/* function from fold.c */
#ifndef __VIENNA_RNA_PACKAGE_SNOFOLD_H__
#define __VIENNA_RNA_PACKAGE_SNOFOLD_H__

#include "data_structures.h"

//Normal fold

/**
*** snofold is the stem folding array for RNAsnoop
**/
float  snofold( const char *sequence,
                const int max_assym,
                const int threshold, 
                const int min_s2,
                const int max_s2,
                const int half_stem,
                const int max_half_stem);
/**
*** Free arrays and structure related to snofold
**/

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