seqdb_src.hpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: seqdb_src.hpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 18:03:10  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
 * PRODUCTION
 * ===========================================================================
 */

#ifndef ALGO_BLAST_API___SEQDB_SRC__HPP
#define ALGO_BLAST_API___SEQDB_SRC__HPP

/*  $Id: seqdb_src.hpp,v 1000.1 2004/06/01 18:03:10 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:  Ilya Dondoshansky
 *
 */

/// @file seqdb_src.hpp
/// Implementation of the BlastSeqSrc interface using the C++ BLAST databases
/// API


#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/core/blast_def.h>
#include <algo/blast/api/blast_types.hpp>

/** @addtogroup AlgoBlast
 *
 * @{
 */

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)

/// Encapsulates the arguments needed to initialize multi-sequence source.
struct SSeqDbSrcNewArgs {
    char* dbname;     /**< Database name */
    bool is_protein; /**< Is this database protein? */
    Int4 first_db_seq; /**< Ordinal id of the first sequence to search */
    Int4 final_db_seq; /**< Ordinal id of the last sequence to search */
};

extern "C" {

/** SeqDb sequence source constructor 
 * @param bssp BlastSeqSrc structure (already allocated) to populate [in]
 * @param args Pointer to SSeqDbSrcNewArgs structure above [in]
 * @return Updated bssp structure (with all function pointers initialized
 */
BlastSeqSrc* SeqDbSrcNew(BlastSeqSrc* bssp, void* args);

/** SeqDb sequence source destructor: frees its internal data structure and the
 * BlastSeqSrc structure itself.
 * @param bssp BlastSeqSrc structure to free [in]
 * @return NULL
 */
BlastSeqSrc* SeqDbSrcFree(BlastSeqSrc* bssp);

}

/** Initialize the sequence source structure.
 * @param dbname BLAST database name [in]
 * @param is_prot Is this a protein or nucleotide database? [in]
 * @param first_seq First ordinal id in the database to search [in]
 * @param last_seq Last ordinal id in the database to search 
 *                 (full database if 0) [in]
 * @param extra_arg Reserved for the future implementation of other database
 *                  restrictions [in]
 */
BlastSeqSrc* 
SeqDbSrcInit(const char* dbname, Boolean is_prot, int first_seq, 
             int last_seq, void* extra_arg);

END_SCOPE(blast)
END_NCBI_SCOPE

/* @} */

/*
 * ===========================================================================
 * $Log: seqdb_src.hpp,v $
 * Revision 1000.1  2004/06/01 18:03:10  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.3
 *
 * Revision 1.3  2004/05/19 14:52:00  camacho
 * 1. Added doxygen tags to enable doxygen processing of algo/blast/core
 * 2. Standardized copyright, CVS $Id string, $Log and rcsid formatting and i
 *    location
 * 3. Added use of @todo doxygen keyword
 *
 * Revision 1.2  2004/04/08 14:46:06  camacho
 * Added missing extern "C" declarations"
 *
 * Revision 1.1  2004/04/06 20:43:54  dondosha
 * Sequence source for CSeqDB BLAST database interface
 *
 * ===========================================================================
 */

#endif /* ALGO_BLAST_API___SEQDB_SRC__HPP */