WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / RNAforester / src / fold_vars.h

diff --git a/binaries/src/ViennaRNA/RNAforester/src/fold_vars.h b/binaries/src/ViennaRNA/RNAforester/src/fold_vars.h
new file mode 100644 (file)
index 0000000..243f504
--- /dev/null
+++ b/binaries/src/ViennaRNA/RNAforester/src/fold_vars.h
@@ -0,0 +1,37 @@
+/* to use floats instead of doubles in pf_fold() comment next line */
+#define LARGE_PF 
+#ifdef  LARGE_PF
+#define FLT_OR_DBL double
+#else
+#define FLT_OR_DBL float
+#endif
+
+extern int  noGU;           /* GU not allowed at all */
+extern int  no_closingGU;   /* GU allowed only inside stacks */
+extern int  tetra_loop;     /* Fold with specially stable 4-loops */
+extern int  energy_set;     /* 0 = BP; 1=any mit GC; 2=any mit AU-parameter */
+extern int  dangles;       /* use dangling end energies (not in part_func!) */
+/*@null@*/
+extern char *nonstandards;  /* contains allowed non standard bases */
+extern double temperature;   /* rescale parameters to this temperature */
+extern int  james_rule;     /* interior loops of size 2 get energy 0.8Kcal and
+                              no mismatches, default 1 */
+extern int  logML;          /* use logarithmic multiloop energy function */
+extern int  cut_point;      /* first position of 2nd strand for co-folding */
+
+struct bond {               /* base pair */
+   int i;
+   int j;
+};
+typedef struct bond bondT;            
+extern bondT  *base_pair; /* list of base pairs */
+
+extern FLT_OR_DBL *pr;          /* base pairing prob. matrix */
+extern int   *iindx;            /* pr[i,j] -> pr[iindx[i]-j] */
+extern double pf_scale;         /* scaling factor to avoid float overflows*/
+extern int    fold_constrained; /* fold with constraints */
+extern int    do_backtrack;     /* calculate pair prob matrix in part_func() */
+extern int    noLonelyPairs;    /* avoid helices of length 1 */
+extern char backtrack_type;     /* usually 'F'; 'C' require (1,N) to be bonded;
+                                  'M' seq is part of a multi loop */
+char * option_string(void);