RNAlib-2.4.5
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 
28 #include <ViennaRNA/model.h>
29 
30 unsigned int vrna_sequence_length_max(unsigned int options);
31 
32 
33 int vrna_nucleotide_IUPAC_identity(char a,
34  char b);
35 
36 
37 void vrna_ptypes_prepare(vrna_fold_compound_t *fc,
38  unsigned int options);
39 
40 
50 char *vrna_ptypes(const short *S,
51  vrna_md_t *md);
52 
53 
58 short *vrna_seq_encode(const char *sequence,
59  vrna_md_t *md);
60 
61 
66 short *vrna_seq_encode_simple(const char *sequence,
67  vrna_md_t *md);
68 
69 
81 int vrna_nucleotide_encode(char c,
82  vrna_md_t *md);
83 
84 
96 char vrna_nucleotide_decode(int enc,
97  vrna_md_t *md);
98 
99 
100 void vrna_aln_encode(const char *sequence,
101  short **S_p,
102  short **s5_p,
103  short **s3_p,
104  char **ss_p,
105  unsigned int **as_p,
106  vrna_md_t *md);
107 
108 
109 unsigned int
110 vrna_get_ptype_md(int i,
111  int j,
112  vrna_md_t *md);
113 
114 
115 unsigned int
116 vrna_get_ptype(int ij,
117  char *ptype);
118 
119 
120 unsigned int
121 vrna_get_ptype_window(int i,
122  int j,
123  char **ptype);
124 
125 
130 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
131 
132 DEPRECATED(char *get_ptypes(const short *S,
133  vrna_md_t *md,
134  unsigned int idx_type),
135  "Use vrna_pytpes() instead");
136 
137 #endif
138 
139 #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:131
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.
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)