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