RNAlib-2.2.5
alphabet.h
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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 
29 #include <ViennaRNA/model.h>
30 
31 int vrna_nucleotide_IUPAC_identity(char a, char b);
32 
42 char *vrna_ptypes( const short *S,
43  vrna_md_t *md);
44 
49 short *vrna_seq_encode( const char *sequence,
50  vrna_md_t *md);
51 
56 short *vrna_seq_encode_simple(const char *sequence,
57  vrna_md_t *md);
58 
70 int vrna_nucleotide_encode( char c,
71  vrna_md_t *md);
72 
84 char vrna_nucleotide_decode(int enc,
85  vrna_md_t *md);
86 
87 void vrna_aln_encode( const char *sequence,
88  short **S_p,
89  short **s5_p,
90  short **s3_p,
91  char **ss_p,
92  unsigned short **as_p,
93  vrna_md_t *md);
94 
99 #ifdef VRNA_BACKWARD_COMPAT
100 
101 DEPRECATED(char *get_ptypes(const short *S, vrna_md_t *md, unsigned int idx_type));
102 
103 #endif
104 
105 #endif
char vrna_nucleotide_decode(int enc, vrna_md_t *md)
Decode a numerical representation of a nucleotide back into nucleotide alphabet.
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)
short * vrna_seq_encode(const char *sequence, vrna_md_t *md)
Get a numerical representation of the nucleotide sequence.
The data structure that contains the complete model details used throughout the calculations.
Definition: model.h:190
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)