int main(int argc, char *argv[]){
struct RNAheat_args_info args_info;
char *string, *input_string, *ns_bases, *c, *ParamFile, *rec_sequence, *rec_id, **rec_rest, *orig_sequence;
int i, length, l, sym;
float T_min, T_max, h;
int mpoints, istty, noconv = 0;
unsigned int input_type;
unsigned int rec_type, read_opt;
string = ParamFile = ns_bases = NULL;
T_min = 0.;
T_max = 100.;
h = 1;
mpoints = 2;
dangles = 2; /* dangles can be 0 (no dangles) or 2, default is 2 */
rec_type = read_opt = 0;
rec_id = rec_sequence = orig_sequence = NULL;
rec_rest = NULL;
/*
#############################################
# check the command line parameters
#############################################
*/
if(RNAheat_cmdline_parser(argc, argv, &args_info) != 0) exit(1);
/* 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){
if((args_info.dangles_arg != 0) && (args_info.dangles_arg != 2))
vrna_message_warning("required dangle model not implemented, falling back to default dangles=2");
else
dangles = args_info.dangles_arg;
}
/* do not allow weak pairs */
if(args_info.noLP_given) noLonelyPairs = 1;
/* 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;
/* do not convert DNA nucleotide "T" to appropriate RNA "U" */
if(args_info.noconv_given) noconv = 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);
/* Tmin */
if(args_info.Tmin_given) T_min = args_info.Tmin_arg;
/* Tmax */
if(args_info.Tmax_given) T_max = args_info.Tmax_arg;
/* step size */
if(args_info.stepsize_given) h = args_info.stepsize_arg;
/* ipoints */
if(args_info.ipoints_given){
mpoints = args_info.ipoints_arg;
if (mpoints < 1) mpoints = 1;
if (mpoints > 100) mpoints = 100;
}
/* free allocated memory of command line data structure */
RNAheat_cmdline_parser_free (&args_info);
/*
#############################################
# begin initializing
#############################################
*/
if (ParamFile!=NULL) read_parameter_file(ParamFile);
if (ns_bases != NULL) {
nonstandards = vrna_alloc(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++;
}
}
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
read_opt |= VRNA_INPUT_NO_REST;
if(istty){
vrna_message_input_seq_simple();
read_opt |= VRNA_INPUT_NOSKIP_BLANK_LINES;
}
/*
#############################################
# main loop: continue until end of file
#############################################
*/
while(
!((rec_type = vrna_file_fasta_read_record(&rec_id, &rec_sequence, &rec_rest, NULL, read_opt))
& (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT))){
/*
########################################################
# init everything according to the data we've read
########################################################
*/
if(rec_id && !istty) printf("%s\n", rec_id);
length = (int)strlen(rec_sequence);
/* convert DNA alphabet to RNA if not explicitely switched off */
if(!noconv) vrna_seq_toRNA(rec_sequence);
/* store case-unmodified sequence */
orig_sequence = strdup(rec_sequence);
/* convert sequence to uppercase letters only */
vrna_seq_toupper(rec_sequence);
if(istty) printf("length = %d\n", length);
/*
########################################################
# done with 'stdin' handling
########################################################
*/
heat_capacity(rec_sequence, T_min, T_max, h, mpoints);
(void) fflush(stdout);
/* clean up */
if(rec_id) free(rec_id);
free(rec_sequence);
free(orig_sequence);
rec_id = rec_sequence = orig_sequence = NULL;
rec_rest = NULL;
/* print user help for the next round if we get input from tty */
if(istty) vrna_message_input_seq_simple();
}
return EXIT_SUCCESS;
}
int main(int argc, char *argv[]){
struct RNAheat_args_info args_info;
char *string, *input_string, *ns_bases, *c, *ParamFile;
int i, length, l, sym;
float T_min, T_max, h;
int mpoints, istty, noconv = 0;
unsigned int input_type;
string = ParamFile = ns_bases = NULL;
T_min = 0.;
T_max = 100.;
h = 1;
mpoints = 2;
dangles = 2; /* dangles can be 0 (no dangles) or 2, default is 2 */
/*
#############################################
# check the command line parameters
#############################################
*/
if(RNAheat_cmdline_parser(argc, argv, &args_info) != 0) exit(1);
/* 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;
if(dangles % 2){
warn_user("using default dangles = 2");
dangles = 2;
}
}
/* do not allow weak pairs */
if(args_info.noLP_given) noLonelyPairs = 1;
/* 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;
/* do not convert DNA nucleotide "T" to appropriate RNA "U" */
if(args_info.noconv_given) noconv = 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);
/* Tmin */
if(args_info.Tmin_given) T_min = args_info.Tmin_arg;
/* Tmax */
if(args_info.Tmax_given) T_max = args_info.Tmax_arg;
/* step size */
if(args_info.stepsize_given) h = args_info.stepsize_arg;
/* ipoints */
if(args_info.ipoints_given){
mpoints = args_info.ipoints_arg;
if (mpoints < 1) mpoints = 1;
if (mpoints > 100) mpoints = 100;
}
/* free allocated memory of command line data structure */
RNAheat_cmdline_parser_free (&args_info);
/*
#############################################
# begin initializing
#############################################
*/
if (ParamFile!=NULL) read_parameter_file(ParamFile);
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++;
}
}
istty = isatty(fileno(stdout))&&isatty(fileno(stdin));
/*
#############################################
# main loop: continue until end of file
#############################################
*/
do {
/*
########################################################
# handle user input from 'stdin'
########################################################
*/
if(istty) print_tty_input_seq();
/* skip fasta headers and comments */
while((input_type = get_input_line(&input_string, 0)) & VRNA_INPUT_FASTA_HEADER){
printf(">%s\n", input_string);
/* skip fasta headers and comments */
free(input_string);
}
/* break on any error, EOF or quit request */
if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)){ break;}
/* else assume a proper sequence of letters of a certain alphabet (RNA, DNA, etc.) */
else{
string = strdup(input_string);
length = (int) strlen(string);
free(input_string);
}
if(noconv) str_RNA2RNA(string);
else str_DNA2RNA(string);
if (istty) printf("length = %d\n", length);
heat_capacity(string, T_min, T_max, h, mpoints);
free(string);
(void) fflush(stdout);
} while (1);
return 0;
}
