1 #ifndef VIENNA_RNA_PACKAGE_ALPHABET_H
2 #define VIENNA_RNA_PACKAGE_ALPHABET_H
5 #define VRNA_BACKWARD_COMPAT
7 #ifdef DEPRECATION_WARNINGS
9 # define DEPRECATED(func) func __attribute__ ((deprecated))
11 # define DEPRECATED(func) func
14 # define DEPRECATED(func) func
82 void vrna_aln_encode(
const char *sequence,
87 unsigned short **as_p,
94 #ifdef VRNA_BACKWARD_COMPAT
96 DEPRECATED(
char *get_ptypes(
const short *S,
vrna_md_t *md,
unsigned int idx_type));
int vrna_nucleotide_encode(char c, vrna_md_t *md)
Encode a nucleotide character to numerical value.
The model details data structure and its corresponding modifiers.
short * vrna_seq_encode_simple(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence (simple version)
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:187
char vrna_nucleotide_decode(int enc, vrna_md_t *md)
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
short * vrna_seq_encode(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence.
char * vrna_ptypes(const short *S, vrna_md_t *md)
Get an array of the numerical encoding for each possible base pair (i,j)