int main(int argc, char *argv[]){
char *rec_sequence, *structure;
double min_en;
rec_sequence = structure = NULL;
/* initialization */
if (argc>1) {
read_parameter_file(argv[1]);
// printf("Params: '%s'\n",argv[1]);
}
/* main loop: continue until end of file */
while (!(get_multi_input_line(&rec_sequence, 0) & (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT) )) {
/* init everything according to the data we've read */
int length = (int)strlen(rec_sequence);
structure = (char *)space(sizeof(char) *(length+1));
/* actual computations */
min_en = fold_par(rec_sequence, structure);
printf("%s\n%s (%6.2f)\n", rec_sequence, structure, min_en);
fflush(stdout);
/* clean up */
free(rec_sequence); free(structure);
rec_sequence = structure = NULL;
}
return EXIT_SUCCESS;
}
int main(int argc, char *argv[]){
struct RNAinverse_args_info args_info;
int input_type;
char *input_string, *start, *structure, *rstart, *str2, *line;
char *ParamFile=NULL, *c, *ns_bases;
int i,j, length, l, hd, sym;
double energy=0., kT;
int pf, mfe, istty;
int repeat, found;
do_backtrack = 0; pf = 0; mfe = 1;
repeat = 0;
input_type = 0;
input_string = ns_bases = NULL;
init_rand();
/*
#############################################
# check the command line parameters
#############################################
*/
if(RNAinverse_cmdline_parser (argc, argv, &args_info) != 0) exit(1);
/* temperature */
if(args_info.temp_given) temperature = args_info.temp_arg;
/* do not take special tetra loop energies into account */
if(args_info.noTetra_given) tetra_loop=0;
/* set dangle model */
if(args_info.dangles_given) dangles = args_info.dangles_arg;
/* do not allow wobble pairs (GU) */
if(args_info.noGU_given) noGU = 1;
/* do not allow weak closing pairs (AU,GU) */
if(args_info.noClosingGU_given) no_closingGU = 1;
/* set energy model */
if(args_info.energyModel_given) energy_set = args_info.energyModel_arg;
/* take another energy parameter set */
if(args_info.paramFile_given) ParamFile = strdup(args_info.paramFile_arg);
/* Allow other pairs in addition to the usual AU,GC,and GU pairs */
if(args_info.nsp_given) ns_bases = strdup(args_info.nsp_arg);
/* alter the alphabet */
if(args_info.alphabet_given){
symbolset=args_info.alphabet_arg;
/* symbolset should only have uppercase characters */
for (l = 0; l < (int)strlen(symbolset); l++)
symbolset[l] = toupper(symbolset[l]);
}
/* set function for optimization */
if(args_info.function_given){
if(strlen(args_info.function_arg) > 2){
RNAinverse_cmdline_parser_print_help(); exit(EXIT_FAILURE);
}
else{
if((*args_info.function_arg == 'm') || (*(args_info.function_arg+1) == 'm')) mfe = 1;
if((*args_info.function_arg == 'p') || (*(args_info.function_arg+1) == 'p')) pf = 1;
}
}
/* set repeat */
if(args_info.repeat_given) repeat = args_info.repeat_arg;
/* set final cost */
if(args_info.final_given) final_cost = args_info.final_arg;
/* do we wannabe verbose */
if(args_info.verbose_given) inv_verbose = 1;
/* free allocated memory of command line data structure */
RNAinverse_cmdline_parser_free (&args_info);
kT = (temperature+273.15)*1.98717/1000.0;
istty = (isatty(fileno(stdout))&&isatty(fileno(stdin)));
if (ParamFile!=NULL)
read_parameter_file(ParamFile);
give_up = (repeat<0);
do {
/*
########################################################
# handle user input from 'stdin'
########################################################
*/
if(istty)
print_tty_input_seq_str("Input structure & start string\n"
"(lower case letters for const positions) and 0 or empty line for random start string\n");
input_type = get_multi_input_line(&input_string, 0);
/* we are waiting for a structure (i.e. something like a constraint) so we skip all sequences, fasta-headers and misc lines */
while(input_type & (VRNA_INPUT_SEQUENCE | VRNA_INPUT_MISC | VRNA_INPUT_FASTA_HEADER)){
if(!istty && (input_type & VRNA_INPUT_FASTA_HEADER)) printf(">%s\n", input_string);
free(input_string); input_string = NULL;
input_type = get_multi_input_line(&input_string, 0);
}
if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) break;
if(input_type & (VRNA_INPUT_CONSTRAINT)){
structure = (char *)space(sizeof(char) * (strlen(input_string) + 1));
(void)sscanf(input_string, "%s", structure); /* scanf gets rid of trailing junk */
length = (int)strlen(structure);
free(input_string); input_string = NULL;
input_type = get_multi_input_line(&input_string, VRNA_INPUT_NOSKIP_BLANK_LINES | VRNA_INPUT_NOSKIP_COMMENTS);
}
if(input_type & VRNA_INPUT_QUIT) break;
start = (char *)space(sizeof(char) * (length+1));
/* now we assume to get a sequence (input_string may be empty as well) */
if(input_type & VRNA_INPUT_SEQUENCE){
(void)strncpy(start, input_string, length);
start[length] = '\0';
free(input_string); input_string = NULL;
}
/* fallback to empty start sequence */
else start[0] = '\0';
/*
########################################################
# done with 'stdin' handling
########################################################
*/
if (ns_bases != NULL) {
nonstandards = space(33);
c=ns_bases;
i=sym=0;
if (*c=='-') {
sym=1; c++;
}
while (*c!='\0') {
if (*c!=',') {
nonstandards[i++]=*c++;
nonstandards[i++]=*c;
if ((sym)&&(*c!=*(c-1))) {
nonstandards[i++]=*c;
nonstandards[i++]=*(c-1);
}
}
c++;
}
}
str2 = (char *) space((unsigned)length+1);
if (istty) printf("length = %d\n", length);
if (repeat!=0) found = (repeat>0)? repeat : (-repeat);
else found = 1;
/* initialize_fold(length); <- obsolete (hopefully commenting this out does not affect anything crucial ;) */
rstart = (char *) space((unsigned)length+1);
while(found>0) {
char *string;
string = (char *) space((unsigned)length+1);
strcpy(string, start);
for (i=0; i<length; i++) {
/* lower case characters are kept fixed, any other character
not in symbolset is replaced by a random character */
if (islower(string[i])) continue;
if (string[i]=='\0' || (strchr(symbolset,string[i])==NULL))
string[i]=symbolset[int_urn(0,strlen(symbolset)-1)];
}
strcpy(rstart, string); /* remember start string */
if (mfe) {
energy = inverse_fold(string, structure);
if( (repeat>=0) || (energy<=0.0) ) {
found--;
hd = hamming(rstart, string);
printf("%s %3d", string, hd);
if (energy>0) { /* no solution found */
printf(" d= %g\n", energy);
if(istty) {
energy = fold(string,str2);
printf("%s\n", str2);
}
} else printf("\n");
}
}
if (pf) {
if (!(mfe && give_up && (energy>0))) {
/* unless we gave up in the mfe part */
double prob, min_en, sfact=1.07;
/* get a reasonable pf_scale */
min_en = fold(string,str2);
pf_scale = exp(-(sfact*min_en)/kT/length);
/* init_pf_fold(length); <- obsolete (hopefully commenting this out does not affect anything crucial ;) */
energy = inverse_pf_fold(string, structure);
prob = exp(-energy/kT);
hd = hamming(rstart, string);
printf("%s %3d (%g)\n", string, hd, prob);
free_pf_arrays();
}
if (!mfe) found--;
}
(void) fflush(stdout);
free(string);
}
free(rstart);
free_arrays();
free(structure);
free(str2);
free(start);
(void) fflush(stdout);
} while (1);
return 0;
}
