RNAlib-2.5.1
snofold.h
1/* function from fold.c */
2#ifndef VIENNA_RNA_PACKAGE_SNOFOLD_H
3#define VIENNA_RNA_PACKAGE_SNOFOLD_H
4
6
7#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
8
9/* Normal fold */
10
14int snofold(const char *sequence,
15 char *structure,
16 const int max_assym,
17 const int threshold,
18 const int min_s2,
19 const int max_s2,
20 const int half_stem,
21 const int max_half_stem);
22
23
28void snofree_arrays(const int length); /* free arrays for mfe folding */
29
30
31void snoinitialize_fold(int length); /* allocate arrays for folding */
32
33
34void snoupdate_fold_params(void); /* recalculate parameters */
35
36
37int snoloop_energy(short *ptable,
38 short *s,
39 short *s1,
40 int i);
41
42
43void snoexport_fold_arrays(int **indx_p,
44 int **mLoop_p,
45 int **cLoop,
46 folden ***fold_p,
47 folden ***fold_p_XS);
48
49
50char *snobacktrack_fold_from_pair(const char *sequence,
51 int i,
52 int j);
53
54
55/* alifold */
56float alisnofold(const char **strings,
57 const int max_assym,
58 const int threshloop,
59 const int min_s2,
60 const int max_s2,
61 const int half_stem,
62 const int max_half_stem);
63
64
65void alisnofree_arrays(const int length);
66
67
68char *alisnobacktrack_fold_from_pair(const char **sequence,
69 int i,
70 int j,
71 int *cov);
72
73
74extern double cv_fact /* =1 */;
75extern double nc_fact /* =1 */;
76
77/* max number of mismatch >>>>>..(( )).>>>> */
78#define MISMATCH 3
79
80#endif
81
82#endif
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
Various data structures and pre-processor macros.
Data structure for RNAsnoop (fold energy list)
Definition: basic.h:239