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