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snofold.h
1 /* function from fold.c */
2 #ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__
3 #define __VIENNA_RNA_PACKAGE_SNOFOLD_H__
4
5 #include "data_structures.h"
6
7 /* Normal fold */
8
12 int snofold( const char *sequence,
13 char *structure,
14 const int max_assym,
15 const int threshold,
16 const int min_s2,
17 const int max_s2,
18 const int half_stem,
19 const int max_half_stem);
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,
28 short *s,
29 short *s1,
30 int i);
31 void snoexport_fold_arrays( int **indx_p,
32 int **mLoop_p,
33 int **cLoop,
34 folden ***fold_p,
35 folden ***fold_p_XS);
36 char * snobacktrack_fold_from_pair( const char *sequence,
37 int i,
38 int j);
39 /* alifold */
40 float alisnofold( const char **strings,
41 const int max_assym,
42 const int threshloop,
43 const int min_s2,
44 const int max_s2,
45 const int half_stem,
46 const int max_half_stem);
47 void alisnofree_arrays(const int length);
48 char *alisnobacktrack_fold_from_pair(const char **sequence,
49 int i,
50 int j,
51 int *cov);
52 extern double cv_fact /* =1 */;
53 extern double nc_fact /* =1 */;
54
55 /* max number of mismatch >>>>>..(( )).>>>> */
56 #define MISMATCH 3
57
58 #endif