phi_extend.h

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: phi_extend.h,v $
 * PRODUCTION Revision 1000.2  2004/06/01 18:04:25  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
 * PRODUCTION
 * ===========================================================================
 */

/* $Id: phi_extend.h,v 1000.2 2004/06/01 18:04:25 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 offical 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 phi_extend.h
 * Word finder for PHI-BLAST
 */

#include <algo/blast/core/blast_extend.h>
#include <algo/blast/core/blast_util.h>

#ifndef PHI_EXTEND__H
#define PHI_EXTEND__H

#ifdef __cplusplus
extern "C" {
#endif

Int2 PHIBlastWordFinder(BLAST_SequenceBlk* subject, 
        BLAST_SequenceBlk* query, LookupTableWrap* lookup_wrap,
        Int4** matrix, const BlastInitialWordParameters* word_params,
        Blast_ExtendWord* ewp, Uint4* q_offsets, Uint4* s_offsets,
        Int4 max_hits, BlastInitHitList* init_hitlist, 
        BlastUngappedStats* ungapped_stats);

#ifdef __cplusplus
}
#endif

#endif /* PHI_EXTEND__H */