alphabet.h
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#ifndef VIENNA_RNA_PACKAGE_ALPHABET_H
#define VIENNA_RNA_PACKAGE_ALPHABET_H
/* make this interface backward compatible with RNAlib < 2.2.0 */
#define VRNA_BACKWARD_COMPAT
#ifdef DEPRECATION_WARNINGS
# ifdef __GNUC__
# define DEPRECATED(func) func __attribute__ ((deprecated))
# else
# define DEPRECATED(func) func
# endif
#else
# define DEPRECATED(func) func
#endif
#include <ViennaRNA/model.h>
int vrna_nucleotide_IUPAC_identity(char a, char b);
char *vrna_ptypes( const short *S,
vrna_md_t *md);
short *vrna_seq_encode( const char *sequence,
vrna_md_t *md);
short *vrna_seq_encode_simple(const char *sequence,
vrna_md_t *md);
int vrna_nucleotide_encode( char c,
vrna_md_t *md);
char vrna_nucleotide_decode(int enc,
vrna_md_t *md);
void vrna_aln_encode( const char *sequence,
short **S_p,
short **s5_p,
short **s3_p,
char **ss_p,
unsigned short **as_p,
vrna_md_t *md);
#ifdef VRNA_BACKWARD_COMPAT
DEPRECATED(char *get_ptypes(const short *S, vrna_md_t *md, unsigned int idx_type));
#endif
#endif
vrna_nucleotide_encode
int vrna_nucleotide_encode(char c, vrna_md_t *md)
Encode a nucleotide character to numerical value.
model.h
The model details data structure and its corresponding modifiers.
vrna_seq_encode_simple
short * vrna_seq_encode_simple(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence (simple version)
vrna_md_s
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:188
vrna_nucleotide_decode
char vrna_nucleotide_decode(int enc, vrna_md_t *md)
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
vrna_seq_encode
short * vrna_seq_encode(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence.
vrna_ptypes
char * vrna_ptypes(const short *S, vrna_md_t *md)
Get an array of the numerical encoding for each possible base pair (i,j)