int count_word_char(char* str, char* charset)
{
int i;
int nb;
i = 0;
nb = 0;
while (str[i])
{
while (str[i] && is_sep_char(str[i], charset))
i = i + 1;
if (str[i])
nb = nb + 1;
while (str[i] && !is_sep_char(str[i], charset))
i = i + 1;
}
return (nb);
}
int assign_sp_code(char *line, struct sp_list *sp_code, int num_sp_code)
{
char *pt;
char buf[100];
int i = 0;
int num_sp = 0;
pt = line;
while(((*pt) != '\0') && ((*pt) != ';')) {
buf[0] = '\0';
if( !is_sep_char(*pt) ) {
i = 0;
while(!is_sep_char(*pt)) {
buf[i++] = *pt;
pt++;
}
buf[i] = '\0';
}
if( (buf[0] != '\0') && ((*pt) == '[') ) {
if( num_sp < num_sp_code ) {
strcpy(sp_code[num_sp].name, buf);
}
pt++;
i = 0;
while(!is_sep_char(*pt)) {
buf[i++] = *pt;
pt++;
}
buf[i] = '\0';
if( (i > 0) && (num_sp < num_sp_code) ) {
sp_code[num_sp].id = atoi(buf);
}
num_sp++;
if( num_sp > num_sp_code ) {
fatalf("overflow: number of species %d vs. %d\n", num_sp, num_sp_code);
}
buf[0] = '\0';
}
pt++;
}
return(num_sp);
}
int add_word_char(char* str, char** tab, int* i, char* charset)
{
int index;
index = 0;
while (str[index] && !is_sep_char(str[index], charset))
index = index + 1;
*tab = calloc(index + 1, sizeof(**tab));
if (!*tab)
return (1);
*tab = id_strncpy(*tab, str, index);
*i = *i + index;
return (0);
}
/* RFC 2616, section 2.2. */
static int is_token_char(char c)
{
return !iscntrl((int) (unsigned char) c) && !is_sep_char((int) (unsigned char) c);
}
struct p_tree *read_one_line(char *one_line) {
struct p_tree *p = NULL, *q = NULL, *t = NULL;
struct p_tree *stack[STACK_SIZE];
char buf[100];
char *pt;
int i, top = 0;
double b_len = 1;
// int count_gene = 0;
int state;
int temp_len;
int temp_id = -1;
pt = one_line;
while(*pt != '\0' && *pt != ';') {
if( !is_sep_char(*pt) ) {
i = 0;
while(!is_sep_char(*pt)) {
buf[i++] = *pt;
pt++;
}
buf[i] = '\0';
// count_gene++;
state = NAME;
p = (struct p_tree *) ckalloc(sizeof(struct p_tree));
init_tree(p);
// p->nid = count_node;
// count_node++;
temp_len = strlen(buf) + 1;
p->name = (char *) ckalloc(temp_len * sizeof(char));
strcpy(p->name, buf);
buf[0] = '\0';
// p->gid = count_gene;
p->left = NULL;
p->right = NULL;
}
switch (*pt)
{
case ':':
pt++;
if (sscanf(pt, "%lf", &b_len) != 1) {
printf("branch length error %s\n", pt);
exit(EXIT_FAILURE);
}
while (!is_sep_char(*pt))
pt++;
break;
case '(':
p = (struct p_tree *) ckalloc(sizeof(struct p_tree));
init_tree(p);
// p->nid = count_node;
// count_node++;
p->left = NULL;
p->right = NULL;
stack[top++] = p;
pt++;
state = LPAR;
break;
case '[':
pt++;
i = 0;
while(!is_sep_char(*pt)) {
buf[i++] = *pt;
pt++;
}
buf[i] = '\0';
temp_id = atoi(buf);
p->nid = temp_id;
buf[0] = '\0';
state = LBR;
break;
case ']':
pt++;
state = RBR;
break;
case ',':
p->b_len = b_len;
q = stack[top-1];
if( q->left == NULL ) {
if( temp_id != -1 ) {
p->sp_code = temp_id;
temp_id = -1;
}
q->left = p;
}
else if( q->right == NULL ) {
p->sp_code = temp_id;
temp_id = -1;
q->right = p;
}
else {
t = (struct p_tree *) ckalloc(sizeof(struct p_tree));
init_tree(t);
// t->nid = count_node;
// count_node++;
if( temp_id != -1 ) {
q->sp_code = temp_id;
temp_id = -1;
}
t->left = q;
t->right = NULL;
stack[top-1] = t;
}
q = stack[top-1];
p->parent = q;
pt++;
state = COMMA;
break;
case ')':
if( top == 0 ) {
printf("tree description unbalanced\n");
exit(EXIT_FAILURE);
}
else
{
q = stack[--top];
p->parent = q;
p->b_len = b_len;
if( q->right == NULL )
{
if( temp_id != -1 ) {
p->sp_code = temp_id;
temp_id = -1;
}
q->right = p;
p = q;
}
else {
t = (struct p_tree *) ckalloc(sizeof(struct p_tree));
init_tree(t);
// t->nid = count_node;
// count_node++;
if( temp_id != -1 ) {
p->sp_code = temp_id;
temp_id = -1;
}
t->left = q;
t->right = p;
stack[top-1] = t;
p = t;
}
pt++;
}
state = RPAR;
break;
case ';':
break;
default:
printf("undefined symbol\n");
exit(EXIT_FAILURE);
break;
}
}
p->b_len = 1;
if( temp_id != -1 ) {
p->sp_code = temp_id;
}
return p;
}