//sample usage:
int main(){
int i=3;
char *q = NULL;
Sasprintf(q, "select * from tab");
Sasprintf(q, "%s where col%i is not null", q, i);
printf("%s\n", q);
}
void mem_leak_asprintf() {
int col_number=3, person_number=27;
/*NOT OK , free cause fail below Sasprintf*/
char *q;
/* fail with Sasprintf because it tries to free immutable string */
q = "asdsad";
/*free(NULL) cause segfault*/
q = NULL;
/* q should be initialize with strdup or set to null in order to use
Sasprintf macro otherwise a segfault is raised*/
q = strdup("select ");
/*memory leak for each of following steps*/
/*asprintf(&q, "%scol%i \n", q, col_number);*/
/*asprintf(&q, "%sfrom tab \n", q);*/
/*asprintf(&q, "%swhere person_id = %i", q, person_number);*/
int i = 3;
Sasprintf(q, "select * from tab");
Sasprintf(q, "%s where col%i is not null", q, i);
printf("%s\n", q);
/* only free the last allocated memory */
free(q);
}
phylo parseNewick(char *in) {
phylo p;
int lbrack = 0;
int rbrack = 0;
int comma = 0;
// dimension the phylo struct
for (int i = 0; i < strlen(in); i++)
{
// printf("%c", in[i]);
if (in[i] == 40) lbrack++;
else if (in[i] == 41) rbrack++;
else if (in[i] == 44) comma++;
}
if (lbrack != rbrack) error("Imbalanced parentheses in phylogeny file");
p.nnodes = lbrack + comma + 1;
p.parent = mem1d_i(p.nnodes);
p.ndaughter = mem1d_i(p.nnodes);
p.depth = mem1d_i(p.nnodes);
p.bl = mem1d_d(p.nnodes);
p.taxon = mem2d1_c(p.nnodes);
p.age = mem1d_d(p.nnodes);
// Move through the newick format tree character by character
int i = 0;
// start outside parentheses, one hypothetical node proximal to root node
int node = -1;
int parent = -2;
int nodeCount = 0;
int tmpn;
while ((i < strlen(in)) && (in[i] != 59))
{
// descend a branch, making new node for the parenthesis descended thru
if (in[i] == 40) // "("
{
parent = node;
// make a new node, set node to index of final row
nodeCount++;
node = nodeCount-1;
p.parent[node] = parent;
// first run case, since root has no parent data
if (node == 0) {
p.depth[node] = 0;
} else {
p.depth[node] = p.depth[parent] + 1;
p.ndaughter[parent]++;
}
/* printf("%c DOWN %d(%d)\n", in[i], node, parent);
printf(" new node %d, parent %d, depth %d\n",
node, p.parent[node], p.depth[node]); */
i++;
}
// sibling taxon, ignore
else if (in[i] == 44) // ","
{
node = parent;
parent = p.parent[node];
// printf("%c ACROSS %d(%d)\n", in[i], node, parent);
i++;
}
// back up a node to parent, keep track of locn with node
else if (in[i] == 41) // ")"
{
node = parent;
parent = p.parent[node];
// printf("%c UP %d(%d)\n", in[i], node, parent);
i++;
}
else
{
// Now, check for new taxa, or new interior name
//! \todo deal with quoted labels
// Is there nodename here? I.e., not `:' or `['
if ((in[i] != 58) && (in[i] != 91))
{
// Is it a new terminal? I.e., not following a `)'
if (in[i-1] != 41)
{
// creat new node
parent = node;
nodeCount++;
node = nodeCount-1;
p.parent[node] = parent;
p.depth[node] = p.depth[parent] + 1;
p.ndaughter[parent]++;
/* printf("%c TERM %d(%d)\n", in[i], node, parent);
printf(" new node %d, parent %d, depth %d\n", node,
p.parent[node], p.depth[node]); */
}
char *tmp = NULL; tmpn = 0;
// check for name, I.e. not `:' nor `['
while ((in[i] != 58) && (in[i] != 91) &&
(in[i] != 44) && (in[i] != 41) && (in[i] != 40) &&
(in[i] != 59))
{
if (!tmpn) {
asprintf(&tmp, "%c", in[i]); tmpn++;
} else {
char *tmp2 = tmp;
asprintf(&tmp, "%s%c", tmp2, in[i]); tmpn++;
free(tmp2);
}
i++;
}
// was there any taxon name?
asprintf(&p.taxon[node], "%s", tmp);
// printf(" taxon name %s\n", tmp);
free(tmp);
}
// are there bls?
if (in[i] == 58)
{
i++; // skip over delimiter `:'
char *tmp = NULL; tmpn = 0;
// bead bl string, I.e. not `['
while ((in[i] != 91) &&
(in[i] != 44) && (in[i] != 41) && (in[i] != 40) &&
(in[i] != 59)) // watch out for final `;'
{
if (!tmpn) {
asprintf(&tmp, "%c", in[i]); tmpn++;
} else {
Sasprintf(tmp, "%s%c", tmp, in[i]); tmpn++;
}
i++;
}
p.bl[node] = atof(tmp);
// printf(" taxon bl %f\n", p.bl[node]);
free(tmp);
}
// are there notes?
if (in[i] == 91)
// Discard note
while ((in[i] != 44) && (in[i] != 41) && (in[i] != 40) &&
(in[i] != 59))
i++;
}
}
/* printf("%s\n", in);
for (int n = 0; n < p.nnodes; n++)
printf("%3d %3d %3d %3d %5.2f %s\n", n, p.parent[n], p.depth[n],
p.ndaughter[n], p.bl[n], p.taxon[n]); */
return p;
}
