/*
* Position (of a struct in the map) to ip: Converts the node position
* `map_pos' to its relative ip.
*/
void postoip(u_int map_pos, inet_prefix ipstart, inet_prefix *ret)
{
ret->family=ipstart.family;
if(ipstart.family==AF_INET) {
ret->data[0]=map_pos + ipstart.data[0];
ret->len=4;
} else {
ret->len=16;
inet_copy_ipdata_raw(ret->data, &ipstart);
sum_int(map_pos, ret->data);
}
ret->bits=ret->len*8;
}
void init_scores(data *d) {
const int alph_size = d->m.alph_size;
const int width = d->m.width;
const double *bg = d->alph.prob;
glam2_scorer *s = &d->scorer;
int i, j;
d->match_scores = xmalloc2(width, (alph_size+1) * sizeof(double));
XMALLOC(d->delete_scores, width);
XMALLOC(d->insert_scores, width);
for (i = 0; i < width; ++i) {
const int *residue_counts = d->m.residue_counts[i];
const int match_count = sum_int(residue_counts, alph_size);
const int delete_count = d->m.delete_counts[i];
const int insert_count = d->m.insert_counts[i];
const int aligned_seq = match_count + delete_count;
const double ds = beta_ratio_a(&s->d_prior, delete_count, match_count);
const double ms = beta_ratio_b(&s->d_prior, delete_count, match_count);
const double is = beta_ratio_a(&s->i_prior, insert_count, aligned_seq);
const double js = beta_ratio_b(&s->i_prior, insert_count, aligned_seq);
dmix_ratios(&s->e_prior, d->match_scores[i], residue_counts);
if (i+1 < width) {
for (j = 0; j < alph_size; ++j)
d->match_scores[i][j] = xlog(js * ms * d->match_scores[i][j] / bg[j]);
d->delete_scores[i] = xlog(ds * js);
d->insert_scores[i] = xlog(is);
} else { /* no insertions after last column: special case */
for (j = 0; j < alph_size; ++j)
d->match_scores[i][j] = xlog(ms * d->match_scores[i][j] / bg[j]);
d->delete_scores[i] = xlog(ds);
d->insert_scores[i] = -DBL_MAX; /* overflow risk? */
}
/* overflow risk? */
d->match_scores[i][alph_size] = -DBL_MAX; /* mask character forbidden */
}
}