--- /dev/null
+/* Last changed Time-stamp: <2003-04-23 11:56:44 ivo> */
+/*
+ Ineractive Access to folding Routines
+
+ c Ivo L Hofacker
+ Vienna RNA package
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <ctype.h>
+#include <unistd.h>
+#include <string.h>
+#include "fold_vars.h"
+#include "utils.h"
+#include "read_epars.h"
+#include "Lfold.h"
+#include "RNALfold_cmdl.h"
+
+/*@unused@*/
+static char rcsid[] = "$Id: RNALfold.c,v 1.2 2003/07/14 13:38:47 ivo Exp $";
+
+int main(int argc, char *argv[]){
+ struct RNALfold_args_info args_info;
+ char *input_string, *c, *string, *structure, *ParamFile, *ns_bases, *rec_sequence, *rec_id, **rec_rest, *orig_sequence;
+ int i, length, l, sym, r, istty, noconv, maxdist, zsc;
+ double energy, min_en, min_z;
+ unsigned int input_type;
+ unsigned int rec_type, read_opt;
+
+ string = structure = ParamFile = ns_bases = NULL;
+ do_backtrack = 1;
+ noconv = 0;
+ dangles = 2;
+ maxdist = 150;
+ zsc = 0;
+ min_z = -2.0;
+ gquad = 0;
+ rec_type = read_opt = 0;
+ rec_id = rec_sequence = orig_sequence = NULL;
+ rec_rest = NULL;
+
+ /*
+ #############################################
+ # check the command line parameters
+ #############################################
+ */
+ if(RNALfold_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){
+ if((args_info.dangles_arg < 0) || (args_info.dangles_arg > 3))
+ warn_user("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);
+ /* set the maximum base pair span */
+ if(args_info.span_given) maxdist = args_info.span_arg;
+ if(args_info.zscore_given){
+#ifdef USE_SVM
+ zsc = 1;
+ if(args_info.zscore_arg != -2)
+ min_z = args_info.zscore_arg;
+#else
+ nrerror("\'z\' option is available only if compiled with SVM support!");
+#endif
+ }
+ /* gquadruplex support */
+ if(args_info.gquad_given) gquad = 1;
+
+ /* check for errorneous parameter options */
+ if(maxdist < 0){
+ RNALfold_cmdline_parser_print_help();
+ exit(EXIT_FAILURE);
+ }
+
+ /* free allocated memory of command line data structure */
+ RNALfold_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));
+ read_opt |= VRNA_INPUT_NO_REST;
+ if(istty){
+ print_tty_input_seq();
+ read_opt |= VRNA_INPUT_NOSKIP_BLANK_LINES;
+ }
+ /*
+ #############################################
+ # main loop: continue until end of file
+ #############################################
+ */
+ while(
+ !((rec_type = read_record(&rec_id, &rec_sequence, &rec_rest, 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) str_DNA2RNA(rec_sequence);
+ /* store case-unmodified sequence */
+ orig_sequence = strdup(rec_sequence);
+ /* convert sequence to uppercase letters only */
+ str_uppercase(rec_sequence);
+
+ if(istty) printf("length = %d\n", length);
+ /*
+ ########################################################
+ # done with 'stdin' handling
+ ########################################################
+ */
+
+ min_en = (zsc) ? Lfoldz((const char *)rec_sequence, NULL, maxdist, zsc, min_z) : Lfold((const char *)rec_sequence, NULL, maxdist);
+ printf("%s\n", orig_sequence);
+
+ if (istty)
+ printf("\n minimum free energy = %6.2f kcal/mol\n", min_en);
+ else
+ printf(" (%6.2f)\n", min_en);
+
+ (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) print_tty_input_seq();
+ }
+ return EXIT_SUCCESS;
+}
+
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