int live_or_die(board_t *self, int row, int col) {
int curr = board_get(self, row, col);
int top_row = CIRC(row - 1, self->num_rows);
int bottom_row = (row + 1)%self->num_rows;
int left_col = CIRC(col - 1, self->num_cols);
int right_col = (col + 1)%self->num_cols;
int neighbors = board_get(self, top_row, left_col) +
board_get(self, top_row, col) +
board_get(self, top_row, right_col) +
board_get(self, row, left_col) +
board_get(self, row, right_col) +
board_get(self, bottom_row, left_col) +
board_get(self, bottom_row, col) +
board_get(self, bottom_row, right_col);
if (curr == 1 && neighbors < 2)
return 0; // dies of loneliness
else if (curr == 1 && neighbors > 3)
return 0; // dies of overcrowding
else if (curr == 1 && (neighbors == 2 || neighbors == 3))
return 1; // stays alive
else if (curr == 0 && neighbors == 3)
return 1; // born
return 0; // stays dead
}
static size_t computeoffset(
double threshold,
double penalty,
bool reverse,
const unsigned char *seq,
size_t seq_length,
size_t size,
base_score score,
const panda_nt *primer,
size_t primerlen) {
/* Circular buffer of probabilities of primer alignment indexed by the offset. */
double probabilities[primerlen];
double bestpr = exp(primerlen * threshold);
size_t bestindex = 0;
size_t index;
if (primerlen > seq_length) {
return 0;
}
for (index = 0; index < primerlen; index++) {
probabilities[index] = -INFINITY;
}
for (index = 0; index < seq_length; index++) {
ptrdiff_t x;
double last_pr = exp(probabilities[CIRC(index, primerlen)] / (index + 1)) - index * penalty;
/* The last bucket in the buffer holds the probability of a complete alignment. If it so better than we have seen previously, store it. */
if (last_pr > bestpr) {
bestpr = last_pr;
bestindex = index + 1;
}
probabilities[CIRC(index, primerlen)] = 0;
for (x = (ptrdiff_t) (primerlen > index ? index : primerlen - 1); x >= 0; x--) {
if (!PANDA_NT_IS_N(primer[x])) {
panda_nt nt;
double p;
double notp;
score(&seq[size * (reverse ? (seq_length - index - 1) : index)], &nt, &p, ¬p);
probabilities[CIRC(index - x, primerlen)] += ((nt & primer[x]) != 0) ? p : notp;
}
}
}
return bestindex;
}
