/*
* 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;
}
/*
* Destroy the specified tree, calling the destructor destroy
* for each node and then freeing the tree itself.
*/
void rbtree_destroy(struct rbtree *tree, void (*destroy)(void *))
{
if (!tree)
return;
if (rbtree_first(tree))
_rbdestroy(tree, rbtree_first(tree), destroy);
free(tree);
}
/** call timeouts handlers, and return how long to wait for next one or -1 */
static void handle_timeouts(struct event_base* base, struct timeval* now,
struct timeval* wait)
{
struct event* p;
#ifndef S_SPLINT_S
wait->tv_sec = (time_t)-1;
#endif
while((rbnode_t*)(p = (struct event*)rbtree_first(base->times))
!=RBTREE_NULL) {
#ifndef S_SPLINT_S
if(p->ev_timeout.tv_sec > now->tv_sec ||
(p->ev_timeout.tv_sec==now->tv_sec &&
p->ev_timeout.tv_usec > now->tv_usec)) {
/* there is a next larger timeout. wait for it */
wait->tv_sec = p->ev_timeout.tv_sec - now->tv_sec;
if(now->tv_usec > p->ev_timeout.tv_usec) {
wait->tv_sec--;
wait->tv_usec = 1000000 - (now->tv_usec -
p->ev_timeout.tv_usec);
} else {
wait->tv_usec = p->ev_timeout.tv_usec
- now->tv_usec;
}
return;
}
#endif
/* event times out, remove it */
(void)rbtree_delete(base->times, p);
p->ev_events &= ~EV_TIMEOUT;
fptr_ok(fptr_whitelist_event(p->ev_callback));
(*p->ev_callback)(p->ev_fd, EV_TIMEOUT, p->ev_arg);
}
}
/*
* 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;
}
static void rbtree_1(CuTest *tc)
{
/* tree should be empty on start. */
CuAssert(tc, "empty tree?", (rbtree_first((rbtree_t*)tree) == &rbtree_null_node));
CuAssert(tc, "empty tree?", (rbtree_last((rbtree_t*)tree) == &rbtree_null_node));
test_tree_integrity(tc, tree);
}
/**
* 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;
}
net_interface_t *net_interface_first()
{
rbtree_node_t *retval;
retval = rbtree_first(interface_tree);
return ((retval) ? (((tree_node_t *) retval)->ni) : NULL);
}
/*****************************************************************************
* 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);
}
}
}
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;
}
/**************************************************************************
* 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 char *rbtree_next(char *node)
{
char *parent;
if (rbtree_get_right(node))
return rbtree_first(rbtree_get_right(node));
while ((parent = rb_get_parent(node)) && rbtree_get_right(parent) == node)
node = parent;
return parent;
}
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);
}
}
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;
}
/** sum up the zone trees, in_use only */
static size_t sumtrees_inuse(struct val_neg_cache* neg)
{
size_t res = 0;
struct val_neg_zone* z;
struct val_neg_data* d;
RBTREE_FOR(z, struct val_neg_zone*, &neg->tree) {
/* get count of highest parent for num in use */
d = (struct val_neg_data*)rbtree_first(&z->tree);
if(d && (rbnode_t*)d!=RBTREE_NULL)
res += d->count;
}
return res;
}
/***********************************************************************
* 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;
}
/*
* Look for a node matching key in tree.
* Returns a pointer to the node if found, else NULL.
*/
struct rbnode *rbtree_find_node(struct rbtree *tree, void *key)
{
struct rbnode *node = rbtree_first(tree);
int res;
while (node != rbnil(tree)) {
if ((res = tree->compar(key, node->data)) == 0) {
return (node);
}
node = res < 0 ? node->left : node->right;
}
return (NULL);
}
/*****************************************************************************
* 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");
}
/**************************************************************************
* 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;
}
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;
}
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;
}
}
}
/*
* Delete node 'z' from the tree and return its data pointer.
*/
void *rbtree_delete(struct rbtree *tree, struct rbnode *z)
{
struct rbnode *x, *y;
void *data = z->data;
if (z->left == rbnil(tree) || z->right == rbnil(tree)) {
y = z;
} else {
y = rbsuccessor(tree, z);
}
x = (y->left == rbnil(tree)) ? y->right : y->left;
if ((x->parent = y->parent) == rbtree_root(tree)) {
rbtree_first(tree) = x;
} else {
if (y == y->parent->left) {
y->parent->left = x;
} else {
y->parent->right = x;
}
}
if (y->color == black) {
rbrepair(tree, x);
}
if (y != z) {
y->left = z->left;
y->right = z->right;
y->parent = z->parent;
y->color = z->color;
z->left->parent = z->right->parent = y;
if (z == z->parent->left) {
z->parent->left = y;
} else {
z->parent->right = y;
}
}
free(z);
tree->num_nodes--;
return (data);
}
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);
}
/**************************************************************************
* 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);
}
/*
* If a node matching "data" already exists, a pointer to
* the existant node is returned. Otherwise we return NULL.
*/
struct rbnode *rbtree_insert(struct rbtree *tree, void *data)
{
struct rbnode *node = rbtree_first(tree);
struct rbnode *parent = rbtree_root(tree);
int res;
/* Find correct insertion point. */
while (node != rbnil(tree)) {
parent = node;
if ((res = tree->compar(data, node->data)) == 0) {
return (node);
}
node = res < 0 ? node->left : node->right;
}
node = (struct rbnode *) malloc(sizeof(*node));
node->data = data;
node->left = node->right = rbnil(tree);
node->parent = parent;
if (parent == rbtree_root(tree) || tree->compar(data, parent->data) < 0) {
parent->left = node;
} else {
parent->right = node;
}
node->color = red;
/*
* If the parent node is black we are all set, if it is red we have
* the following possible cases to deal with. We iterate through
* the rest of the tree to make sure none of the required properties
* is violated.
*
* 1) The uncle is red. We repaint both the parent and uncle black
* and repaint the grandparent node red.
*
* 2) The uncle is black and the new node is the right child of its
* parent, and the parent in turn is the left child of its parent.
* We do a left rotation to switch the roles of the parent and
* child, relying on further iterations to fixup the old parent.
*
* 3) The uncle is black and the new node is the left child of its
* parent, and the parent in turn is the left child of its parent.
* We switch the colors of the parent and grandparent and perform
* a right rotation around the grandparent. This makes the former
* parent the parent of the new node and the former grandparent.
*
* Note that because we use a sentinel for the root node we never
* need to worry about replacing the root.
*/
while (node->parent->color == red) {
struct rbnode *uncle;
if (node->parent == node->parent->parent->left) {
uncle = node->parent->parent->right;
if (uncle->color == red) {
node->parent->color = black;
uncle->color = black;
node->parent->parent->color = red;
node = node->parent->parent;
} else { /* if (uncle->color == black) */
if (node == node->parent->right) {
node = node->parent;
rotate_left(tree, node);
}
node->parent->color = black;
node->parent->parent->color = red;
rotate_right(tree, node->parent->parent);
}
} else { /* if (node->parent == node->parent->parent->right) */
uncle = node->parent->parent->left;
if (uncle->color == red) {
node->parent->color = black;
uncle->color = black;
node->parent->parent->color = red;
node = node->parent->parent;
} else { /* if (uncle->color == black) */
if (node == node->parent->left) {
node = node->parent;
rotate_right(tree, node);
}
node->parent->color = black;
node->parent->parent->color = red;
rotate_left(tree, node->parent->parent);
}
}
}
tree->num_nodes++;
rbtree_first(tree)->color = black; /* first node is always black */
return (NULL);
}
static void rbtree_7(CuTest *tc)
{
CuAssert(tc, "rbtree_first(tree) == findsmallest(tree->root)", rbtree_first(tree) == findsmallest(tree->root));
CuAssert(tc, "rbtree_last(tree) == findlargest(tree->root)", rbtree_last(tree) == findlargest(tree->root));
}
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;
}
static void rbtree_remove(char *node, char **tree)
{
char *parent = rb_get_parent(node);
char *left = rbtree_get_left(node);
char *right = rbtree_get_right(node);
char *next;
int color;
if (!left)
next = right;
else if (!right)
next = left;
else
next = rbtree_first(right);
if (parent)
rb_set_child(next, parent, rbtree_get_left(parent) == node);
else
*tree = next;
if (left && right) {
color = rb_get_color(next);
rb_set_color(rb_get_color(node), next);
rb_set_left(left, next);
rb_set_parent(next, left);
if (next != right) {
parent = rb_get_parent(next);
rb_set_parent(rb_get_parent(node), next);
node = rbtree_get_right(next);
rb_set_left(node, parent);
rb_set_right(right, next);
rb_set_parent(next, right);
} else {
rb_set_parent(parent, next);
parent = next;
node = rbtree_get_right(next);
}
} else {
color = rb_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)
rb_set_parent(parent, node);
/*
* The 'easy' cases.
*/
if (color == RB_RED)
return;
if (node && rb_is_red(node)) {
rb_set_color(RB_BLACK, node);
return;
}
do {
if (node == *tree)
break;
if (node == rbtree_get_left(parent)) {
char *sibling = rbtree_get_right(parent);
if (rb_is_red(sibling)) {
rb_set_color(RB_BLACK, sibling);
rb_set_color(RB_RED, parent);
rb_rotate_left(parent, tree);
sibling = rbtree_get_right(parent);
}
if ((!rbtree_get_left(sibling) || rb_is_black(rbtree_get_left(sibling))) &&
(!rbtree_get_right(sibling) || rb_is_black(rbtree_get_right(sibling)))) {
rb_set_color(RB_RED, sibling);
node = parent;
parent = rb_get_parent(parent);
continue;
}
if (!rbtree_get_right(sibling) || rb_is_black(rbtree_get_right(sibling))) {
rb_set_color(RB_BLACK, rbtree_get_left(sibling));
rb_set_color(RB_RED, sibling);
rb_rotate_right(sibling, tree);
sibling = rbtree_get_right(parent);
}
rb_set_color(rb_get_color(parent), sibling);
rb_set_color(RB_BLACK, parent);
rb_set_color(RB_BLACK, rbtree_get_right(sibling));
rb_rotate_left(parent, tree);
node = *tree;
break;
} else {
char *sibling = rbtree_get_left(parent);
if (rb_is_red(sibling)) {
rb_set_color(RB_BLACK, sibling);
rb_set_color(RB_RED, parent);
rb_rotate_right(parent, tree);
sibling = rbtree_get_left(parent);
}
if ((!rbtree_get_left(sibling) || rb_is_black(rbtree_get_left(sibling))) &&
(!rbtree_get_right(sibling) || rb_is_black(rbtree_get_right(sibling)))) {
rb_set_color(RB_RED, sibling);
node = parent;
parent = rb_get_parent(parent);
continue;
}
if (!rbtree_get_left(sibling) || rb_is_black(rbtree_get_left(sibling))) {
rb_set_color(RB_BLACK, rbtree_get_right(sibling));
rb_set_color(RB_RED, sibling);
rb_rotate_left(sibling, tree);
sibling = rbtree_get_left(parent);
}
rb_set_color(rb_get_color(parent), sibling);
rb_set_color(RB_BLACK, parent);
rb_set_color(RB_BLACK, rbtree_get_left(sibling));
rb_rotate_right(parent, tree);
node = *tree;
break;
}
} while (rb_is_black(node));
if (node)
rb_set_color(RB_BLACK, node);
}
