alifold.h

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#ifndef __VIENNA_RNA_PACKAGE_ALIFOLD_H__
#define __VIENNA_RNA_PACKAGE_ALIFOLD_H__

#include "data_structures.h"

extern  double  cv_fact;
extern  double  nc_fact;

/*
##############################################
# MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #
##############################################
*/

void update_alifold_params(void);


float  alifold( const char **strings,
                char *structure);


float  circalifold( const char **strings,
                    char *structure);

void    free_alifold_arrays(void);

int get_mpi(char *Alseq[],
            int n_seq,
            int length,
            int *mini);

float   **readribosum(char *name);

float   energy_of_alistruct(const char **sequences,
                            const char *structure,
                            int n_seq,
                            float *energy);

float   energy_of_ali_gquad_structure(const char **sequences,
                                      const char *structure,
                                      int n_seq,
                                      float *energy);

/*
#############################################################
# some helper functions that might be useful in the library #
#############################################################
*/

void encode_ali_sequence( const char *sequence,
                          short *S,
                          short *s5,
                          short *s3,
                          char *ss,
                          unsigned short *as,
                          int circ);

void  alloc_sequence_arrays(const char **sequences,
                            short ***S,
                            short ***S5,
                            short ***S3,
                            unsigned short ***a2s,
                            char ***Ss,
                            int circ);

void  free_sequence_arrays( unsigned int n_seq,
                            short ***S,
                            short ***S5,
                            short ***S3,
                            unsigned short ***a2s,
                            char ***Ss);

/*
#############################################################
# PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #
#############################################################
*/


float alipf_fold_par( const char **sequences,
                      char *structure,
                      plist **pl,
                      pf_paramT *parameters,
                      int calculate_bppm,
                      int is_constrained,
                      int is_circular);

float alipf_fold( const char **sequences,
                  char *structure,
                  plist **pl);

float alipf_circ_fold(const char **sequences,
                      char *structure,
                      plist **pl);


FLT_OR_DBL *export_ali_bppm(void);

void  free_alipf_arrays(void);

char  *alipbacktrack(double *prob);


int get_alipf_arrays(short ***S_p,
         short ***S5_p,
         short ***S3_p,
         unsigned short ***a2s_p,
         char ***Ss_p,
         FLT_OR_DBL **qb_p,
         FLT_OR_DBL **qm_p,
         FLT_OR_DBL **q1k_p,
         FLT_OR_DBL **qln_p,
         short **pscore);

#endif