RNAlib-2.2.9

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alphabet.h
Go to the documentation of this file.
1 #ifndef VIENNA_RNA_PACKAGE_ALPHABET_H
2 #define VIENNA_RNA_PACKAGE_ALPHABET_H
3
4 /* make this interface backward compatible with RNAlib < 2.2.0 */
5 #define VRNA_BACKWARD_COMPAT
6
7 #ifdef DEPRECATION_WARNINGS
8 # ifdef __GNUC__
9 # define DEPRECATED(func) func __attribute__ ((deprecated))
10 # else
11 # define DEPRECATED(func) func
12 # endif
13 #else
14 # define DEPRECATED(func) func
15 #endif
16
26 #include <ViennaRNA/model.h>
27
28 int vrna_nucleotide_IUPAC_identity(char a, char b);
29
39 char *vrna_ptypes( const short *S,
40 vrna_md_t *md);
41
46 short *vrna_seq_encode( const char *sequence,
47 vrna_md_t *md);
48
53 short *vrna_seq_encode_simple(const char *sequence,
54 vrna_md_t *md);
55
67 int vrna_nucleotide_encode( char c,
68 vrna_md_t *md);
69
81 char vrna_nucleotide_decode(int enc,
82 vrna_md_t *md);
83
84 void vrna_aln_encode( const char *sequence,
85 short **S_p,
86 short **s5_p,
87 short **s3_p,
88 char **ss_p,
89 unsigned short **as_p,
90 vrna_md_t *md);
91
96 #ifdef VRNA_BACKWARD_COMPAT
97
98 DEPRECATED(char *get_ptypes(const short *S, vrna_md_t *md, unsigned int idx_type));
99
100 #endif
101
102 #endif
vrna_nucleotide_encode
int vrna_nucleotide_encode(char c, vrna_md_t *md)
Encode a nucleotide character to numerical value.
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:188
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_seq_encode
short * vrna_seq_encode(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence.
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)