snofold.h
/* function from fold.c */
#ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__
#define __VIENNA_RNA_PACKAGE_SNOFOLD_H__
#include "data_structures.h"
/* Normal fold */
int snofold( const char *sequence,
char *structure,
const int max_assym,
const int threshold,
const int min_s2,
const int max_s2,
const int half_stem,
const int max_half_stem);
void snofree_arrays(const int length); /* free arrays for mfe folding */
void snoinitialize_fold(int length); /* allocate arrays for folding */
void snoupdate_fold_params(void); /* recalculate parameters */
int snoloop_energy(short *ptable,
short *s,
short *s1,
int i);
void snoexport_fold_arrays( int **indx_p,
int **mLoop_p,
int **cLoop,
folden ***fold_p,
folden ***fold_p_XS);
char * snobacktrack_fold_from_pair( const char *sequence,
int i,
int j);
/* alifold */
float alisnofold( const char **strings,
const int max_assym,
const int threshloop,
const int min_s2,
const int max_s2,
const int half_stem,
const int max_half_stem);
void alisnofree_arrays(const int length);
char *alisnobacktrack_fold_from_pair(const char **sequence,
int i,
int j,
int *cov);
extern double cv_fact /* =1 */;
extern double nc_fact /* =1 */;
/* max number of mismatch >>>>>..(( )).>>>> */
#define MISMATCH 3
#endif