text: /* Last changed Time-stamp: <2008-06-27 17:21:42 ivo> */
  
  /*
         global variables to change behaviour of folding routines
  			  Vienna RNA package
  */
  #include <string.h>
  #include <stdio.h>
  #include "fold_vars.h"
  
  int  noGU = 0;           /* GU not allowed at all */
  int  no_closingGU = 0;   /* GU allowed only inside stacks */
  int  tetra_loop = 1;     /* Fold with specially stable 4-loops */
  int  energy_set = 0;     /* 0 = BP; 1=any with GC; 2=any with AU parameters */
  int  dangles = 1;	 /* use dangling end energies */
  char *nonstandards = (char *)0; /* contains allowed non standard bases */
  double temperature = 37.0;
  int  james_rule = 1;     /* interior loops of size 2 get energy 0.8Kcal and
  			    no mismatches (no longer used) */
  int  oldAliEn   = 0;     /* use old alifold-energies (without removing gaps) */
  int  ribo       = 0;     /* use ribosum instead of classic covariance term */
  char *RibosumFile = NULL; /* TODO: compile ribosums into program
  			     Warning: this variable will vanish */
  
  struct bond  *base_pair;
  
  FLT_OR_DBL *pr;          /* base pairing prob. matrix */
  int  *iindx;             /* pr[i,j] -> pr[iindx[i]-j] */
  double pf_scale=- 1;     /* scaling factor to avoid floating point overflows */
  int   fold_constrained = 0; /* fold with constraints */
  int   do_backtrack=1;     /* calculate pair prob matrix in part_func() */
  int    noLonelyPairs = 0; /* avoid helices of length 1 */
  char backtrack_type='F';  /* 'C' require (1,N) to be bonded;
  			     'M' seq is part of s multi loop */
  
  int *cut_points;
  int *strand;
  char * option_string(void) {
    static char options[100];
    *options = '\0';
    if (noGU) strcat(options, "-noGU ");
    if (no_closingGU) strcat(options, "-noCloseGU ");
    if (!tetra_loop) strcat(options, "-4 ");
    if (noLonelyPairs) strcat(options, "-noLP ");
    if (fold_constrained) strcat(options, "-C ");
    if (dangles!=1) sprintf(options+strlen(options), "-d%d ", dangles);
    if (temperature!=37.0) 
      sprintf(options+strlen(options), "-T %f ", temperature);
    return options;
  }
  