyl_read_tree(treefile, &phyltree);
phyl_free_tree(&phyltree);
}
}
else
phyl_read_tree(treefile, &phyltree);
read_genomes(genomefile, &population);
if ((num_trees == 1) && (tree_generation == genome_generation))
{
if ((tree_dist = (double *) malloc((population.size * population.size - 1) / 2 * sizeof(double))) == NULL)
fprintf(stderr, "Failed to allocate array of tree distances\n");
else
{
if ((reconst_dist = (double *) malloc(population.size * (population.size - 1) / 2 * sizeof(double))) == NULL)
fprintf(stderr, "Failed to allocate array of reconstructed distances\n");
else
{
if (outfile_name)
{
sprintf(buf, "%s-%05ld.gpd", outfile_name, tree_generation);
outfile = fopen(buf, "w");
fprintf(outfile, "# generation %ld\n", tree_generation);
}
num_data = 0;
for (i = 0; i < population.size; i++)
{
for (j = 0; j < i; j++)
{
tree_d = phyl_leafdistance(&phyltree, population.seq[i].name, population.seq[j].name);
if (tree_d < 0)
{
fprintf(stderr, "Generation %ld: Trees and genomes inconsistent: error #%f\n", tree_generation, tree_d);
break;
}
rec_d = diffchar_distance(population.seq[i].genome.length,
population.seq[i].genome.g,
population.seq[j].genome.length, population.seq[j].genome.g);
change_rate = rec_d / (population.seq[i].genome.length);
rec_d1 = 1.0 - 256.0 / 255.0 * change_rate;
if (rec_d1 > 0.0)
{
rec_d = log(rec_d1);
tree_dist[num_data] = tree_d;
reconst_dist[num_data] = rec_d;
num_data++;
if (outfile)
fprintf(outfile, "%f %f\n", tree_d, rec_d);
}
else if (outfile)
fprintf(outfile, "# Infinite distance (log operand: %f)\n", rec_d1);
}
if (j < i)
break;
}
if (outfile_name && outfile)
fclose(outfile);
if ((ret_code = linear_regression(num_data, tree_dist, reconst_dist, &lambda, &y0, &r)) < 0)
{
fprintf(stderr, "Error #%d in linear regression\n", ret_code);
}
else
{
mutation_rate = 1.0 - exp(lambda);
if (corrfile)
fprintf(corrfile, "%ld %f\n", tree_generation, r);
if (mutfile)
fprintf(mutfile, "%ld %f\n", tree_generation, mutation_rate);
}
free(reconst_dist);
}
free(tree_dist);
}
}
phyl_free_tree(&phyltree);
free_population(&population);
#ifdef MEMDEBUG
print_MemdebugStatistics();
#endif
}
if (mutfile)
fclose(mutfile);
if (corrfile != stdout)
fclose(corrfile);
fclose(treefile);
fclose(genomefile);
return (EXIT_SUCCESS);
}
int main(int argc, char **argv)
{
extern int optind, opterr;
extern char *optarg;
int optchar;
char *treefile_name = NULL, *genomefile_name = NULL, *outfile_basename = NULL, g_outfile_name[FILENAME_MAX];
FILE *treefile, *genomefile, *outfile;
long generation, g, num_trees, i;
int ret_code;
genomefile_name = NULL;
treefile_name = NULL;
outfile_basename = NULL;
generation = -1;
phyl_init_tree(&phyltree);
while ((optchar = getopt(argc, argv, "t:g:o:h")) != -1)
{
switch (optchar)
{
case 'g':
genomefile_name = optarg;
break;
case 't':
treefile_name = optarg;
break;
case 'o':
outfile_basename = optarg;
break;
case 'h':
printf("distcorr -- a hack to visualize correlation between\n");
printf(" phylogenetic and edit distances\n");
printf("Usage of command line options:\n");
printf("-g <filename>: Specify genome file\n");
printf("-t <filename>: Specify tree file\n");
printf("-o <outfile>: specify output file basename:");
printf("-h: Print this info and exit\n");
exit (EXIT_SUCCESS);
}
}
if (treefile_name == NULL)
{
fprintf(stderr, "no tree file specified -- exit\n");
exit (EXIT_FAILURE);
}
if ((treefile = fopen(treefile_name, "r")) == NULL)
{
fprintf(stderr, "failed to open tree file \"%s\" -- exit\n", treefile_name);
exit (EXIT_FAILURE);
}
if (genomefile_name == NULL)
{
fprintf(stderr, "no tree file specified -- exit\n");
exit (EXIT_FAILURE);
}
if ((genomefile = fopen(genomefile_name, "r")) == NULL)
{
fprintf(stderr, "failed to open genome file \"%s\" -- exit\n", genomefile_name);
exit (EXIT_FAILURE);
}
while (!feof(treefile) && !ferror(treefile) && !feof(genomefile) && !ferror(genomefile))
{
get_line(buf, 256, treefile);
if (feof(treefile) || ferror(treefile))
break;
if (buf[0] != 'g')
{
fprintf(stderr, "error in header of treefile after generation %ld -- exit\n", generation);
exit (EXIT_FAILURE);
}
generation = strtol(buf + 1, (char **) NULL, 10);
get_line(buf, 256, genomefile);
if (feof(genomefile) || ferror(genomefile))
break;
if (buf[0] != 'g')
{
fprintf(stderr, "error in header of genomefile after generation %ld -- exit\n", g);
exit (EXIT_FAILURE);
}
g = strtol(buf + 1, (char **) NULL, 10);
if (g != generation)
{
fprintf(stderr, "treefile: g=%ld, genomefile: g=%ld -- out of sync\n", generation, g);
break;
}
get_line(buf, 256, treefile);
num_trees = strtol(buf, NULL, 10);
if (num_trees < 1)
{
fprintf(stderr, "%ld trees in treefile at generation %ld\n", num_trees, generation);
break;
}
if (num_trees > 1)
{
fprintf(stderr, "distcorr: multiple trees in treefile\n");
for (i = 0; i < num_trees; i++)
{
if ((ret_code = phyl_read_tree(treefile, &phyltree)) < 0)
fprintf(stderr, "error #%d while reading tree #%ld of generation %ld\n", ret_code, i, generation);
phyl_free_tree(&phyltree);
}
read_population(genomefile, g);
free_population();
continue;
}
if ((ret_code = phyl_read_tree(treefile, &phyltree)) < 0)
{
fprintf(stderr, "error #%d while reading tree #%ld of generation %ld\n", ret_code, i, generation);
break;
}
if ((ret_code = read_population(genomefile, g)) < 0)
{
fprintf(stderr, "error %d reading genomes of generation %ld\n", ret_code, g);
phyl_free_tree(&phyltree);
break;
}
if (outfile_basename)
{
sprintf(g_outfile_name, "%s-%06ld-dc.gpd", outfile_basename, generation);
if ((outfile = fopen(g_outfile_name, "w")) == NULL)
{
fprintf(stderr, "failed to open \"%s\" for output -- exit\n", g_outfile_name);
exit (EXIT_FAILURE);
}
}
else
outfile = stdout;
ret_code = distcorr(outfile, generation);
if (ret_code < 0)
fprintf(stderr, "error %d in distcorr\n", ret_code);
if (outfile_basename)
fclose(outfile);
free_population();
phyl_free_tree(&phyltree);
}
fclose(treefile);
fclose(genomefile);
return (EXIT_SUCCESS);
}
