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

[jabaws.git] / binaries / src / ViennaRNA / lib / fold_vars.c

diff --git a/binaries/src/ViennaRNA/lib/fold_vars.c b/binaries/src/ViennaRNA/lib/fold_vars.c
new file mode 100644 (file)
index 0000000..8d11b09
--- /dev/null
+++ b/binaries/src/ViennaRNA/lib/fold_vars.c
@@ -0,0 +1,88 @@
+/* Last changed Time-stamp: <2008-06-27 17:21:42 ivo> */
+
+/**
+*** \file fold_vars.c
+*** global variables to change behaviour of folding routines<BR>
+*** Also there are some functions that make the live easier when
+*** using functions of the Vienna RNA package
+**/
+#include <string.h>
+#include <stdio.h>
+#include "fold_vars.h"
+
+int         circ = 0;
+
+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 = 2;          /* 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 */
+
+int         csv = 0;              /*generate comma seperated output*/
+
+bondT       *base_pair = NULL;
+
+FLT_OR_DBL  *pr = NULL;           /* base pairing prob. matrix */
+
+int         *iindx = NULL;        /* 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;
+
+int         gquad = 0;            /* consider g-qudruplexes in the calculations */
+
+PUBLIC 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;
+}
+
+PUBLIC void set_model_details(model_detailsT *md){
+  if(md){
+    md->dangles     = dangles;
+    md->special_hp  = tetra_loop;
+    md->noLP        = noLonelyPairs;
+    md->noGU        = noGU;
+    md->noGUclosure = no_closingGU;
+    md->logML       = logML;
+    md->gquad       = gquad;
+  }
+}