/*
* Returns true if any node in tree1 intersects with any node from tree2.
*/
int mm_trees_intersect(char *tree1, char *tree2)
{
char *node_a, *node_b;
node_a = rbtree_first(tree1);
while (node_a) {
node_b = rbtree_first(tree2);
while (node_b) {
/* Don't compare nodes to themselves */
if (node_a == node_b) {
node_b = rbtree_next(node_b);
continue;
}
/* If the runs are equal they intersect */
if (rbtree_compare_runs(node_b, node_a) == 0 ||
rbtree_compare_runs(node_a, node_b) == 0) {
fprintf(stderr, "(%p, %p) ", node_a, node_b);
return !0;
}
node_b = rbtree_next(node_b);
}
node_a = rbtree_next(node_a);
}
return 0;
}
/**
* Assemble the rrsets in the anchors, ready for use by validator.
* @param anchors: trust anchor storage.
* @return: false on error.
*/
static int
anchors_assemble_rrsets(struct val_anchors* anchors)
{
struct trust_anchor* ta;
struct trust_anchor* next;
size_t nods, nokey;
lock_basic_lock(&anchors->lock);
ta=(struct trust_anchor*)rbtree_first(anchors->tree);
while((rbnode_type*)ta != RBTREE_NULL) {
next = (struct trust_anchor*)rbtree_next(&ta->node);
lock_basic_lock(&ta->lock);
if(ta->autr || (ta->numDS == 0 && ta->numDNSKEY == 0)) {
lock_basic_unlock(&ta->lock);
ta = next; /* skip */
continue;
}
if(!anchors_assemble(ta)) {
log_err("out of memory");
lock_basic_unlock(&ta->lock);
lock_basic_unlock(&anchors->lock);
return 0;
}
nods = anchors_ds_unsupported(ta);
nokey = anchors_dnskey_unsupported(ta);
if(nods) {
log_nametypeclass(0, "warning: unsupported "
"algorithm for trust anchor",
ta->name, LDNS_RR_TYPE_DS, ta->dclass);
}
if(nokey) {
log_nametypeclass(0, "warning: unsupported "
"algorithm for trust anchor",
ta->name, LDNS_RR_TYPE_DNSKEY, ta->dclass);
}
if(nods == ta->numDS && nokey == ta->numDNSKEY) {
char b[257];
dname_str(ta->name, b);
log_warn("trust anchor %s has no supported algorithms,"
" the anchor is ignored (check if you need to"
" upgrade unbound and "
#ifdef HAVE_LIBRESSL
"libressl"
#else
"openssl"
#endif
")", b);
(void)rbtree_delete(anchors->tree, &ta->node);
lock_basic_unlock(&ta->lock);
if(anchors->dlv_anchor == ta)
anchors->dlv_anchor = NULL;
anchors_delfunc(&ta->node, NULL);
ta = next;
continue;
}
lock_basic_unlock(&ta->lock);
ta = next;
}
lock_basic_unlock(&anchors->lock);
return 1;
}
/*
* Tries to allocate a suitably sized run from the free list.
*
* Returns the size of the allocated run and a pointer to it.
* Returns 0 and NULL if no suitably sized run can be found.
*/
static size_t mmrun_allocate_freerun(size_t size, char **allocated)
{
/* Nothing to do if the free list is empty */
if (free_runs) {
/*
* Scan the free list linearly for a run that is of
* the correct size (address ordered first-fit)
*/
int run_size;
char *run = rbtree_first(free_runs);
while (run && mmrun_get_largesize(run) < size) {
run = rbtree_next(run);
}
/* If no run is found return NULL */
if (!run) {
*allocated = NULL;
return 0;
}
/* Remove the run from the free list */
rbtree_remove(run, &free_runs);
run_size = mmrun_get_largesize(run);
run_size = mmrun_split(size, run);
*allocated = run;
return run_size;
}
*allocated = NULL;
return 0;
}
/*****************************************************************************
* Reads frequency attributes into the pre-allocated freqs array.
****************************************************************************/
static void parse_freq_attrs(PS_T *ps, const char* tag, const xmlChar **attrs) {
int i, ncore, seen, *idx;
char *end_ptr;
double value, sum;
RBNODE_T *node;
bool seen_bad;
ncore = rbtree_size(ps->alph_ids);
// initilize the freqs array
if (ps->freqs == NULL) ps->freqs = mm_malloc(sizeof(double) * ncore);
// reset freqs array;
for (i = 0; i < ncore; i++) ps->freqs[i] = -1;
seen = 0;
seen_bad = false;
sum = 0.0;
// iterate over attributes
for (i = 0; attrs[i] != NULL; i += 2) {
idx = (int*)rbtree_get(ps->alph_ids, attrs[i]);
if (idx != NULL) {
assert(*idx < ncore);
if (ps->freqs[*idx] != -1) {
dreme_attr_parse_error(ps, PARSE_ATTR_DUPLICATE, tag, (const char*)attrs[i], NULL);
continue;
}
seen++;
errno = 0; // reset because we're about to check it
value = strtod((const char*)attrs[i+1], &end_ptr);
// allow out of range values, mainly because freqs can be very close to zero
if (end_ptr == (const char*)attrs[i+1] || (errno && errno != ERANGE) || value < 0 || value > 1) {
dreme_attr_parse_error(ps, PARSE_ATTR_BAD_VALUE, tag, (const char*)attrs[i], (const char*)attrs[i+1]);
ps->freqs[*idx] = 0; // mark frequence as seen, even though it's bad
seen_bad = true;
continue;
}
ps->freqs[*idx] = value;
sum += value;
}
}
// check we got everthing
if (seen < ncore) {
// identify what we're missing
for (node = rbtree_first(ps->alph_ids); node != NULL; node = rbtree_next(node)) {
idx = (int*)rbtree_value(node);
if (ps->freqs[*idx] == -1) {
dreme_attr_parse_error(ps, PARSE_ATTR_MISSING, tag, (char*)rbtree_key(node), NULL);
}
}
} else if (!seen_bad) {
// check the frequencies sum to 1
double delta = sum - 1;
delta = (delta < 0 ? -delta : delta);
if (delta > (0.001 * ncore)) {
// dreme writes background probabilities to 3 decimal places so assuming
// the error on each is at maximum 0.001 then the total error for the
// sum must be less than or equal to 0.004
error(ps, "Probabilities of %s do not sum to 1, got %g .\n", tag, sum);
}
}
}
/**************************************************************************
* Puts counts into the spacing bins.
**************************************************************************/
void bin_matches(int margin, int bin_size, RBTREE_T *sequences, MOTIF_T *primary_motif, SECONDARY_MOTIF_T *secondary_motif, int *matches) {
int primary_len, secondary_len, secondary, secondary_pos, primary_rc, secondary_rc, quad, distance, max_distance;
RBNODE_T *node;
SECONDARY_MOTIF_T *smotif;
SEQUENCE_T *sequence;
SPACING_T *spacing;
primary_len = get_motif_trimmed_length(primary_motif);
smotif = secondary_motif;
secondary_len = get_motif_trimmed_length(smotif->motif);
// Note that distance counts from zero
max_distance = margin - secondary_len;
// for each sequence
for (node = rbtree_first(sequences); node != NULL; node = rbtree_next(node)) {
sequence = (SEQUENCE_T*)rbtree_value(node);
secondary = matches[sequence->index];
// check for a match
if (!secondary) continue;
// convert the encoded form into easier to use form
primary_rc = sequence->primary_match < 0;
secondary_rc = secondary < 0;
secondary_pos = (secondary_rc ? -secondary : secondary);
// calculate the distance (counts from zero) and side
if (secondary_pos <= margin) {
distance = margin - secondary_pos - secondary_len + 1;
if (primary_rc) {//rotate reference direction
quad = RIGHT;
} else {
quad = LEFT;
}
} else {
distance = secondary_pos - margin - primary_len - 1;
if (primary_rc) {//rotate reference direction
quad = LEFT;
} else {
quad = RIGHT;
}
}
// check that we're within the acceptable range
if (distance < 0 || distance > max_distance) {
die("Secondary motif match not within margin as it should be due to prior checks!");
}
// calculate the strand
if (secondary_rc == primary_rc) {
quad |= SAME;
} else {
quad |= OPPO;
}
// add a count to the frequencies
spacing = smotif->spacings+(quad);
spacing->bins[(int)(distance / bin_size)] += 1;
smotif->total_spacings += 1;
}
}
static bool
_predicate (void)
{
int i;
KeyValuePair_t n;
struct rbtree tree;
KeyValuePair_t *node;
struct rbtree_node *result;
rbtree_init (&tree, _compareFn, 0);
for (i = 0; i < TreeSize; i++) {
node = malloc (sizeof (KeyValuePair_t));
node->key = i;
node->val = TreeSize + i;
rbtree_insert ((struct rbtree_node *) &node->node, &tree);
}
// Lookup the nodes.
for (i = 0; i < TreeSize; i++) {
KeyValuePair_t *kvResult;
n.key = i;
kvResult = rbtree_container_of (rbtree_lookup ((struct rbtree_node *) &n.node, &tree), KeyValuePair_t, node);
if (kvResult->key != i || kvResult->val != TreeSize + i) {
return false;
}
}
// This lookup should fail.
n.key = TreeSize;
result = rbtree_lookup ((struct rbtree_node *) &n.node, &tree);
if (result != NULL) {
return false;
}
//iterate (rbtree_first(&tree), iterateFn);
result = rbtree_first(&tree);
while (result) {
KeyValuePair_t *kvResult = rbtree_container_of (result, KeyValuePair_t, node);
struct rbtree_node *n = result;
result = rbtree_next (result);
rbtree_remove (n, &tree);
free (kvResult);
}
// This lookup should fail because we just cleared the tree.
n.key = TreeSize;
n.key = 0;
result = rbtree_lookup ((struct rbtree_node *) &n.node, &tree);
if (result != NULL) {
return false;
}
return true;
}
tb_t *
tb_find(struct rbtree *rb, const void *tc_ptr)
{
struct tb_t tb;
uint16_t tc_boundaries[1] = {1};
struct rbtree_elem *found;
struct tb_t *ret;
tb.num_insns = 0;
tb.tc_boundaries = tc_boundaries;
tb.tc_ptr = (void *)tc_ptr;
if (!(found = rbtree_find(rb, &tb.tc_elem))) {
return NULL;
}
ASSERT( rbtree_next(found) == rbtree_end(rb)
|| tc_less(found, rbtree_next(found), NULL));
ret = rbtree_entry(found, struct tb_t, tc_elem);
return ret;
}
net_interface_t *net_interface_next(net_interface_t *intp)
{
rbtree_node_t *retval;
tree_node_t temp;
temp.ni = intp;
retval = rbtree_next(interface_tree, &temp.header, cmpfn);
return ((retval) ? (((tree_node_t *) retval)->ni) : NULL);
}
static inline char *mmbin_get_available(char *bin)
{
char *run = rbtree_first(bin);
/* Bitmap will be zero for any full run */
while (run && !mmrun_get_bitmap(run)) {
run = rbtree_next(run);
}
return run;
}
static void
_freeTree (struct rbtree *tree)
{
struct rbtree_node *node = rbtree_first(tree);
while (node)
{
AddrToIndex *aiNode = rbtree_container_of (node, AddrToIndex, node);
node = rbtree_next (node);
free (aiNode);
}
}
//void *map_next(map_iterator *mi, pair *p) {
void *map_next(map_iterator *mi) {
rbnode *node;
node = rbtree_next((rbtree_iterator *)mi->iter);
if (node == NULL) {
return NULL;
}
// p->first = RBNODE_KEY(node);
// p->second = RBNODE_VAL(node);
// return p;
return RBNODE_VAL(node);
// return make_pair(RBNODE_KEY(node), RBNODE_VAL(node), NULL);
}
/** returns true if the node is terminal so no deeper domain names exist */
static int
is_terminal(struct local_data* d)
{
/* for empty nonterminals, the deeper domain names are sorted
* right after them, so simply check the next name in the tree
*/
struct local_data* n = (struct local_data*)rbtree_next(&d->node);
if(n == (struct local_data*)RBTREE_NULL)
return 1; /* last in tree, no deeper node */
if(dname_strict_subdomain(n->name, n->namelabs, d->name, d->namelabs))
return 0; /* there is a deeper node */
return 1;
}
/***********************************************************************
* Convert a tree of motifs into an array of motifs with a count.
* This is intended to allow backwards compatibility with the older
* version.
***********************************************************************/
void motif_tree_to_array(RBTREE_T *motif_tree, MOTIF_T **motif_array, int *num) {
int count, i;
MOTIF_T *motifs;
RBNODE_T *node;
count = rbtree_size(motif_tree);
motifs = mm_malloc(sizeof(MOTIF_T) * count);
for (i = 0, node = rbtree_first(motif_tree); node != NULL; i++, node = rbtree_next(node)) {
copy_motif((MOTIF_T*)rbtree_value(node), motifs+i);
}
*motif_array = motifs;
*num = count;
}
/*****************************************************************************
* MEME > training_set > /alphabet
* Read in the number of symbols in the alphabet and if it is nucleotide or
* amino-acid (RNA is apparently classed as nucleotide).
****************************************************************************/
void mxml_end_alphabet(void *ctx) {
PARMSG_T *message;
CTX_T *data;
RBNODE_T *node;
char *id, symbol;
bool *exists;
int i;
data = (CTX_T*)ctx;
if (data->alph == NULL) { // Custom alphabet
alph_reader_done(data->alph_rdr);
// report any errors that the alphabet reader found
while (alph_reader_has_message(data->alph_rdr)) {
message = alph_reader_next_message(data->alph_rdr);
if (message->severity == SEVERITY_ERROR) {
local_error(data, "Alphabet error: %s.\n", message->message);
} else {
local_warning(data, "Alphabet warning: %s.\n", message->message);
}
parmsg_destroy(message);
}
// try to get an alphabet
data->alph = alph_reader_alphabet(data->alph_rdr);
alph_reader_destroy(data->alph_rdr);
data->alph_rdr = NULL;
} else { // legacy alphabet
exists = mm_malloc(sizeof(bool) * alph_size_core(data->alph));
// set list to false
for (i = 0; i < alph_size_core(data->alph); i++) exists[i] = false;
// check that id's were defined for all the core alphabet symbols
for (node = rbtree_first(data->letter_lookup); node != NULL; node = rbtree_next(node)) {
id = (char*)rbtree_key(node);
symbol = ((char*)rbtree_value(node))[0];
if (exists[alph_indexc(data->alph, symbol)]) {
// duplicate!
local_error(data, "The letter identifier %s is not the first to refer to symbol %c.\n", id, symbol);
}
exists[alph_indexc(data->alph, symbol)] = true;
}
// now check for missing identifiers
for (i = 0; i < alph_size_core(data->alph); i++) {
if (!exists[i]) {
// missing id for symbol
local_error(data, "The symbol %c does not have an assigned identifier.\n", alph_char(data->alph, i));
}
}
free(exists);
}
}
int
forwards_next_root(struct iter_forwards* fwd, uint16_t* dclass)
{
struct iter_forward_zone key;
rbnode_t* n;
struct iter_forward_zone* p;
if(*dclass == 0) {
/* first root item is first item in tree */
n = rbtree_first(fwd->tree);
if(n == RBTREE_NULL)
return 0;
p = (struct iter_forward_zone*)n;
if(dname_is_root(p->name)) {
*dclass = p->dclass;
return 1;
}
/* root not first item? search for higher items */
*dclass = p->dclass + 1;
return forwards_next_root(fwd, dclass);
}
/* find class n in tree, we may get a direct hit, or if we don't
* this is the last item of the previous class so rbtree_next() takes
* us to the next root (if any) */
key.node.key = &key;
key.name = (uint8_t*)"\000";
key.namelen = 1;
key.namelabs = 0;
key.dclass = *dclass;
n = NULL;
if(rbtree_find_less_equal(fwd->tree, &key, &n)) {
/* exact */
return 1;
} else {
/* smaller element */
if(!n || n == RBTREE_NULL)
return 0; /* nothing found */
n = rbtree_next(n);
if(n == RBTREE_NULL)
return 0; /* no higher */
p = (struct iter_forward_zone*)n;
if(dname_is_root(p->name)) {
*dclass = p->dclass;
return 1;
}
/* not a root node, return next higher item */
*dclass = p->dclass+1;
return forwards_next_root(fwd, dclass);
}
}
/*
* Utility function for tree visualisation.
* Use gdb to call it.
*/
void mm_print_tree(char *tree)
{
if (!tree) {
printf("Empty\n");
return;
}
char *node = rbtree_first(tree);
while (node) {
printf("%p ", node);
node = rbtree_next(node);
}
printf("\n");
}
/** iterate over the kiddies of the given name and set their parent ptr */
static void
set_kiddo_parents(struct local_zone* z, struct local_zone* match,
struct local_zone* newp)
{
/* both zones and z are locked already */
/* in the sorted rbtree, the kiddies of z are located after z */
/* z must be present in the tree */
struct local_zone* p = z;
p = (struct local_zone*)rbtree_next(&p->node);
while(p!=(struct local_zone*)RBTREE_NULL &&
p->dclass == z->dclass && dname_strict_subdomain(p->name,
p->namelabs, z->name, z->namelabs)) {
/* update parent ptr */
/* only when matches with existing parent pointer, so that
* deeper child structures are not touched, i.e.
* update of x, and a.x, b.x, f.b.x, g.b.x, c.x, y
* gets to update a.x, b.x and c.x */
lock_rw_wrlock(&p->lock);
if(p->parent == match)
p->parent = newp;
lock_rw_unlock(&p->lock);
p = (struct local_zone*)rbtree_next(&p->node);
}
}
int router_list(struct router_t* router, int (*func)(void* param, struct node_t* node), void* param)
{
int r = 0;
struct rbitem_t* item;
const struct rbtree_node_t* node;
locker_lock(&router->locker);
node = rbtree_first(&router->rbtree);
while (node && 0 == r)
{
item = rbtree_entry(node, struct rbitem_t, link);
r = func(param, item->node);
node = rbtree_next(node);
}
locker_unlock(&router->locker);
return r;
}
/**************************************************************************
* Calculate the total number of pvalue calculations that will be done
* by the program. This number is used to correct the pvalues for multiple
* tests using a bonferoni correction.
**************************************************************************/
int calculate_test_count(int margin, int bin, int test_max, RBTREE_T *secondary_motifs) {
int total_tests, quad_opt_count, quad_bin_count;
SECONDARY_MOTIF_T *smotif;
RBNODE_T *node;
total_tests = 0;
for (node = rbtree_first(secondary_motifs); node != NULL; node = rbtree_next(node)) {
smotif = (SECONDARY_MOTIF_T*)rbtree_value(node);
//the number of possible values for spacings in one quadrant
quad_opt_count = margin - get_motif_trimmed_length(smotif->motif) + 1;
//the number of bins in one quadrant (excluding a possible leftover bin)
quad_bin_count = (int)(quad_opt_count / bin) + (quad_opt_count % bin ? 1 : 0);
//add the number of tested bins
total_tests += (test_max < quad_bin_count ? test_max : quad_bin_count) * 4;
}
return total_tests;
}
void start_net_interfaces_lib(void)
{
tree_node_t *ptr = (tree_node_t *) rbtree_first(interface_tree);
/*
* Now loop and start drivers.
*/
while (ptr) {
if (ptr->ni && ptr->ni->drv && ptr->ni->drv->start_fn(ptr->ni->unit)) {
kerrprintf("Failed starting %s\n", ptr->ni->name);
} else {
kmsgprintf("Interface %s started, MTU %u\n",
ptr->ni->name,
ptr->ni->mtu);
}
ptr = (tree_node_t *) rbtree_next(interface_tree, &ptr->header, cmpfn);
}
}
/**************************************************************************
* compute the list of ids for the most significant spacing
**************************************************************************/
void compute_idset(int margin, int bin_size, RBTREE_T *sequences, MOTIF_T *primary_motif, SECONDARY_MOTIF_T *secondary_motif, int *matches) {
int primary_len, secondary_len, secondary, secondary_pos, primary_rc, secondary_rc, quad, distance;
RBNODE_T *node;
SEQUENCE_T *sequence;
if (secondary_motif->sig_count == 0) return;
primary_len = get_motif_trimmed_length(primary_motif);
secondary_len = get_motif_trimmed_length(secondary_motif->motif);
// for each sequence
for (node = rbtree_first(sequences); node != NULL; node = rbtree_next(node)) {
sequence = (SEQUENCE_T*)rbtree_value(node);
secondary = matches[sequence->index];
// check for a match
if (!secondary) continue;
// convert the encoded form into easier to use form
primary_rc = sequence->primary_match < 0;
secondary_rc = secondary < 0;
secondary_pos = (secondary_rc ? -secondary : secondary);
// calculate the distance and side
// note that distance can be zero meaning the primary is next to the secondary
if (secondary_pos <= margin) {
distance = margin - secondary_pos - secondary_len + 1;
quad = LEFT;
} else {
distance = secondary_pos - margin - primary_len;
quad = RIGHT;
}
// calculate the strand
if (secondary_rc == primary_rc) {
quad |= SAME;
} else {
quad |= OPPO;
}
// add the sequence id to the set if the bin matches
if (quad == secondary_motif->sigs->quad && (distance / bin_size) == secondary_motif->sigs->bin) {
secondary_motif->seq_count += 1;
secondary_motif->seqs = (int*)mm_realloc(secondary_motif->seqs, sizeof(int) * secondary_motif->seq_count);
secondary_motif->seqs[secondary_motif->seq_count-1] = sequence->index;
}
}
}
void rbtree_remove(struct rbtree_node *node, struct rbtree *tree)
{
struct rbtree_node *parent = get_parent(node);
struct rbtree_node *left = node->left;
struct rbtree_node *right = node->right;
struct rbtree_node *next;
enum rb_color color;
if (node == tree->first)
tree->first = rbtree_next(node);
if (node == tree->last)
tree->last = rbtree_prev(node);
if (!left)
next = right;
else if (!right)
next = left;
else
next = get_first(right);
if (parent)
set_child(next, parent, parent->left == node);
else
tree->root = next;
if (left && right) {
color = get_color(next);
set_color(get_color(node), next);
next->left = left;
set_parent(next, left);
if (next != right) {
parent = get_parent(next);
set_parent(get_parent(node), next);
node = next->right;
parent->left = node;
next->right = right;
set_parent(next, right);
} else {
set_parent(parent, next);
parent = next;
node = next->right;
}
} else {
color = get_color(node);
node = next;
}
/*
* 'node' is now the sole successor's child and 'parent' its
* new parent (since the successor can have been moved).
*/
if (node)
set_parent(parent, node);
/*
* The 'easy' cases.
*/
if (color == RB_RED)
return;
if (node && is_red(node)) {
set_color(RB_BLACK, node);
return;
}
do {
if (node == tree->root)
break;
if (node == parent->left) {
struct rbtree_node *sibling = parent->right;
if (is_red(sibling)) {
set_color(RB_BLACK, sibling);
set_color(RB_RED, parent);
rotate_left(parent, tree);
sibling = parent->right;
}
if ((!sibling->left || is_black(sibling->left))
&& (!sibling->right || is_black(sibling->right))) {
set_color(RB_RED, sibling);
node = parent;
parent = get_parent(parent);
continue;
}
if (!sibling->right || is_black(sibling->right)) {
set_color(RB_BLACK, sibling->left);
set_color(RB_RED, sibling);
rotate_right(sibling, tree);
sibling = parent->right;
}
set_color(get_color(parent), sibling);
set_color(RB_BLACK, parent);
set_color(RB_BLACK, sibling->right);
rotate_left(parent, tree);
node = tree->root;
break;
} else {
struct rbtree_node *sibling = parent->left;
if (is_red(sibling)) {
set_color(RB_BLACK, sibling);
set_color(RB_RED, parent);
rotate_right(parent, tree);
sibling = parent->left;
}
if ((!sibling->left || is_black(sibling->left))
&& (!sibling->right || is_black(sibling->right))) {
set_color(RB_RED, sibling);
node = parent;
parent = get_parent(parent);
continue;
}
if (!sibling->left || is_black(sibling->left)) {
set_color(RB_BLACK, sibling->right);
set_color(RB_RED, sibling);
rotate_left(sibling, tree);
sibling = parent->left;
}
set_color(get_color(parent), sibling);
set_color(RB_BLACK, parent);
set_color(RB_BLACK, sibling->left);
rotate_right(parent, tree);
node = tree->root;
break;
}
} while (is_black(node));
if (node)
set_color(RB_BLACK, node);
}
void
xfrd_write_state(struct xfrd_state* xfrd)
{
rbnode_t* p;
const char* statefile = xfrd->nsd->options->xfrdfile;
FILE *out;
time_t now = xfrd_time();
DEBUG(DEBUG_XFRD,1, (LOG_INFO, "xfrd: write file %s", statefile));
out = fopen(statefile, "w");
if(!out) {
log_msg(LOG_ERR, "xfrd: Could not open file %s for writing: %s",
statefile, strerror(errno));
return;
}
fprintf(out, "%s\n", XFRD_FILE_MAGIC);
fprintf(out, "# This file is written on exit by nsd xfr daemon.\n");
fprintf(out, "# This file contains slave zone information:\n");
fprintf(out, "# * timeouts (when was zone data acquired)\n");
fprintf(out, "# * state (OK, refreshing, expired)\n");
fprintf(out, "# * which master transfer to attempt next\n");
fprintf(out, "# The file is read on start (but not on reload) by nsd xfr daemon.\n");
fprintf(out, "# You can edit; but do not change statement order\n");
fprintf(out, "# and no fancy stuff (like quoted \"strings\").\n");
fprintf(out, "#\n");
fprintf(out, "# If you remove a zone entry, it will be refreshed.\n");
fprintf(out, "# This can be useful for an expired zone; it revives\n");
fprintf(out, "# the zone temporarily, from refresh-expiry time.\n");
fprintf(out, "# If you delete the file all slave zones are updated.\n");
fprintf(out, "#\n");
fprintf(out, "# Note: if you edit this file while nsd is running,\n");
fprintf(out, "# it will be overwritten on exit by nsd.\n");
fprintf(out, "\n");
fprintf(out, "filetime: %lld\t# %s\n", (long long)now, ctime(&now));
fprintf(out, "# The number of zone entries in this file\n");
fprintf(out, "numzones: %d\n", (int)xfrd->zones->count);
fprintf(out, "\n");
for(p = rbtree_first(xfrd->zones); p && p!=RBTREE_NULL; p=rbtree_next(p))
{
xfrd_zone_t* zone = (xfrd_zone_t*)p;
fprintf(out, "zone: \tname: %s\n", zone->apex_str);
fprintf(out, "\tstate: %d", (int)zone->state);
fprintf(out, " # %s", zone->state==xfrd_zone_ok?"OK":(
zone->state==xfrd_zone_refreshing?"refreshing":"expired"));
fprintf(out, "\n");
fprintf(out, "\tmaster: %d\n", zone->master_num);
fprintf(out, "\tnext_master: %d\n", zone->next_master);
fprintf(out, "\tround_num: %d\n", zone->round_num);
fprintf(out, "\tnext_timeout: %d",
(zone->zone_handler_flags&EV_TIMEOUT)?(int)zone->timeout.tv_sec:0);
if((zone->zone_handler_flags&EV_TIMEOUT)) {
neato_timeout(out, "\t# =", zone->timeout.tv_sec);
}
fprintf(out, "\n");
xfrd_write_state_soa(out, "soa_nsd", &zone->soa_nsd,
zone->soa_nsd_acquired, zone->apex);
xfrd_write_state_soa(out, "soa_disk", &zone->soa_disk,
zone->soa_disk_acquired, zone->apex);
xfrd_write_state_soa(out, "soa_notify", &zone->soa_notified,
zone->soa_notified_acquired, zone->apex);
fprintf(out, "\n");
}
fprintf(out, "%s\n", XFRD_FILE_MAGIC);
DEBUG(DEBUG_XFRD,1, (LOG_INFO, "xfrd: written %d zones to state file",
(int)xfrd->zones->count));
fclose(out);
}
int rrset_canonical_equal(struct regional* region,
struct ub_packed_rrset_key* k1, struct ub_packed_rrset_key* k2)
{
struct rbtree_t sortree1, sortree2;
struct canon_rr *rrs1, *rrs2, *p1, *p2;
struct packed_rrset_data* d1=(struct packed_rrset_data*)k1->entry.data;
struct packed_rrset_data* d2=(struct packed_rrset_data*)k2->entry.data;
struct ub_packed_rrset_key fk;
struct packed_rrset_data fd;
size_t flen[2];
uint8_t* fdata[2];
/* basic compare */
if(k1->rk.dname_len != k2->rk.dname_len ||
k1->rk.flags != k2->rk.flags ||
k1->rk.type != k2->rk.type ||
k1->rk.rrset_class != k2->rk.rrset_class ||
query_dname_compare(k1->rk.dname, k2->rk.dname) != 0)
return 0;
if(d1->ttl != d2->ttl ||
d1->count != d2->count ||
d1->rrsig_count != d2->rrsig_count ||
d1->trust != d2->trust ||
d1->security != d2->security)
return 0;
/* init */
memset(&fk, 0, sizeof(fk));
memset(&fd, 0, sizeof(fd));
fk.entry.data = &fd;
fd.count = 2;
fd.rr_len = flen;
fd.rr_data = fdata;
rbtree_init(&sortree1, &canonical_tree_compare);
rbtree_init(&sortree2, &canonical_tree_compare);
if(d1->count > RR_COUNT_MAX || d2->count > RR_COUNT_MAX)
return 1; /* protection against integer overflow */
rrs1 = regional_alloc(region, sizeof(struct canon_rr)*d1->count);
rrs2 = regional_alloc(region, sizeof(struct canon_rr)*d2->count);
if(!rrs1 || !rrs2) return 1; /* alloc failure */
/* sort */
canonical_sort(k1, d1, &sortree1, rrs1);
canonical_sort(k2, d2, &sortree2, rrs2);
/* compare canonical-sorted RRs for canonical-equality */
if(sortree1.count != sortree2.count)
return 0;
p1 = (struct canon_rr*)rbtree_first(&sortree1);
p2 = (struct canon_rr*)rbtree_first(&sortree2);
while(p1 != (struct canon_rr*)RBTREE_NULL &&
p2 != (struct canon_rr*)RBTREE_NULL) {
flen[0] = d1->rr_len[p1->rr_idx];
flen[1] = d2->rr_len[p2->rr_idx];
fdata[0] = d1->rr_data[p1->rr_idx];
fdata[1] = d2->rr_data[p2->rr_idx];
if(canonical_compare(&fk, 0, 1) != 0)
return 0;
p1 = (struct canon_rr*)rbtree_next(&p1->node);
p2 = (struct canon_rr*)rbtree_next(&p2->node);
}
return 1;
}
/**************************************************************************
* Dump sequence matches sorted by the name of the sequence.
*
* Outputs Columns:
* 1) Trimmed lowercase sequence with uppercase matches.
* 2) Position of the secondary match within the whole sequence.
* 3) Sequence fragment that the primary matched.
* 4) Strand of the primary match (+|-)
* 5) Sequence fragment that the secondary matched.
* 6) Strand of the secondary match (+|-)
* 7) Is the primary match on the same strand as the secondary (s|o)
* 8) Is the secondary match downstream or upstream (d|u)
* 9) The gap between the primary and secondary matches
* 10) The name of the sequence
* 11) The p-value of the bin containing the match (adjusted for # of bins)
* ---if the FASTA input file sequence names are in Genome Browser format:
* 12-14) Position of primary match in BED coordinates
* 15) Position of primary match in Genome Browser coordinates
* 16-18) Position of secondary match in BED coordinates
* 19) Position of secondary match in Genome Browser coordinates
*
* If you wish to sort based on the gap column:
* Sort individual output:
* sort -n -k 9,9 -o seqs_primary_secondary.txt seqs_primary_secondary.txt
* Or sort all outputs:
* for f in seqs_*.txt; do sort -n -k 9,9 -o $f $f; done
* Or to get just locations of primary motif in BED coordinates
* where the secondary is on the opposite strand, upstream with a gap of 118bp:
* awk '$7=="o" && $8=="u" && $9==118 {print $12"\t"$13"\t"$14;}' seqs_primary_secondary.txt
*
**************************************************************************/
static void dump_sequence_matches(FILE *out, int margin, int bin,
double sigthresh, BOOLEAN_T sig_only, RBTREE_T *sequences,
MOTIF_T *primary_motif, SECONDARY_MOTIF_T *secondary_motif,
ARRAY_T **matches) {
RBNODE_T *node;
SEQUENCE_T *sequence;
int idx, seqlen, i, j, start, end, secondary, secondary_pos, primary_len, secondary_len, distance;
BOOLEAN_T primary_rc, secondary_rc, downstream;
char *buffer, *seq, *primary_match, *secondary_match;
ARRAY_T *secondary_array;
ALPH_T *alph;
// get the alphabet
alph = get_motif_alph(primary_motif);
// allocate a buffer for copying the trimmed sequence into and modify it
seqlen = margin * 2 + get_motif_trimmed_length(primary_motif);
buffer = (char*)mm_malloc(sizeof(char) * (seqlen + 1));
// get the lengths of the motifs
primary_len = get_motif_trimmed_length(primary_motif);
secondary_len = get_motif_trimmed_length(secondary_motif->motif);
// allocate some strings for storing the matches
primary_match = (char*)mm_malloc(sizeof(char) * (primary_len + 1));
secondary_match = (char*)mm_malloc(sizeof(char) * (secondary_len + 1));
// add null byte at the end of the match strings
primary_match[primary_len] = '\0';
secondary_match[secondary_len] = '\0';
// iterate over all the sequences
for (node = rbtree_first(sequences); node != NULL; node = rbtree_next(node)) {
sequence = (SEQUENCE_T*)rbtree_value(node);
primary_rc = get_array_item(0, sequence->primary_matches) < 0;
//secondary = matches[sequence->index];
secondary_array = matches[sequence->index];
if (! secondary_array) continue;
int n_secondary_matches = get_array_length(secondary_array);
for (idx=0; idx<n_secondary_matches; idx++) {
secondary = get_array_item(idx, secondary_array);
secondary_rc = secondary < 0;
secondary_pos = abs(secondary);
// calculate the distance
if (secondary_pos <= margin) {
distance = margin - secondary_pos - secondary_len + 1;
downstream = primary_rc;
} else {
distance = secondary_pos - margin - primary_len - 1;
downstream = !primary_rc;
}
// copy the trimmed sequence
seq = sequence->data;
for (i = 0; i < seqlen; ++i) {
buffer[i] = (alph_is_case_insensitive(alph) ? tolower(seq[i]) : seq[i]);
}
buffer[seqlen] = '\0';
// uppercase primary
start = margin;
end = margin + primary_len;
for (i = start, j = 0; i < end; ++i, ++j) {
buffer[i] = (alph_is_case_insensitive(alph) ? toupper(buffer[i]) : buffer[i]);
primary_match[j] = buffer[i];
}
// uppercase secondary
// note orign was one, subtract 1 to make origin zero as required for arrays
start = secondary_pos -1;
end = start + secondary_len;
for (i = start, j = 0; i < end; ++i, ++j) {
buffer[i] = (alph_is_case_insensitive(alph) ? toupper(buffer[i]) : buffer[i]);
secondary_match[j] = buffer[i];
}
// get the p-value of the seconndary match
SPACING_T *spacings;
if (secondary_rc == primary_rc) {
spacings = downstream ? secondary_motif->spacings+(SAME+RIGHT) : secondary_motif->spacings+(SAME+LEFT);
} else {
spacings = downstream ? secondary_motif->spacings+(OPPO+RIGHT) : secondary_motif->spacings+(OPPO+LEFT);
}
double p_value = spacings->pvalue[distance/bin];
// skip match if not significant and only reporting significant matches
if (sig_only && (p_value > sigthresh)) continue;
// output line to file
fprintf(out, "%s %3d %s %s %s %s %s %s %3d %s %.1e",
buffer,
secondary_pos,
primary_match,
(primary_rc ? "-" : "+"),
secondary_match,
(secondary_rc ? "-" : "+"),
(secondary_rc == primary_rc ? "s" : "o"),
(downstream ? "d" : "u"),
distance,
sequence->name,
p_value
);
// Parse the sequence name to see if we can get genomic coordinates
// and print additional columns with primary and secondary matches
// in both BED and Genome Browser coordinates.
char *chr_name;
size_t chr_name_len;
int start_pos, end_pos;
if (parse_genomic_coordinates_helper(
sequence->name,
&chr_name,
&chr_name_len,
&start_pos,
&end_pos))
{
// Get the start and end of the primary match in
// 0-relative, half-open genomic coordinates.
int p_start = start_pos + fabs(get_array_item(0, sequence->primary_matches)) - 1;
int p_end = p_start + primary_len;
// Get the start and end of the secondary match in
// 0-relative, half-open genomic coordinates.
int s_start, s_end;
if ( (!primary_rc && downstream) || (primary_rc && !downstream) ) {
s_start = p_end + distance;
s_end = s_start + secondary_len;
} else {
s_end = p_start - distance;
s_start = s_end - secondary_len;
}
fprintf(out, " %s %d %d %s:%d-%d",
chr_name, p_start, p_end, chr_name, p_start+1, p_end);
fprintf(out, " %s %d %d %s:%d-%d\n",
chr_name, s_start, s_end, chr_name, s_start+1, s_end);
} else {
fprintf(out, "\n");
}
} // secondary match
} // primary match
free(buffer);
free(primary_match);
free(secondary_match);
}
/**
* Remove NSEC records between start and end points.
* By walking the tree, the tree is sorted canonically.
* @param neg: negative cache.
* @param zone: the zone
* @param el: element to start walking at.
* @param nsec: the nsec record with the end point
*/
static void wipeout(struct val_neg_cache* neg, struct val_neg_zone* zone,
struct val_neg_data* el, struct ub_packed_rrset_key* nsec)
{
struct packed_rrset_data* d = (struct packed_rrset_data*)nsec->
entry.data;
uint8_t* end;
size_t end_len;
int end_labs, m;
rbnode_t* walk, *next;
struct val_neg_data* cur;
uint8_t buf[257];
/* get endpoint */
if(!d || d->count == 0 || d->rr_len[0] < 2+1)
return;
if(ntohs(nsec->rk.type) == LDNS_RR_TYPE_NSEC) {
end = d->rr_data[0]+2;
end_len = dname_valid(end, d->rr_len[0]-2);
end_labs = dname_count_labels(end);
} else {
/* NSEC3 */
if(!nsec3_get_nextowner_b32(nsec, 0, buf, sizeof(buf)))
return;
end = buf;
end_labs = dname_count_size_labels(end, &end_len);
}
/* sanity check, both owner and end must be below the zone apex */
if(!dname_subdomain_c(el->name, zone->name) ||
!dname_subdomain_c(end, zone->name))
return;
/* detect end of zone NSEC ; wipe until the end of zone */
if(query_dname_compare(end, zone->name) == 0) {
end = NULL;
}
walk = rbtree_next(&el->node);
while(walk && walk != RBTREE_NULL) {
cur = (struct val_neg_data*)walk;
/* sanity check: must be larger than start */
if(dname_canon_lab_cmp(cur->name, cur->labs,
el->name, el->labs, &m) <= 0) {
/* r == 0 skip original record. */
/* r < 0 too small! */
walk = rbtree_next(walk);
continue;
}
/* stop at endpoint, also data at empty nonterminals must be
* removed (no NSECs there) so everything between
* start and end */
if(end && dname_canon_lab_cmp(cur->name, cur->labs,
end, end_labs, &m) >= 0) {
break;
}
/* this element has to be deleted, but we cannot do it
* now, because we are walking the tree still ... */
/* get the next element: */
next = rbtree_next(walk);
/* now delete the original element, this may trigger
* rbtree rebalances, but really, the next element is
* the one we need.
* But it may trigger delete of other data and the
* entire zone. However, if that happens, this is done
* by deleting the *parents* of the element for deletion,
* and maybe also the entire zone if it is empty.
* But parents are smaller in canonical compare, thus,
* if a larger element exists, then it is not a parent,
* it cannot get deleted, the zone cannot get empty.
* If the next==NULL, then zone can be empty. */
if(cur->in_use)
neg_delete_data(neg, cur);
walk = next;
}
}
query_state_type
query_axfr(struct nsd *nsd, struct query *query)
{
domain_type *closest_match;
domain_type *closest_encloser;
int exact;
int added;
uint16_t total_added = 0;
if (query->axfr_is_done)
return QUERY_PROCESSED;
if (query->maxlen > AXFR_MAX_MESSAGE_LEN)
query->maxlen = AXFR_MAX_MESSAGE_LEN;
assert(!query_overflow(query));
/* only keep running values for most packets */
query->tsig_prepare_it = 0;
query->tsig_update_it = 1;
if(query->tsig_sign_it) {
/* prepare for next updates */
query->tsig_prepare_it = 1;
query->tsig_sign_it = 0;
}
if (query->axfr_zone == NULL) {
/* Start AXFR. */
exact = namedb_lookup(nsd->db,
query->qname,
&closest_match,
&closest_encloser);
query->domain = closest_encloser;
query->axfr_zone = domain_find_zone(closest_encloser);
if (!exact
|| query->axfr_zone == NULL
|| query->axfr_zone->apex != query->domain)
{
/* No SOA no transfer */
RCODE_SET(query->packet, RCODE_NOTAUTH);
return QUERY_PROCESSED;
}
query->axfr_current_domain
= (domain_type *) rbtree_first(nsd->db->domains->names_to_domains);
query->axfr_current_rrset = NULL;
query->axfr_current_rr = 0;
if(query->tsig.status == TSIG_OK) {
query->tsig_sign_it = 1; /* sign first packet in stream */
}
query_add_compression_domain(query, query->domain, QHEADERSZ);
assert(query->axfr_zone->soa_rrset->rr_count == 1);
added = packet_encode_rr(query,
query->axfr_zone->apex,
&query->axfr_zone->soa_rrset->rrs[0]);
if (!added) {
/* XXX: This should never happen... generate error code? */
abort();
}
++total_added;
} else {
/*
* Query name and EDNS need not be repeated after the
* first response packet.
*/
query->edns.status = EDNS_NOT_PRESENT;
buffer_set_limit(query->packet, QHEADERSZ);
QDCOUNT_SET(query->packet, 0);
query_prepare_response(query);
}
/* Add zone RRs until answer is full. */
assert(query->axfr_current_domain);
while ((rbnode_t *) query->axfr_current_domain != RBTREE_NULL) {
if (!query->axfr_current_rrset) {
query->axfr_current_rrset = domain_find_any_rrset(
query->axfr_current_domain,
query->axfr_zone);
query->axfr_current_rr = 0;
}
while (query->axfr_current_rrset) {
if (query->axfr_current_rrset != query->axfr_zone->soa_rrset
&& query->axfr_current_rrset->zone == query->axfr_zone)
{
while (query->axfr_current_rr < query->axfr_current_rrset->rr_count) {
added = packet_encode_rr(
query,
query->axfr_current_domain,
&query->axfr_current_rrset->rrs[query->axfr_current_rr]);
if (!added)
goto return_answer;
++total_added;
++query->axfr_current_rr;
}
}
query->axfr_current_rrset = query->axfr_current_rrset->next;
query->axfr_current_rr = 0;
}
assert(query->axfr_current_domain);
query->axfr_current_domain
= (domain_type *) rbtree_next((rbnode_t *) query->axfr_current_domain);
}
/* Add terminating SOA RR. */
assert(query->axfr_zone->soa_rrset->rr_count == 1);
added = packet_encode_rr(query,
query->axfr_zone->apex,
&query->axfr_zone->soa_rrset->rrs[0]);
if (added) {
++total_added;
query->tsig_sign_it = 1; /* sign last packet */
query->axfr_is_done = 1;
}
return_answer:
AA_SET(query->packet);
ANCOUNT_SET(query->packet, total_added);
NSCOUNT_SET(query->packet, 0);
ARCOUNT_SET(query->packet, 0);
/* check if it needs tsig signatures */
if(query->tsig.status == TSIG_OK) {
if(query->tsig.updates_since_last_prepare >= AXFR_TSIG_SIGN_EVERY_NTH) {
query->tsig_sign_it = 1;
}
}
query_clear_compression_tables(query);
return QUERY_IN_AXFR;
}
int main()
{
int i, count = 30;
key_t key;
RBTreeNodeHandle root = NULL;
int test_addr = 0;
key_t search_key = -1;
key_t delete_key = -1;
srand(1103515245);
for (i = 1; i < count; ++i)
{
key = rand() % count;
test_addr = key;
AGILE_LOGI("key = %d", key);
root = rbtree_insert(root, key, (void *)&test_addr);
if (!(i % 188)){
AGILE_LOGI("[i = %d] set search key %d", i, key);
search_key = key;
}
if (!(i % 373)){
AGILE_LOGI("[i = %d] set delete key %d", i, key);
delete_key = key;
}
if (search_key > 0){
if (rbtree_get(root, search_key))
{
AGILE_LOGI("[i = %d] search key %d success!", i, search_key);
search_key = -1;
}
else
{
AGILE_LOGI("[i = %d] search key %d error!", i, search_key);
return (-1);
}
}
if (delete_key > 0)
{
AGILE_LOGI("****** Before delete: node number: %d, repeatKeyNum: %d", rbtree_dump(root, 0), rbtree_debug_getRepeatNum());
if (rbtree_delete(&root, delete_key) == 0)
{
AGILE_LOGI("[i = %d] delete key %d success (%d)", i, delete_key, ++deleteNum);
delete_key = -1;
}
else
{
AGILE_LOGI("[i = %d] delete key %d error", i, delete_key);
return -1;
}
AGILE_LOGI("****** After delete: node number: %d", rbtree_dump(root, 0));
/*return 0;*/
}
/*rbtree_dump(root, 1);*/
}
{
RBTreeNodeHandle n;
i = 0;
for (n = rbtree_first(root); n; n = rbtree_next(n)) {
AGILE_LOGI("index %d: key - %lld", i, n->key);
i++;
}
}
return 0;
}
/*
* Load background file frequencies into the array.
*/
ARRAY_T* get_file_frequencies(ALPH_T *alph, char *bg_filename, ARRAY_T *freqs) {
regmatch_t matches[4];
STR_T *line;
char chunk[BG_CHUNK_SIZE+1], letter[2], *key;
int size, terminate, offset, i;
FILE *fp;
regex_t bgfreq;
double freq;
RBTREE_T *letters;
RBNODE_T *node;
regcomp_or_die("bg freq", &bgfreq, BGFREQ_RE, REG_EXTENDED);
letters = rbtree_create(rbtree_strcasecmp, rbtree_strcpy, free, rbtree_dblcpy, free);
line = str_create(100);
if (!(fp = fopen(bg_filename, "r"))) {
die("Unable to open background file \"%s\" for reading.\n", bg_filename);
}
terminate = feof(fp);
while (!terminate) {
size = fread(chunk, sizeof(char), BG_CHUNK_SIZE, fp);
chunk[size] = '\0';
terminate = feof(fp);
offset = 0;
while (offset < size) {
// skip mac newline
if (str_len(line) == 0 && chunk[offset] == '\r') {
offset++;
continue;
}
// find next new line
for (i = offset; i < size; ++i) {
if (chunk[i] == '\n') break;
}
// append portion up to the new line or end of chunk
str_append(line, chunk+offset, i - offset);
// read more if we didn't find a new line
if (i == size && !terminate) break;
// move the offset past the new line
offset = i + 1;
// handle windows new line
if (str_char(line, -1) == '\r') str_truncate(line, -1);
// remove everything to the right of a comment character
for (i = 0; i < str_len(line); ++i) {
if (str_char(line, i) == '#') {
str_truncate(line, i);
break;
}
}
// check the line for a single letter followed by a number
if (regexec_or_die("bg freq", &bgfreq, str_internal(line), 4, matches, 0)) {
// parse the letter and frequency value
regex_strncpy(matches+1, str_internal(line), letter, 2);
freq = regex_dbl(matches+2, str_internal(line));
// check the frequency is acceptable
if (freq < 0 || freq > 1) {
die("The background file lists the illegal probability %g for "
"the letter %s.\n", freq, letter);
} else if (freq == 0) {
die("The background file lists a probability of zero for the "
"letter %s\n", letter);
}
if (freq >= 0 && freq <= 1) rbtree_put(letters, letter, &freq);
}
str_clear(line);
}
}
// finished with the file so clean up file parsing stuff
fclose(fp);
str_destroy(line, FALSE);
regfree(&bgfreq);
// guess the alphabet
if (*alph == INVALID_ALPH) {
switch (rbtree_size(letters)) {
case PROTEIN_ASIZE:
*alph = PROTEIN_ALPH;
break;
case DNA_ASIZE:
*alph = DNA_ALPH;
break;
default:
die("Number of single character entries in background does not match "
"an alphabet.\n");
}
}
// make the background
if (freqs == NULL) freqs = allocate_array(alph_size(*alph, ALL_SIZE));
assert(get_array_length(freqs) >= alph_size(*alph, ALL_SIZE));
init_array(-1, freqs);
for (node = rbtree_first(letters); node != NULL; node = rbtree_next(node)) {
key = (char*)rbtree_key(node);
i = alph_index(*alph, key[0]);
freq = *((double*)rbtree_value(node));
if (i == -1) {
die("Background contains letter %s which is not in the %s alphabet.\n",
key, alph_name(*alph));
}
if (get_array_item(i, freqs) != -1) {
die("Background contains letter %s which has the same meaning as an "
"already listed letter.\n", key);
}
set_array_item(i, freq, freqs);
}
// check that all items were set
for (i = 0; i < alph_size(*alph, ALPH_SIZE); i++) {
if (get_array_item(i, freqs) == -1) {
die("Background is missing letter %c.\n", alph_char(*alph, i));
}
}
// disabled for backwards compatability (AMA test was failing)
//normalize_subarray(0, ALPH_ASIZE[*alph], 0.0, freqs);
// calculate the values of the ambiguous letters from the concrete ones
calc_ambigs(*alph, FALSE, freqs);
// cleanup
rbtree_destroy(letters);
// return result
return freqs;
}
/** remove a random item */
static void remove_item(struct val_neg_cache* neg)
{
int n, i;
struct val_neg_data* d;
rbnode_t* walk;
struct val_neg_zone* z;
lock_basic_lock(&neg->lock);
if(neg->tree.count == 0) {
lock_basic_unlock(&neg->lock);
return; /* nothing to delete */
}
/* pick a random zone */
walk = rbtree_first(&neg->tree); /* first highest parent, big count */
z = (struct val_neg_zone*)walk;
n = random() % (int)(z->count);
if(negverbose)
printf("neg stress delete zone %d\n", n);
i=0;
walk = rbtree_first(&neg->tree);
z = (struct val_neg_zone*)walk;
while(i!=n+1 && walk && walk != RBTREE_NULL && !z->in_use) {
walk = rbtree_next(walk);
z = (struct val_neg_zone*)walk;
if(z->in_use)
i++;
}
if(!walk || walk == RBTREE_NULL) {
lock_basic_unlock(&neg->lock);
return;
}
if(!z->in_use) {
lock_basic_unlock(&neg->lock);
return;
}
if(negverbose)
log_nametypeclass(0, "delete zone", z->name, 0, 0);
/* pick a random nsec item. - that is in use */
walk = rbtree_first(&z->tree); /* first is highest parent */
d = (struct val_neg_data*)walk;
n = random() % (int)(d->count);
if(negverbose)
printf("neg stress delete item %d\n", n);
i=0;
walk = rbtree_first(&z->tree);
d = (struct val_neg_data*)walk;
while(i!=n+1 && walk && walk != RBTREE_NULL && !d->in_use) {
walk = rbtree_next(walk);
d = (struct val_neg_data*)walk;
if(d->in_use)
i++;
}
if(!walk || walk == RBTREE_NULL) {
lock_basic_unlock(&neg->lock);
return;
}
if(d->in_use) {
if(negverbose)
log_nametypeclass(0, "neg delete item:", d->name, 0, 0);
neg_delete_data(neg, d);
}
lock_basic_unlock(&neg->lock);
}
