RNAlib-2.4.3
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 VRNA_WARN_DEPRECATED
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 
34 int vrna_nucleotide_IUPAC_identity(char a,
35  char b);
36 
37 
38 void vrna_ptypes_prepare(vrna_fold_compound_t *fc,
39  unsigned int options);
40 
41 
51 char *vrna_ptypes(const short *S,
52  vrna_md_t *md);
53 
54 
59 short *vrna_seq_encode(const char *sequence,
60  vrna_md_t *md);
61 
62 
67 short *vrna_seq_encode_simple(const char *sequence,
68  vrna_md_t *md);
69 
70 
82 int vrna_nucleotide_encode(char c,
83  vrna_md_t *md);
84 
85 
97 char vrna_nucleotide_decode(int enc,
98  vrna_md_t *md);
99 
100 
101 void vrna_aln_encode(const char *sequence,
102  short **S_p,
103  short **s5_p,
104  short **s3_p,
105  char **ss_p,
106  unsigned int **as_p,
107  vrna_md_t *md);
108 
109 
114 #ifdef VRNA_BACKWARD_COMPAT
115 
116 DEPRECATED(char *get_ptypes(const short *S,
117  vrna_md_t *md,
118  unsigned int idx_type));
119 
120 #endif
121 
122 #endif
char vrna_nucleotide_decode(int enc, vrna_md_t *md)
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:130
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:189
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.
char * vrna_ptypes(const short *S, vrna_md_t *md)
Get an array of the numerical encoding for each possible base pair (i,j)