PUBLIC float alifold(const char **strings, char *structure){
int length, energy, s, n_seq;
circ = 0;
length = (int) strlen(strings[0]);
if (length>init_length) init_alifold(length);
if ((P==NULL)||(fabs(P->temperature - temperature)>1e-6)) {
update_fold_params(); P = scale_parameters();
}
for (s=0; strings[s]!=NULL; s++);
n_seq = s;
alloc_sequence_arrays(strings, &S, &S5, &S3, &a2s, &Ss, circ);
make_pscores((const short **) S, strings, n_seq, structure);
energy = fill_arrays((const char **)strings);
backtrack((const char **)strings, 0);
parenthesis_structure(structure, length);
free_sequence_arrays(n_seq, &S, &S5, &S3, &a2s, &Ss);
if (backtrack_type=='C')
return (float) c[indx[length]+1]/(n_seq*100.);
else if (backtrack_type=='M')
return (float) fML[indx[length]+1]/(n_seq*100.);
else
return (float) f5[length]/(n_seq*100.);
}
PUBLIC paramT *copy_parameters(void) {
paramT *copy;
if (p.id != id) scale_parameters();
copy = (paramT *) space(sizeof(paramT));
memcpy(copy, &p, sizeof(paramT));
return copy;
}
PUBLIC void update_alifold_params(void){
if(P) free(P);
P = scale_parameters();
make_pair_matrix();
if (init_length < 0) init_length=0;
}
duplexT duplexfold(const char *s1, const char *s2) {
int i, j, l1, Emin=INF, i_min=0, j_min=0;
char *struc;
duplexT mfe;
n1 = (int) strlen(s1);
n2 = (int) strlen(s2);
if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {
update_fold_params(); P = scale_parameters();
make_pair_matrix();
}
c = (int **) space(sizeof(int *) * (n1+1));
for (i=1; i<=n1; i++) c[i] = (int *) space(sizeof(int) * (n2+1));
encode_seq(s1, s2);
for (i=1; i<=n1; i++) {
for (j=n2; j>0; j--) {
int type, type2, E, k,l;
type = pair[S1[i]][S2[j]];
c[i][j] = type ? P->DuplexInit : INF;
if (!type) continue;
if (i>1) c[i][j] += P->dangle5[type][SS1[i-1]];
if (j<n2) c[i][j] += P->dangle3[type][SS2[j+1]];
if (type>2) c[i][j] += P->TerminalAU;
for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {
for (l=j+1; l<=n2; l++) {
if (i-k+l-j-2>MAXLOOP) break;
type2 = pair[S1[k]][S2[l]];
if (!type2) continue;
E = LoopEnergy(i-k-1, l-j-1, type2, rtype[type],
SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1]);
c[i][j] = MIN2(c[i][j], c[k][l]+E);
}
}
E = c[i][j];
if (i<n1) E += P->dangle3[rtype[type]][SS1[i+1]];
if (j>1) E += P->dangle5[rtype[type]][SS2[j-1]];
if (type>2) E += P->TerminalAU;
if (E<Emin) {
Emin=E; i_min=i; j_min=j;
}
}
}
struc = backtrack(i_min, j_min);
if (i_min<n1) i_min++;
if (j_min>1 ) j_min--;
l1 = strchr(struc, '&')-struc;
/*
printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", struc, i_min+1-l1, i_min,
j_min, j_min+strlen(struc)-l1-2, Emin*0.01);
*/
mfe.i = i_min;
mfe.j = j_min;
mfe.energy = (float) Emin/100.;
mfe.structure = struc;
if (!delay_free) {
for (i=1; i<=n1; i++) free(c[i]);
free(c);
free(S1); free(S2); free(SS1); free(SS2);
}
return mfe;
}
