1#ifndef VIENNA_RNA_PACKAGE_ALPHABET_H
2#define VIENNA_RNA_PACKAGE_ALPHABET_H
4#ifdef VRNA_WARN_DEPRECATED
6# define DEPRECATED(func, msg) func __attribute__ ((deprecated("", msg)))
7# elif defined(__GNUC__)
8# define DEPRECATED(func, msg) func __attribute__ ((deprecated(msg)))
10# define DEPRECATED(func, msg) func
13# define DEPRECATED(func, msg) func
33vrna_sequence_length_max(
unsigned int options);
37vrna_nucleotide_IUPAC_identity(
char a,
43 unsigned int options);
114vrna_aln_encode(
const char *sequence,
124vrna_get_ptype_md(
int i,
130vrna_get_ptype(
int ij,
135vrna_get_ptype_window(
int i,
144#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
146DEPRECATED(
char *get_ptypes(
const short *S,
148 unsigned int idx_type),
149 "Use vrna_pytpes() instead");
The Basic Fold Compound API.
char vrna_nucleotide_decode(int enc, vrna_md_t *md)
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
char * vrna_ptypes(const short *S, vrna_md_t *md)
Get an array of the numerical encoding for each possible base pair (i,j)
short * vrna_seq_encode(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence.
int vrna_nucleotide_encode(char c, vrna_md_t *md)
Encode a nucleotide character to numerical value.
short * vrna_seq_encode_simple(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence (simple version)
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:148
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180
The model details data structure and its corresponding modifiers.