char *getNextToken(char **tokenStream) {
char *token = stString_getNextWord(tokenStream);
if(token != NULL) {
char *cA = stString_replace(token, "\"", "");
free(token);
token = stString_replace(cA, "'", "");
free(cA);
}
return token;
}
static int64_t *getInts(const char *string, int64_t *arrayLength) {
int64_t *iA = st_malloc(sizeof(int64_t) * strlen(string));
char *cA = stString_copy(string);
char *cA2 = cA;
char *cA3;
*arrayLength = 0;
while ((cA3 = stString_getNextWord(&cA)) != NULL) {
int64_t i = sscanf(cA3, "%" PRIi64 "", &iA[(*arrayLength)++]);
(void) i;
assert(i == 1);
free(cA3);
}
free(cA2);
return iA;
}
stTree *stTree_parseNewickString(const char *string) {
//lax newick tree parser
char *cA = stString_replace(string, "(", " ( ");
char *cA2 = stString_replace(cA, ")", " ) ");
free(cA);
cA = cA2;
cA2 = stString_replace(cA, ":", " : ");
free(cA);
cA = cA2;
cA2 = stString_replace(cA, ",", " , ");
free(cA);
cA = cA2;
cA2 = stString_replace(cA, ";", " ; ");
free(cA);
cA = cA2;
char *token = stString_getNextWord(&cA);
assert(token != NULL);
stTree *tree = tree_parseNewickStringP(&token, &cA);
assert(*token == ';');
free(cA2);
free(token);
return tree;
}
/*
* Gets the next token from the list.
*/
static void tree_parseNewickTreeString_getNextToken(char **token, char **newickTreeString) {
assert(*token != NULL);
free(*token);
*token = stString_getNextWord(newickTreeString);
assert(*token != NULL); //Newick string must terminate with ';'
}