NCBI C++ ToolKit
Macros | Enumerations | Variables
blast_encoding.h File Reference

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent manner by the BLAST engine. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_export.h>
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Macros

#define BLAST2NA_SIZE   4
 Size of compressed nucleic acid alphabet. More...
 
#define BLASTNA_SIZE   16
 Size of nucleic acid alphabet. More...
 
#define BLASTAA_SIZE   28
 Size of aminoacid alphabet. More...
 
#define BLASTNA_SEQ_CODE   99
 Identifies the blastna alphabet, for use in blast only. More...
 
#define BLASTAA_SEQ_CODE   11
 == Seq_code_ncbistdaa More...
 
#define NCBI4NA_SEQ_CODE   4
 == Seq_code_ncbi4na More...
 

Enumerations

enum  EBlastEncoding {
  eBlastEncodingProtein = 0 , eBlastEncodingNucleotide = 1 , eBlastEncodingNcbi4na = 2 , eBlastEncodingNcbi2na = 3 ,
  eBlastEncodingError = 255
}
 Different types of sequence encodings for sequence retrieval from the BLAST database. More...
 

Variables

const Uint1 NCBI4NA_TO_BLASTNA []
 Translates between ncbi4na and blastna. More...
 
const Uint1 BLASTNA_TO_NCBI4NA []
 Translates between blastna and ncbi4na. More...
 
const Uint1 IUPACNA_TO_BLASTNA []
 Translates between iupacna and blastna. More...
 
const Uint1 IUPACNA_TO_NCBI4NA []
 Translates between iupacna and ncbi4na. More...
 
const Uint1 AMINOACID_TO_NCBISTDAA []
 Translates between ncbieaa and ncbistdaa. More...
 
const char NCBISTDAA_TO_AMINOACID []
 Translates between ncbieaa and ncbistdaa. More...
 
const char BLASTNA_TO_IUPACNA []
 Translates between blastna and iupacna. More...
 
const char NCBI4NA_TO_IUPACNA []
 Translates between ncbi4na and iupacna. More...
 
const Uint1 kProtSentinel
 Sentinel byte for protein sequences. More...
 
const Uint1 kNuclSentinel
 Sentinel nibble for nucleotide sequences. More...
 

Detailed Description

Declarations of static arrays used to define some NCBI encodings to be used in a toolkit independent manner by the BLAST engine.

Definition in file blast_encoding.h.

Modified on Mon Apr 22 04:05:51 2024 by modify_doxy.py rev. 669887