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RNAlib-2.4.17
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Functions to cope with various aspects related to the nucleotide sequence alphabet. More...
Functions to cope with various aspects related to the nucleotide sequence alphabet.
Collaboration diagram for Utilities to deal with Nucleotide Alphabets:Files | |
| file | alphabet.h |
| Functions to process, convert, and generally handle different nucleotide and/or base pair alphabets. | |
| file | sequence.h |
| Functions and data structures related to sequence representations ,. | |
Data Structures | |
| struct | vrna_sequence_s |
| Data structure representing a nucleotide sequence. More... | |
| struct | vrna_alignment_s |
Typedefs | |
| typedef struct vrna_sequence_s | vrna_seq_t |
| Typename for nucleotide sequence representation data structure vrna_sequence_s. | |
Enumerations | |
| enum | vrna_seq_type_e { VRNA_SEQ_UNKNOWN, VRNA_SEQ_RNA, VRNA_SEQ_DNA } |
| A enumerator used in vrna_sequence_s to distinguish different nucleotide sequences. More... | |
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. More... | |
| 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... | |
| struct vrna_sequence_s |
Data structure representing a nucleotide sequence.
Data Fields | |
| vrna_seq_type_e | type |
| The type of sequence. | |
| char * | string |
| The string representation of the sequence. | |
| short * | encoding |
| The integer representation of the sequence. | |
| unsigned int | length |
| The length of the sequence. | |
| struct vrna_alignment_s |
Collaboration diagram for vrna_alignment_s:| enum vrna_seq_type_e |
#include <ViennaRNA/sequence.h>
A enumerator used in vrna_sequence_s to distinguish different nucleotide sequences.
| Enumerator | |
|---|---|
| VRNA_SEQ_UNKNOWN | Nucleotide sequence represents an Unkown type. |
| VRNA_SEQ_RNA | Nucleotide sequence represents an RNA type. |
| VRNA_SEQ_DNA | Nucleotide sequence represents a DNA type. |
| char* vrna_ptypes | ( | const short * | S, |
| vrna_md_t * | md | ||
| ) |
#include <ViennaRNA/alphabet.h>
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 | ||
| ) |
#include <ViennaRNA/alphabet.h>
Get a numerical representation of the nucleotide sequence.
| sequence | The input sequence in upper-case letters |
| md | A pointer to a vrna_md_t data structure that specifies the conversion type |
| int vrna_nucleotide_encode | ( | char | c, |
| vrna_md_t * | md | ||
| ) |
#include <ViennaRNA/alphabet.h>
Encode a nucleotide character to numerical value.
This function encodes a nucleotide character to its numerical representation as required by many functions in RNAlib.
| c | The nucleotide character to encode |
| md | The model details that determine the kind of encoding |
| char vrna_nucleotide_decode | ( | int | enc, |
| vrna_md_t * | md | ||
| ) |
#include <ViennaRNA/alphabet.h>
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
| enc | The encoded nucleotide |
| md | The model details that determine the kind of decoding |