blastx_options.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: blastx_options.hpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 18:02:54  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

#ifndef ALGO_BLAST_API___BLASTX_OPTIONS__HPP
#define ALGO_BLAST_API___BLASTX_OPTIONS__HPP

/*  $Id: blastx_options.hpp,v 1000.2 2004/06/01 18:02:54 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.
 *
 * ===========================================================================
 *
 * Authors:  Christiam Camacho
 *
 */

/// @file blastx_options.hpp
/// Declares the CBlastxOptionsHandle class.


#include <algo/blast/api/blast_prot_options.hpp>

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


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)

/// Handle to the translated nucleotide-protein options to the BLAST algorithm.
///
/// Adapter class for translated nucleotide-protein BLAST comparisons.
/// Exposes an interface to allow manipulation the options that are relevant to
/// this type of search.

class NCBI_XBLAST_EXPORT CBlastxOptionsHandle : 
                                            public CBlastProteinOptionsHandle
{
public:

    /// Creates object with default options set
    CBlastxOptionsHandle(EAPILocality locality = CBlastOptions::eLocal);
    ~CBlastxOptionsHandle() {}

    /******************* Query setup options ************************/
    objects::ENa_strand GetStrandOption() const { 
        return m_Opts->GetStrandOption();
    }
    void SetStrandOption(objects::ENa_strand strand) {
        m_Opts->SetStrandOption(strand);
    }

    int GetQueryGeneticCode() const { return m_Opts->GetQueryGeneticCode(); }
    void SetQueryGeneticCode(int gc) { m_Opts->SetQueryGeneticCode(gc); }

    /************************ Scoring options ************************/
    // is this needed or can we use a sentinel for the frame shift penalty?
    bool GetOutOfFrameMode() const { return m_Opts->GetOutOfFrameMode(); }
    void SetOutOfFrameMode(bool m = true) { m_Opts->SetOutOfFrameMode(m); }

    int GetFrameShiftPenalty() const { return m_Opts->GetFrameShiftPenalty(); }
    void SetFrameShiftPenalty(int p) { m_Opts->SetFrameShiftPenalty(p); }

protected:
    void SetLookupTableDefaults();
    void SetQueryOptionDefaults();
    void SetScoringOptionsDefaults();
    void SetHitSavingOptionsDefaults();

private:
    CBlastxOptionsHandle(const CBlastxOptionsHandle& rhs);
    CBlastxOptionsHandle& operator=(const CBlastxOptionsHandle& rhs);
};

END_SCOPE(blast)
END_NCBI_SCOPE


/* @} */


/*
 * ===========================================================================
 * $Log: blastx_options.hpp,v $
 * Revision 1000.2  2004/06/01 18:02:54  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 *
 * Revision 1.6  2004/05/04 13:09:20  camacho
 * Made copy-ctor & assignment operator private
 *
 * Revision 1.5  2004/03/19 14:53:24  camacho
 * Move to doxygen group AlgoBlast
 *
 * Revision 1.4  2004/01/20 15:19:24  camacho
 * Provide missing default parameters to default ctor
 *
 * Revision 1.3  2004/01/16 20:42:58  bealer
 * - Add locality flag for blast options handle classes.
 *
 * Revision 1.2  2003/12/09 12:40:22  camacho
 * Added windows export specifiers
 *
 * Revision 1.1  2003/11/26 18:22:17  camacho
 * +Blast Option Handle classes
 *
 * ===========================================================================
 */

#endif  /* ALGO_BLAST_API___BLASTX_OPTIONS__HPP */