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/* $Id: lookup_wrap.h,v 1.18 2008/01/31 23:55:42 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: Ilya Dondoshansky
*
*/
/** @file lookup_wrap.h
* Wrapper for all lookup tables used in BLAST
*/
#ifndef ALGO_BLAST_CORE__LOOKUP_WRAP__H
#define ALGO_BLAST_CORE__LOOKUP_WRAP__H
#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/blast_options.h>
#include <algo/blast/core/blast_rps.h>
#include <algo/blast/core/blast_stat.h>
#ifdef __cplusplus
extern "C" {
#endif
/** Wrapper structure for different types of BLAST lookup tables */
typedef struct LookupTableWrap {
ELookupTableType lut_type; /**< What kind of a lookup table it is? */
void* lut; /**< Pointer to the actual lookup table structure */
void* read_indexed_db; /**< function used to retrieve hits
from an indexed database */
} LookupTableWrap;
/** Create the lookup table for all query words.
* @param query The query sequence [in]
* @param lookup_options What kind of lookup table to build? [in]
* @param lookup_segments Locations on query to be used for lookup table
* construction [in]
* @param sbp Scoring block containing matrix [in]
* @param lookup_wrap_ptr The initialized lookup table [out]
* @param rps_info Structure containing RPS blast setup information [in]
* @param error_msg message with warning or errors [in|out]
*/
NCBI_XBLAST_EXPORT
Int2 LookupTableWrapInit(BLAST_SequenceBlk* query,
const LookupTableOptions* lookup_options,
const QuerySetUpOptions* query_options,
BlastSeqLoc* lookup_segments, BlastScoreBlk* sbp,
LookupTableWrap** lookup_wrap_ptr, const BlastRPSInfo *rps_info,
Blast_Message* *error_msg);
/** Deallocate memory for the lookup table */
NCBI_XBLAST_EXPORT
LookupTableWrap* LookupTableWrapFree(LookupTableWrap* lookup);
/** Default size of offset arrays filled in a single ScanSubject call. */
#define OFFSET_ARRAY_SIZE 4096
/** Determine the size of the offsets arrays to be filled by
* the ScanSubject function.
*/
NCBI_XBLAST_EXPORT
Int4 GetOffsetArraySize(LookupTableWrap* lookup);
#ifdef __cplusplus
}
#endif
#endif /* !ALGO_BLAST_CORE__LOOKUP_WRAP__H */
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