1 #ifndef VIENNA_RNA_PACKAGE_ALPHABET_H 2 #define VIENNA_RNA_PACKAGE_ALPHABET_H 4 #ifdef VRNA_WARN_DEPRECATED 5 # if defined(__clang__) 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 31 unsigned int vrna_sequence_length_max(
unsigned int options);
34 int vrna_nucleotide_IUPAC_identity(
char a,
39 unsigned int options);
101 void vrna_aln_encode(
const char *sequence,
111 vrna_get_ptype_md(
int i,
117 vrna_get_ptype(
int ij,
122 vrna_get_ptype_window(
int i,
131 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY 133 DEPRECATED(
char *get_ptypes(
const short *S,
135 unsigned int idx_type),
136 "Use vrna_pytpes() instead");
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
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:177
short * vrna_seq_encode(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence.
char vrna_nucleotide_decode(int enc, vrna_md_t *md)
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
int vrna_nucleotide_encode(char c, vrna_md_t *md)
Encode a nucleotide character to numerical value.
char * vrna_ptypes(const short *S, vrna_md_t *md)
Get an array of the numerical encoding for each possible base pair (i,j)