1 /* function from fold.c */
2 #ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__
3 #define __VIENNA_RNA_PACKAGE_SNOFOLD_H__
5 #include "data_structures.h"
10 *** snofold is the stem folding array for RNAsnoop
12 int snofold( const char *sequence,
19 const int max_half_stem);
21 *** Free arrays and structure related to snofold
24 void snofree_arrays(const int length); /* free arrays for mfe folding */
25 void snoinitialize_fold(int length); /* allocate arrays for folding */
26 void snoupdate_fold_params(void); /* recalculate parameters */
27 int snoloop_energy(short *ptable,
31 void snoexport_fold_arrays( int **indx_p,
36 char * snobacktrack_fold_from_pair( const char *sequence,
40 float alisnofold( const char **strings,
46 const int max_half_stem);
47 void alisnofree_arrays(const int length);
48 char *alisnobacktrack_fold_from_pair(const char **sequence,
52 extern double cv_fact /* =1 */;
53 extern double nc_fact /* =1 */;
55 /* max number of mismatch >>>>>..(( )).>>>> */