/* $Id: blast_nascan.h,v 1.6 2009/05/27 17:39:36 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
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 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 */

/** @file blast_nascan.h
 *  Routines for scanning nucleotide BLAST lookup tables.
 */

#ifndef ALGO_BLAST_CORE__BLAST_NTSCAN__H
#define ALGO_BLAST_CORE__BLAST_NTSCAN__H

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/core/lookup_wrap.h>

#ifdef __cplusplus
extern "C" {
#endif

/** Generic prototype for nucleotide subject scanning routines */
typedef Int4 (*TNaScanSubjectFunction)(const LookupTableWrap* lookup_wrap,
                                  const BLAST_SequenceBlk* subject,
                                  Int4 start_offset,
                                  BlastOffsetPair* NCBI_RESTRICT offset_pairs,
                                  Int4 max_hits, 
                                  Int4* end_offset);

/** Choose the most appropriate function to scan through
 * nucleotide subject sequences
 * @param lookup_wrap Structure containing lookup table [in][out]
 */
NCBI_XBLAST_EXPORT
void BlastChooseNucleotideScanSubject(LookupTableWrap *lookup_wrap);

/** Return the most generic function to scan through
 * nucleotide subject sequences
 * @param lookup_wrap Structure containing lookup table [in][out]
 */
NCBI_XBLAST_EXPORT
void * BlastChooseNucleotideScanSubjectAny(LookupTableWrap *lookup_wrap);

#ifdef __cplusplus
}
#endif

#endif /* !ALGO_BLAST_CORE__BLAST_NTSCAN__H */