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/* $Id: blast_encoding.c,v 1.7 2008/01/24 21:25:45 kazimird 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.c
* Definitions of static arrays defined in blast_encoding.h.
* @sa blast_encoding.h
*/
#ifndef SKIP_DOXYGEN_PROCESSING
static char const rcsid[] =
"$Id: blast_encoding.c,v 1.7 2008/01/24 21:25:45 kazimird Exp $";
#endif /* SKIP_DOXYGEN_PROCESSING */
#include <algo/blast/core/blast_encoding.h>
const Uint1 NCBI4NA_TO_BLASTNA[BLASTNA_SIZE] = {
15, /* Gap, 0 */
0, /* A, 1 */
1, /* C, 2 */
6, /* M, 3 */
2, /* G, 4 */
4, /* R, 5 */
9, /* S, 6 */
13, /* V, 7 */
3, /* T, 8 */
8, /* W, 9 */
5, /* Y, 10 */
12, /* H, 11 */
7, /* K, 12 */
11, /* D, 13 */
10, /* B, 14 */
14 /* N, 15 */
};
const Uint1 BLASTNA_TO_NCBI4NA[BLASTNA_SIZE] = {
1, /* A, 0 */
2, /* C, 1 */
4, /* G, 2 */
8, /* T, 3 */
5, /* R, 4 */
10, /* Y, 5 */
3, /* M, 6 */
12, /* K, 7 */
9, /* W, 8 */
6, /* S, 9 */
14, /* B, 10 */
13, /* D, 11 */
11, /* H, 12 */
7, /* V, 13 */
15, /* N, 14 */
0 /* Gap, 15 */
};
const char BLASTNA_TO_IUPACNA[BLASTNA_SIZE] = {
'A', 'C', 'G', 'T', 'R', 'Y', 'M', 'K',
'W', 'S', 'B', 'D', 'H', 'V', 'N', '-'
};
const char NCBI4NA_TO_IUPACNA[BLASTNA_SIZE] = {
'-', 'A', 'C', 'M', 'G', 'R', 'S', 'V',
'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'
};
const Uint1 IUPACNA_TO_BLASTNA[128]={
15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
15, 0,10, 1,11,15,15, 2,12,15,15, 7,15, 6,14,15,
15,15, 4, 9, 3,15,13, 8,15, 5,15,15,15,15,15,15,
15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,
15,15,15,15,15,15,15,15,15,15,15,15,15,15,15,15};
const Uint1 IUPACNA_TO_NCBI4NA[128]={
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1,14, 2,13, 0, 0, 4,11, 0, 0,12, 0, 3,15, 0,
0, 0, 5, 6, 8, 0, 7, 9, 0,10, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
const Uint1 AMINOACID_TO_NCBISTDAA[128] = {
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,25, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,27,10,11,12,13,26,
14,15,16,17,18,24,19,20,21,22,23, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
const char NCBISTDAA_TO_AMINOACID[BLASTAA_SIZE] = {
'-','A','B','C','D','E','F','G','H','I','K','L','M',
'N','P','Q','R','S','T','V','W','X','Y','Z','U','*',
'O', 'J'};
const Uint1 kProtSentinel = NULLB;
const Uint1 kNuclSentinel = 0xF;
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