RNAlib-2.4.14
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/fold_compound.h>
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 
64 short *
65 vrna_seq_encode(const char *sequence,
66  vrna_md_t *md);
67 
68 
73 short *
74 vrna_seq_encode_simple(const char *sequence,
75  vrna_md_t *md);
76 
77 
89 int
90 vrna_nucleotide_encode(char c,
91  vrna_md_t *md);
92 
93 
105 char
106 vrna_nucleotide_decode(int enc,
107  vrna_md_t *md);
108 
109 
110 void
111 vrna_aln_encode(const char *sequence,
112  short **S_p,
113  short **s5_p,
114  short **s3_p,
115  char **ss_p,
116  unsigned int **as_p,
117  vrna_md_t *md);
118 
119 
120 unsigned int
121 vrna_get_ptype_md(int i,
122  int j,
123  vrna_md_t *md);
124 
125 
126 unsigned int
127 vrna_get_ptype(int ij,
128  char *ptype);
129 
130 
131 unsigned int
132 vrna_get_ptype_window(int i,
133  int j,
134  char **ptype);
135 
136 
141 #ifndef VRNA_DISABLE_BACKWARD_COMPATIBILITY
142 
143 DEPRECATED(char *get_ptypes(const short *S,
144  vrna_md_t *md,
145  unsigned int idx_type),
146  "Use vrna_pytpes() instead");
147 
148 #endif
149 
150 #endif
vrna_fc_s
The most basic data structure required by many functions throughout the RNAlib.
Definition: fold_compound.h:132
model.h
The model details data structure and its corresponding modifiers.
vrna_seq_encode_simple
short * vrna_seq_encode_simple(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence (simple version)
vrna_md_s
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:180
vrna_seq_encode
short * vrna_seq_encode(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence.
vrna_nucleotide_decode
char vrna_nucleotide_decode(int enc, vrna_md_t *md)
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
vrna_nucleotide_encode
int vrna_nucleotide_encode(char c, vrna_md_t *md)
Encode a nucleotide character to numerical value.
vrna_ptypes
char * vrna_ptypes(const short *S, vrna_md_t *md)
Get an array of the numerical encoding for each possible base pair (i,j)
fold_compound.h
The Basic Fold Compound API.