PUBLIC int find_saddle(const char *sequence, const char *struc1, const char *struc2, int max) {
int maxl, maxE, i;
const char *tmp;
move_t *bestpath=NULL;
int dir;
path_fwd = 0;
maxE = INT_MAX - 1;
seq = sequence;
update_fold_params();
make_pair_matrix();
/* nummerically encode sequence */
S = encode_sequence(seq, 0);
S1 = encode_sequence(seq, 1);
maxl=1;
do {
int saddleE;
path_fwd = !path_fwd;
if (maxl>max) maxl=max;
if(path) free(path);
saddleE = find_path_once(struc1, struc2, maxE, maxl);
if (saddleE<maxE) {
maxE = saddleE;
if (bestpath) free(bestpath);
bestpath = path;
path = NULL;
dir = path_fwd;
} else{
free(path);path=NULL;
}
tmp=struc1;
struc1=struc2;
struc2=tmp;
maxl *=2;
} while (maxl<2*max);
free(S); free(S1);
/* (re)set some globals */
path=bestpath;
path_fwd = dir;
return maxE;
}
int find_saddle(char *sequence, char *struc1, char *struc2, int max) {
int maxl, maxE, i;
char *tmp;
move_t *bestpath=NULL;
int dir;
maxE = INT_MAX - 1;
seq = sequence;
update_fold_params();
make_pair_matrix();
/* nummerically encode sequence */
S = (short *) space(sizeof(short)*(strlen(seq)+1));
S1 = (short *) space(sizeof(short)*(strlen(seq)+1));
S[0] = S1[0] = (short) strlen(seq);
for (i=0; i< strlen(seq); i++) {
S[i+1] = encode_char(seq[i]);
S1[i+1] = alias[S[i+1]];
}
maxl=1;
do {
int saddleE;
path_fwd = !path_fwd;
if (maxl>max) maxl=max;
saddleE = find_path_once(struc1, struc2, maxE, maxl);
if (saddleE<maxE) {
maxE = saddleE;
if (bestpath) free(bestpath);
bestpath = path;
dir = path_fwd;
} else
free(path);
tmp=struc1; struc1=struc2; struc2=tmp;
maxl *=2;
} while (maxl<2*max);
free(S); free(S1);
path=bestpath;
path_fwd = dir;
return maxE;
}
