RNAlib-2.5.1
alphabet.h
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1#ifndef VIENNA_RNA_PACKAGE_ALPHABET_H
2#define VIENNA_RNA_PACKAGE_ALPHABET_H
3
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)))
9# else
10# define DEPRECATED(func, msg) func
11# endif
12#else
13# define DEPRECATED(func, msg) func
14#endif
15
30#include <ViennaRNA/model.h>
31
32unsigned int
33vrna_sequence_length_max(unsigned int options);
34
35
36int
37vrna_nucleotide_IUPAC_identity(char a,
38 char b);
39
40
41void
42vrna_ptypes_prepare(vrna_fold_compound_t *fc,
43 unsigned int options);
44
45
55char *
56vrna_ptypes(const short *S,
57 vrna_md_t *md);
58
59
67short *
68vrna_seq_encode(const char *sequence,
69 vrna_md_t *md);
70
71
76short *
77vrna_seq_encode_simple(const char *sequence,
78 vrna_md_t *md);
79
80
92int
94 vrna_md_t *md);
95
96
108char
110 vrna_md_t *md);
111
112
113void
114vrna_aln_encode(const char *sequence,
115 short **S_p,
116 short **s5_p,
117 short **s3_p,
118 char **ss_p,
119 unsigned int **as_p,
120 vrna_md_t *md);
121
122
123unsigned int
124vrna_get_ptype_md(int i,
125 int j,
126 vrna_md_t *md);
127
128
129unsigned int
130vrna_get_ptype(int ij,
131 char *ptype);
132
133
134unsigned int
135vrna_get_ptype_window(int i,
136 int j,
137 char **ptype);
138
139
144#ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
145
146DEPRECATED(char *get_ptypes(const short *S,
147 vrna_md_t *md,
148 unsigned int idx_type),
149 "Use vrna_pytpes() instead");
150
151#endif
152
153#endif
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.