RNAlib-2.5.0
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 
32 unsigned int
33 vrna_sequence_length_max(unsigned int options);
34 
35 
36 int
37 vrna_nucleotide_IUPAC_identity(char a,
38  char b);
39 
40 
41 void
42 vrna_ptypes_prepare(vrna_fold_compound_t *fc,
43  unsigned int options);
44 
45 
55 char *
56 vrna_ptypes(const short *S,
57  vrna_md_t *md);
58 
59 
67 short *
68 vrna_seq_encode(const char *sequence,
69  vrna_md_t *md);
70 
71 
76 short *
77 vrna_seq_encode_simple(const char *sequence,
78  vrna_md_t *md);
79 
80 
92 int
94  vrna_md_t *md);
95 
96 
108 char
110  vrna_md_t *md);
111 
112 
113 void
114 vrna_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 
123 unsigned int
124 vrna_get_ptype_md(int i,
125  int j,
126  vrna_md_t *md);
127 
128 
129 unsigned int
130 vrna_get_ptype(int ij,
131  char *ptype);
132 
133 
134 unsigned int
135 vrna_get_ptype_window(int i,
136  int j,
137  char **ptype);
138 
139 
144 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
145 
146 DEPRECATED(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.
short * vrna_seq_encode_simple(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence (simple version)
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.
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:137
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.