blast_input.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: blast_input.hpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 18:06:40  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.10
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: blast_input.hpp,v 1000.2 2004/06/01 18:06:40 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
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 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author:  Christiam Camacho
 *
 */

/** @file blast_input.hpp
 * Reading FASTA sequences from input file
 */

#ifndef ALGO_BLAST_API___BLAST_INPUT__HPP
#define ALGO_BLAST_API___BLAST_INPUT__HPP

#include <corelib/ncbistd.hpp>
#include <algo/blast/api/blast_aux.hpp>

BEGIN_NCBI_SCOPE

BEGIN_SCOPE(objects)
    class CObjectManager;
END_SCOPE(objects)

BEGIN_SCOPE(blast)


TSeqLocVector
BLASTGetSeqLocFromStream(CNcbiIstream& in, objects::CObjectManager& objmgr, 
                         objects::ENa_strand strand,
                         TSeqPos from, TSeqPos to, int* counter,
                         bool get_lcase_mask = FALSE);


END_SCOPE(blast)
END_NCBI_SCOPE

#endif  /* ALGO_BLAST_API___BLAST_INPUT__HPP */