RNAlib-2.1.9h
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
12int 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);
24void snofree_arrays(const int length); /* free arrays for mfe folding */
25void snoinitialize_fold(int length); /* allocate arrays for folding */
26void snoupdate_fold_params(void); /* recalculate parameters */
27int snoloop_energy(short *ptable,
28 short *s,
29 short *s1,
30 int i);
31void snoexport_fold_arrays( int **indx_p,
32 int **mLoop_p,
33 int **cLoop,
34 folden ***fold_p,
35 folden ***fold_p_XS);
36char * snobacktrack_fold_from_pair( const char *sequence,
37 int i,
38 int j);
39/* alifold */
40float 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);
47void alisnofree_arrays(const int length);
48char *alisnobacktrack_fold_from_pair(const char **sequence,
49 int i,
50 int j,
51 int *cov);
52extern double cv_fact /* =1 */;
53extern double nc_fact /* =1 */;
54
55/* max number of mismatch >>>>>..(( )).>>>> */
56#define MISMATCH 3
57
58#endif
All datastructures and typedefs shared among the Vienna RNA Package can be found here.
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 ...
Definition data_structures.h:509