RNAlib-2.2.7
alphabet.h File Reference

Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets. More...

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Functions

char * vrna_ptypes (const short *S, vrna_md_t *md)
 Get an array of the numerical encoding for each possible base pair (i,j) More...
 
short * vrna_seq_encode (const char *sequence, vrna_md_t *md)
 Get a numerical representation of the nucleotide sequence.
 
short * vrna_seq_encode_simple (const char *sequence, vrna_md_t *md)
 Get a numerical representation of the nucleotide sequence (simple version)
 
int vrna_nucleotide_encode (char c, vrna_md_t *md)
 Encode a nucleotide character to numerical value. More...
 
char vrna_nucleotide_decode (int enc, vrna_md_t *md)
 Decode a numerical representation of a nucleotide back into nucleotide alphabet. More...
 

Detailed Description

Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets.

Function Documentation

char* vrna_ptypes ( const short *  S,
vrna_md_t md 
)

Get an array of the numerical encoding for each possible base pair (i,j)

Note
This array is always indexed in column-wise order, in contrast to previously different indexing between mfe and pf variants!
See also
vrna_idx_col_wise(), vrna_fold_compound_t
int vrna_nucleotide_encode ( char  c,
vrna_md_t md 
)

Encode a nucleotide character to numerical value.

This function encodes a nucleotide character to its numerical representation as required by many functions in RNAlib.

See also
vrna_nucleotide_decode(), vrna_seq_encode()
Parameters
cThe nucleotide character to encode
mdThe model details that determine the kind of encoding
Returns
The encoded nucleotide
char vrna_nucleotide_decode ( int  enc,
vrna_md_t md 
)

Decode a numerical representation of a nucleotide back into nucleotide alphabet.

This function decodes a numerical representation of a nucleotide character back into nucleotide alphabet

See also
vrna_nucleotide_encode(), vrna_seq_encode()
Parameters
encThe encoded nucleotide
mdThe model details that determine the kind of decoding
Returns
The decoded nucleotide character