English
- /*
- * ===========================================================================
- * PRODUCTION $Log: blast_encoding.h,v $
- * PRODUCTION Revision 1000.0 2004/04/12 17:53:18 gouriano
- * PRODUCTION PRODUCTION: IMPORTED [CATCHUP_003] Dev-tree R1.3
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef ALGO_BLAST_CORE___BLAST_ENCODING__H
- #define ALGO_BLAST_CORE___BLAST_ENCODING__H
- /* $Id: blast_encoding.h,v 1000.0 2004/04/12 17:53:18 gouriano Exp $
- * ===========================================================================
- *
- * PUBLIC DOMAIN NOTICE
- * National Center for Biotechnology Information
- *
- * This software/database is a "United States Government Work" under the
- * terms of the United States Copyright Act. It was written as part of
- * the author's official duties as a United States Government employee and
- * thus cannot be copyrighted. This software/database is freely available
- * to the public for use. The National Library of Medicine and the U.S.
- * Government have not placed any restriction on its use or reproduction.
- *
- * Although all reasonable efforts have been taken to ensure the accuracy
- * and reliability of the software and data, the NLM and the U.S.
- * Government do not and cannot warrant the performance or results that
- * may be obtained by using this software or data. The NLM and the U.S.
- * Government disclaim all warranties, express or implied, including
- * warranties of performance, merchantability or fitness for any particular
- * purpose.
- *
- * Please cite the author in any work or product based on this material.
- *
- * ===========================================================================
- *
- * Author: Christiam Camacho
- *
- */
- /** @file blast_encoding.h
- * Declarations of static arrays used to define some NCBI encodings to be used
- * in a toolkit independent manner by the BLAST engine.
- */
- #include <algo/blast/core/ncbi_std.h>
- /** @addtogroup AlgoBlast
- *
- * @{
- */
- #ifdef __cplusplus
- extern "C" {
- #endif
- /* Nucleotide encodings */
- /** Translates between ncbi4na and blastna. The first four elements
- * of this array match ncbi2na. */
- extern const Uint1 NCBI4NA_TO_BLASTNA[];
- /** Translates between blastna and ncbi4na. */
- extern const Uint1 BLASTNA_TO_NCBI4NA[];
- /** Translates between iupacna and blastna. */
- extern const Uint1 IUPACNA_TO_BLASTNA[];
- /** Translates between iupacna and ncbi4na. */
- extern const Uint1 IUPACNA_TO_NCBI4NA[];
- /** Translates between ncbieaa and ncbistdaa. */
- extern const Uint1 AMINOACID_TO_NCBISTDAA[];
- #define BLASTNA_SIZE 16 /**< Size of nucleic acid alphabet */
- #define BLASTAA_SIZE 26 /**< Size of aminoacid alphabet */
- /* Identifies the blastna alphabet, for use in blast only. */
- #define BLASTNA_SEQ_CODE 99
- #define BLASTAA_SEQ_CODE 11 /**< == Seq_code_ncbistdaa */
- #define NCBI4NA_SEQ_CODE 4 /**< == Seq_code_ncbi4na */
- /** @bug FIXME: Should this be removed since it's the same as BLASTAA_SIZE ? */
- #define PSI_ALPHABET_SIZE 26
- #ifdef __cplusplus
- }
- #endif
- /* @} */
- /*
- * ===========================================================================
- * $Log: blast_encoding.h,v $
- * Revision 1000.0 2004/04/12 17:53:18 gouriano
- * PRODUCTION: IMPORTED [CATCHUP_003] Dev-tree R1.3
- *
- * Revision 1.3 2004/04/09 14:48:05 camacho
- * Added doxygen comments
- *
- * Revision 1.2 2004/04/07 19:05:44 camacho
- * Minor fix in #ifdef guards
- *
- * Revision 1.1 2004/04/07 03:10:20 camacho
- * Initial revision
- *
- * ===========================================================================
- */
- #endif /* ALGO_BLAST_CORE___BLAST_ENCODING__H */
