/*-----------------------------------------------------------
* Mise à jour de toutes les cellules de la grille
*----------------------------------------------------------*/
int update_cells (struct ctx_s *ctx) {
int x, y;
int top, bottom, left, right;
int update = 0;
for (x=1; x < ctx->X+1; ++x) {
for (y=1; y < ctx->Y+1; ++y) {
int nb_burning = 0;
left = x - 1;
right = x + 1;
top = y - 1;
bottom = y + 1;
update_neighbor(ctx, left, y, &nb_burning);
update_neighbor(ctx, right, y, &nb_burning);
update_neighbor(ctx, x, top, &nb_burning);
update_neighbor(ctx, x, bottom, &nb_burning);
update += update_self(ctx, x, y, nb_burning);
}
}
return update;
}
/*
* Process an incoming neighbor probe message.
*/
void
accept_probe(u_int32_t src, u_int32_t dst, char *p, int datalen,
u_int32_t level)
{
vifi_t vifi;
if ((vifi = find_vif(src, dst)) == NO_VIF) {
logit(LOG_INFO, 0,
"ignoring probe from non-neighbor %s", inet_fmt(src, s1));
return;
}
update_neighbor(vifi, src, DVMRP_PROBE, p, datalen, level);
}
static void recv_beacon(nbr_state_t *s, Message *msg)
{
nbr_beacon_t *pkt = (nbr_beacon_t*)(msg->data);
uint8_t i;
uint16_t my_addr = sys_id();
bool dup;
nbr_entry_t *nb;
nb = update_neighbor(s, msg->saddr, entohs(pkt->seqno), &dup);
if(nb == NULL) return;
nb->parent = entohs(pkt->parent);
nb->hop = pkt->hopcount;
// find out my address, extract the estimation
for (i = 0; i < pkt->estEntries; i++) {
if (entohs(pkt->estList[i].id) == my_addr) {
//DEBUG("found my entry %d\n", pkt->estList[i].receiveEst);
nb->sendEst = pkt->estList[i].receiveEst;
nb->liveliness++;
}
}
return;
}
/*
* Process an incoming route report message.
*/
void
accept_report(u_int32_t src, u_int32_t dst, char *p, int datalen,
u_int32_t level)
{
vifi_t vifi;
register int width, i, nrt = 0;
int metric;
u_int32_t mask;
u_int32_t origin;
struct newrt rt[4096];
if ((vifi = find_vif(src, dst)) == NO_VIF) {
logit(LOG_INFO, 0,
"ignoring route report from non-neighbor %s", inet_fmt(src, s1));
return;
}
if (!update_neighbor(vifi, src, DVMRP_REPORT, NULL, 0, level))
return;
if (datalen > 2*4096) {
logit(LOG_INFO, 0,
"ignoring oversize (%d bytes) route report from %s",
datalen, inet_fmt(src, s1));
return;
}
while (datalen > 0) { /* Loop through per-mask lists. */
if (datalen < 3) {
logit(LOG_WARNING, 0,
"received truncated route report from %s",
inet_fmt(src, s1));
return;
}
((u_char *)&mask)[0] = 0xff;
width = 1;
if ((((u_char *)&mask)[1] = *p++) != 0) width = 2;
if ((((u_char *)&mask)[2] = *p++) != 0) width = 3;
if ((((u_char *)&mask)[3] = *p++) != 0) width = 4;
if (!inet_valid_mask(ntohl(mask))) {
logit(LOG_WARNING, 0,
"%s reports bogus netmask 0x%08x (%s)",
inet_fmt(src, s1), ntohl(mask), inet_fmt(mask, s2));
return;
}
datalen -= 3;
do { /* Loop through (origin, metric) pairs */
if (datalen < width + 1) {
logit(LOG_WARNING, 0,
"received truncated route report from %s",
inet_fmt(src, s1));
return;
}
origin = 0;
for (i = 0; i < width; ++i)
((char *)&origin)[i] = *p++;
metric = *p++;
datalen -= width + 1;
rt[nrt].mask = mask;
rt[nrt].origin = origin;
rt[nrt].metric = (metric & 0x7f);
++nrt;
} while (!(metric & 0x80));
}
qsort((char*)rt, nrt, sizeof(rt[0]), compare_rts);
start_route_updates();
/*
* If the last entry is default, change mask from 0xff000000 to 0
*/
if (rt[nrt-1].origin == 0)
rt[nrt-1].mask = 0;
logit(LOG_DEBUG, 0, "Updating %d routes from %s to %s", nrt,
inet_fmt(src, s1), inet_fmt(dst, s2));
for (i = 0; i < nrt; ++i) {
if (i != 0 && rt[i].origin == rt[i-1].origin &&
rt[i].mask == rt[i-1].mask) {
logit(LOG_WARNING, 0, "%s reports duplicate route for %s",
inet_fmt(src, s1), inet_fmts(rt[i].origin, rt[i].mask, s2));
continue;
}
update_route(rt[i].origin, rt[i].mask, rt[i].metric,
src, vifi);
}
if (routes_changed && !delay_change_reports)
report_to_all_neighbors(CHANGED_ROUTES);
}
int32_t read_genome(char* read_genome_fname, uintptr_t unfiltered_indiv_ct, uintptr_t* indiv_exclude, uintptr_t indiv_ct, char* person_ids, uintptr_t max_person_id_len, uintptr_t* cluster_merge_prevented, double* cluster_sdistances, double* mds_plot_dmatrix_copy, uint32_t neighbor_n2, double* neighbor_quantiles, uint32_t* neighbor_qindices, uint32_t* ppc_fail_counts, double min_ppc, uintptr_t cluster_ct, uint32_t* cluster_starts, uint32_t* indiv_to_cluster) {
unsigned char* wkspace_mark = wkspace_base;
gzFile gz_infile = NULL;
uint32_t neighbor_load_quantiles = neighbor_quantiles && cluster_sdistances;
uint32_t ppc_warning = 0;
uintptr_t loaded_entry_ct = 0;
uint32_t ppc_fail = 0;
char* idbuf = &(tbuf[MAXLINELEN]);
char* sorted_ids;
uint32_t* id_map;
char* bufptr;
char* fam_id;
char* indiv_id;
uint32_t indiv_idx1;
uint32_t indiv_idx2;
double cur_ibs;
double cur_ppc;
uintptr_t tcoord;
uint32_t uii;
int32_t ii;
int32_t retval;
retval = sort_item_ids(&sorted_ids, &id_map, unfiltered_indiv_ct, indiv_exclude, unfiltered_indiv_ct - indiv_ct, person_ids, max_person_id_len, 0, 1, strcmp_deref);
if (retval) {
goto read_genome_ret_1;
}
if (gzopen_checked(&gz_infile, read_genome_fname, "rb")) {
goto read_genome_ret_OPEN_FAIL;
}
tbuf[MAXLINELEN - 1] = ' ';
// header line
do {
if (!gzgets(gz_infile, tbuf, MAXLINELEN)) {
goto read_genome_ret_READ_FAIL;
}
if (!tbuf[MAXLINELEN - 1]) {
goto read_genome_ret_INVALID_FORMAT_3;
}
bufptr = skip_initial_spaces(tbuf);
} while (is_eoln_kns(*bufptr));
// a little bit of input validation
if (memcmp(bufptr, "FID1", 4)) {
logprint("Error: Invalid --read-genome input file.\n");
goto read_genome_ret_INVALID_FORMAT;
}
while (gzgets(gz_infile, tbuf, MAXLINELEN)) {
if (!tbuf[MAXLINELEN - 1]) {
goto read_genome_ret_INVALID_FORMAT_3;
}
fam_id = skip_initial_spaces(tbuf);
if (is_eoln_kns(*fam_id)) {
continue;
}
indiv_id = next_item(fam_id);
bufptr = next_item_mult(indiv_id, 2);
if (no_more_items(bufptr)) {
goto read_genome_ret_INVALID_FORMAT_4;
}
ii = bsearch_fam_indiv(idbuf, sorted_ids, max_person_id_len, indiv_ct, fam_id, indiv_id);
if (ii == -1) {
continue;
}
indiv_idx1 = id_map[(uint32_t)ii];
fam_id = next_item(indiv_id);
indiv_id = bufptr;
ii = bsearch_fam_indiv(idbuf, sorted_ids, max_person_id_len, indiv_ct, fam_id, indiv_id);
if (ii == -1) {
continue;
}
indiv_idx2 = id_map[(uint32_t)ii];
if (indiv_idx2 == indiv_idx1) {
logprint("Error: FID1/IID1 matches FID2/IID2 in --read-genome input file line.\n");
goto read_genome_ret_INVALID_FORMAT;
}
bufptr = next_item_mult(indiv_id, 8); // distance
fam_id = next_item(bufptr); // repurposed to PPC test value
if (no_more_items(fam_id)) {
goto read_genome_ret_INVALID_FORMAT_4;
}
if (min_ppc != 0.0) {
if (sscanf(fam_id, "%lg", &cur_ppc) != 1) {
logprint("Error: Invalid PPC test value in --read-genome input file.\n");
goto read_genome_ret_INVALID_FORMAT;
}
ppc_fail = (cur_ppc < min_ppc)? 1 : 0;
if (ppc_fail && ppc_fail_counts) {
ppc_fail_counts[indiv_idx1] += 1;
ppc_fail_counts[indiv_idx2] += 1;
}
}
if (sscanf(bufptr, "%lg", &cur_ibs) != 1) {
logprint("Error: Invalid IBS value in --read-genome input file.\n");
goto read_genome_ret_INVALID_FORMAT;
}
if (neighbor_load_quantiles) {
update_neighbor(indiv_ct, neighbor_n2, indiv_idx1, indiv_idx2, cur_ibs, neighbor_quantiles, neighbor_qindices);
}
loaded_entry_ct++;
if (cluster_ct) {
indiv_idx1 = indiv_to_cluster[indiv_idx1];
indiv_idx2 = indiv_to_cluster[indiv_idx2];
if (indiv_idx1 == indiv_idx2) {
if (ppc_fail && (!ppc_warning)) {
logprint("Warning: Initial cluster assignment violates PPC test constraint.\n");
ppc_warning = 1;
}
continue;
}
}
if (indiv_idx2 < indiv_idx1) {
uii = indiv_idx1;
indiv_idx1 = indiv_idx2;
indiv_idx2 = uii;
}
tcoord = tri_coord_no_diag(indiv_idx1, indiv_idx2);
if (ppc_fail) {
set_bit_ul(cluster_merge_prevented, tcoord);
}
if (cluster_sdistances) {
cluster_sdistances[tcoord] += cur_ibs;
}
}
if (!gzeof(gz_infile)) {
goto read_genome_ret_READ_FAIL;
}
if (loaded_entry_ct != (indiv_ct * (indiv_ct - 1)) / 2) {
sprintf(logbuf, "Error: %s does not include all individual pairs.\n", read_genome_fname);
goto read_genome_ret_INVALID_FORMAT_2;
}
if (cluster_sdistances) {
cluster_dist_divide(indiv_ct, cluster_ct, cluster_starts, cluster_sdistances);
}
while (0) {
read_genome_ret_OPEN_FAIL:
retval = RET_OPEN_FAIL;
break;
read_genome_ret_READ_FAIL:
retval = RET_READ_FAIL;
break;
read_genome_ret_INVALID_FORMAT_4:
sprintf(logbuf, "Error: Fewer entries than expected in %s line.\n", read_genome_fname);
logprintb();
retval = RET_INVALID_FORMAT;
break;
read_genome_ret_INVALID_FORMAT_3:
sprintf(logbuf, "Error: Pathologically long line in %s.\n", read_genome_fname);
read_genome_ret_INVALID_FORMAT_2:
logprintb();
read_genome_ret_INVALID_FORMAT:
retval = RET_INVALID_FORMAT;
break;
}
read_genome_ret_1:
wkspace_reset(wkspace_mark);
gzclose_cond(gz_infile);
return retval;
}
