RNAlib-2.4.10
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 
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 
110 unsigned int
111 vrna_get_ptype_md(int i,
112  int j,
113  vrna_md_t *md);
114 
115 
116 unsigned int
117 vrna_get_ptype(int ij,
118  char *ptype);
119 
120 
121 unsigned int
122 vrna_get_ptype_window(int i,
123  int j,
124  char **ptype);
125 
126 
131 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
132 
133 DEPRECATED(char *get_ptypes(const short *S,
134  vrna_md_t *md,
135  unsigned int idx_type),
136  "Use vrna_pytpes() instead");
137 
138 #endif
139 
140 #endif
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)