RNAlib-2.4.16
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 
14 int 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 
28 void snofree_arrays(const int length); /* free arrays for mfe folding */
29 
30 
31 void snoinitialize_fold(int length); /* allocate arrays for folding */
32 
33 
34 void snoupdate_fold_params(void); /* recalculate parameters */
35 
36 
37 int snoloop_energy(short *ptable,
38  short *s,
39  short *s1,
40  int i);
41 
42 
43 void snoexport_fold_arrays(int **indx_p,
44  int **mLoop_p,
45  int **cLoop,
46  folden ***fold_p,
47  folden ***fold_p_XS);
48 
49 
50 char *snobacktrack_fold_from_pair(const char *sequence,
51  int i,
52  int j);
53 
54 
55 /* alifold */
56 float 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 
65 void alisnofree_arrays(const int length);
66 
67 
68 char *alisnobacktrack_fold_from_pair(const char **sequence,
69  int i,
70  int j,
71  int *cov);
72 
73 
74 extern double cv_fact /* =1 */;
75 extern double nc_fact /* =1 */;
76 
77 /* max number of mismatch >>>>>..(( )).>>>> */
78 #define MISMATCH 3
79 
80 #endif
81 
82 #endif
cv_fact
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
node
Data structure for RNAsnoop (fold energy list)
Definition: basic.h:239
basic.h
Various data structures and pre-processor macros.
nc_fact
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...