RNAlib-2.4.8
snofold.h
1 /* function from fold.c */
2 #ifndef VIENNA_RNA_PACKAGE_SNOFOLD_H
3 #define VIENNA_RNA_PACKAGE_SNOFOLD_H
4 
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);
20 
21 
26 void snofree_arrays(const int length); /* free arrays for mfe folding */
27 
28 
29 void snoinitialize_fold(int length); /* allocate arrays for folding */
30 
31 
32 void snoupdate_fold_params(void); /* recalculate parameters */
33 
34 
35 int snoloop_energy(short *ptable,
36  short *s,
37  short *s1,
38  int i);
39 
40 
41 void snoexport_fold_arrays(int **indx_p,
42  int **mLoop_p,
43  int **cLoop,
44  folden ***fold_p,
45  folden ***fold_p_XS);
46 
47 
48 char *snobacktrack_fold_from_pair(const char *sequence,
49  int i,
50  int j);
51 
52 
53 /* alifold */
54 float alisnofold(const char **strings,
55  const int max_assym,
56  const int threshloop,
57  const int min_s2,
58  const int max_s2,
59  const int half_stem,
60  const int max_half_stem);
61 
62 
63 void alisnofree_arrays(const int length);
64 
65 
66 char *alisnobacktrack_fold_from_pair(const char **sequence,
67  int i,
68  int j,
69  int *cov);
70 
71 
72 extern double cv_fact /* =1 */;
73 extern double nc_fact /* =1 */;
74 
75 /* max number of mismatch >>>>>..(( )).>>>> */
76 #define MISMATCH 3
77 
78 #endif
double cv_fact
This variable controls the weight of the covariance term in the energy function of alignment folding ...
Data structure for RNAsnoop (fold energy list)
Definition: basic.h:238
Various data structures and pre-processor macros.
double nc_fact
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance te...