int main(int argc, char *argv[]){
char sequence[MAXSIZE], structure[MAXSIZE];
int i, j;
if (argc == 9) {
i = 1;
while (i < argc) {
if (!strcmp(argv[i], "-s")) {
sequence[0] = '@';
strncpy(sequence + 1, argv[i + 1], strlen(argv[i + 1])); // The sequence starts from index 1
sequence[strlen(argv[i + 1]) + 1] = '\0'; // Remember to end the sequence
i += 2;
} else if (!strcmp(argv[i], "-r")) {
strncpy(structure, argv[i + 1], strlen(argv[i + 1])); // The structure starts from index 0
structure[strlen(argv[i + 1])] = '\0'; // Remember to end the structure
i += 2;
} else if (!strcmp(argv[i], "-c")) {
SCALING_FACTOR = atof(argv[i + 1]);
i += 2;
} else if (!strcmp(argv[i], "-p")) {
PRECISION = atoi(argv[i + 1]);
i += 2;
} else {
printf("Error: Unrecognizable Flag!\n");
printf("Usage:");
printf("%s -s SEQUENCE -r STRUCTURE -c SCALING -p PRECISION\n", argv[0]);
printf("SEQUENCE is the RNA sequence.\n");
printf("STRUCTURE is the RNA structure.\n");
printf("SCALING is used internally as the scaling factor for the recursions.\n");
printf("PRECISION dictates the number of signigicant digits in the resulting distribution.\n");
printf("The length of RNA sequence should be less than %d and larger than or equal to 5.\n", MAXSIZE);
exit(1);
}
}
CheckSequenceAndStructure(sequence, structure);
S0 = encode_seq(sequence + 1);
seqlen = strlen(sequence) - 1;
Initialize_Params();
make_pair_matrix(); // Needed for pair matching.
kT = (temperature + K0) * GASCONST / 1000.0;
ML_base = (double)P -> MLbase / 100;
ML_close = (double)P -> MLclosing / 100;
std::complex<double>** McCaskillZ;
McCaskillZ = runMcCaskill(sequence, structure);
} else {
printf("Usage:");
printf("%s -s SEQUENCE -r STRUCTURE -c SCALING -p PRECISION\n", argv[0]);
printf("SEQUENCE is the RNA sequence.\n");
printf("STRUCTURE is the RNA structure.\n");
printf("SCALING is used internally as the scaling factor for the recursions.\n");
printf("PRECISION dictates the number of signigicant digits in the resulting distribution.\n");
printf("The length of RNA sequence should be less than %d and larger than or equal to 5.\n", MAXSIZE);
exit(1);
}
return 0;
}
float fold(const char *string, char *structure) {
int i, length, energy, bonus=0, bonus_cnt=0;
circ = 0;
length = (int) strlen(string);
if (length>init_length) initialize_fold(length);
if (fabs(P->temperature - temperature)>1e-6) update_fold_params();
encode_seq(string);
BP = (int *)space(sizeof(int)*(length+2));
make_ptypes(S, structure);
energy = fill_arrays(string);
backtrack(string, 0);
#ifdef PAREN
parenthesis_structure(structure, length);
#else
letter_structure(structure, length);
#endif
/* check constraints */
for(i=1;i<=length;i++) {
if((BP[i]<0)&&(BP[i]>-4)) {
bonus_cnt++;
if((BP[i]==-3)&&(structure[i-1]==')')) bonus++;
if((BP[i]==-2)&&(structure[i-1]=='(')) bonus++;
if((BP[i]==-1)&&(structure[i-1]!='.')) bonus++;
}
if(BP[i]>i) {
int l;
bonus_cnt++;
for(l=1; l<=base_pair[0].i; l++)
if((i==base_pair[l].i)&&(BP[i]==base_pair[l].j)) bonus++;
}
}
if (bonus_cnt>bonus) fprintf(stderr,"\ncould not enforce all constraints\n");
bonus*=BONUS;
free(S); free(S1); free(BP);
energy += bonus; /*remove bonus energies from result */
if (backtrack_type=='C')
return (float) c[indx[length]+1]/100.;
else if (backtrack_type=='M')
return (float) fML[indx[length]+1]/100.;
else
return (float) energy/100.;
}
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;
}