RNAlib-2.3.1
alphabet.h
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1 #ifndef VIENNA_RNA_PACKAGE_ALPHABET_H
2 #define VIENNA_RNA_PACKAGE_ALPHABET_H
3 
4 /* make this interface backward compatible with RNAlib < 2.2.0 */
5 #define VRNA_BACKWARD_COMPAT
6 
7 #ifdef DEPRECATION_WARNINGS
8 # ifdef __GNUC__
9 # define DEPRECATED(func) func __attribute__ ((deprecated))
10 # else
11 # define DEPRECATED(func) func
12 # endif
13 #else
14 # define DEPRECATED(func) func
15 #endif
16 
29 #include <ViennaRNA/model.h>
30 
31 unsigned int vrna_sequence_length_max(unsigned int options);
32 
33 int vrna_nucleotide_IUPAC_identity(char a, char b);
34 
44 char *vrna_ptypes( const short *S,
45  vrna_md_t *md);
46 
51 short *vrna_seq_encode( const char *sequence,
52  vrna_md_t *md);
53 
58 short *vrna_seq_encode_simple(const char *sequence,
59  vrna_md_t *md);
60 
72 int vrna_nucleotide_encode( char c,
73  vrna_md_t *md);
74 
86 char vrna_nucleotide_decode(int enc,
87  vrna_md_t *md);
88 
89 void vrna_aln_encode( const char *sequence,
90  short **S_p,
91  short **s5_p,
92  short **s3_p,
93  char **ss_p,
94  unsigned short **as_p,
95  vrna_md_t *md);
96 
101 #ifdef VRNA_BACKWARD_COMPAT
102 
103 DEPRECATED(char *get_ptypes(const short *S, vrna_md_t *md, unsigned int idx_type));
104 
105 #endif
106 
107 #endif
char vrna_nucleotide_decode(int enc, vrna_md_t *md)
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
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)
short * vrna_seq_encode(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:191
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)