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

[jabaws.git] / binaries / src / ViennaRNA / H / snofold.h

diff --git a/binaries/src/ViennaRNA/H/snofold.h b/binaries/src/ViennaRNA/H/snofold.h
new file mode 100644 (file)
index 0000000..15b2f2d
--- /dev/null
+++ b/binaries/src/ViennaRNA/H/snofold.h
@@ -0,0 +1,58 @@
+/* function from fold.c */
+#ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__
+#define __VIENNA_RNA_PACKAGE_SNOFOLD_H__
+
+#include "data_structures.h"
+
+/* Normal fold */
+
+/**
+*** snofold is the stem folding array for RNAsnoop
+**/
+int  snofold( const char *sequence,
+               char *structure,
+                const int max_assym,
+                const int threshold, 
+                const int min_s2,
+                const int max_s2,
+                const int half_stem,
+                const int max_half_stem);
+/**
+*** Free arrays and structure related to snofold
+**/
+
+void   snofree_arrays(const int length);  /* free arrays for mfe folding */
+void   snoinitialize_fold(int length);    /* allocate arrays for folding */
+void   snoupdate_fold_params(void);       /* recalculate parameters */
+int    snoloop_energy(short *ptable,
+                      short *s,
+                      short *s1,
+                      int i);
+void   snoexport_fold_arrays( int **indx_p,
+                              int **mLoop_p,
+                              int **cLoop,
+                              folden ***fold_p,
+                              folden ***fold_p_XS);
+char * snobacktrack_fold_from_pair( const char *sequence,
+                                    int i,
+                                    int j);
+/* alifold */
+float alisnofold( const char **strings,
+                  const int max_assym,
+                  const int threshloop, 
+                  const int min_s2,
+                  const int max_s2,
+                  const int half_stem,
+                  const int max_half_stem);
+void  alisnofree_arrays(const int length);
+char  *alisnobacktrack_fold_from_pair(const char **sequence,
+                                      int i,
+                                      int j,
+                                      int *cov);
+extern double cv_fact /* =1 */;
+extern double nc_fact /* =1 */;
+
+/* max number of mismatch >>>>>..((   )).>>>> */
+#define MISMATCH 3
+
+#endif