#ifndef ALGO_BLAST_API___ADVPROT_OPTIONS__HPP
#define ALGO_BLAST_API___ADVPROT_OPTIONS__HPP

/*  $Id: blast_advprot_options.hpp 472241 2015-07-08 15:24:13Z fongah2 $
 * ===========================================================================
 *
 *                            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:  Tom Madden
 *
 */

/// @file blast_advprot_options.hpp
/// Declares the CBlastAdvancedProteinOptionsHandle class.
/// This class supports protein options such as composition-based stats and 
/// Smith-Waterman that are not implemented for blastx, tblastn, etc.


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

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


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)

/// Handle to the Advanced BLASTP options.
///
/// Adapter class for advanced BLASTP options
/// Exposes an interface to allow manipulation the options that are relevant to
/// this type of search.

class NCBI_XBLAST_EXPORT CBlastAdvancedProteinOptionsHandle : 
                                            public CBlastProteinOptionsHandle
{
public:

    /// Creates object with default options set
    CBlastAdvancedProteinOptionsHandle(EAPILocality locality = CBlastOptions::eLocal);

    CBlastAdvancedProteinOptionsHandle(CRef<CBlastOptions> opt):CBlastProteinOptionsHandle(opt){}

/******************* Gapped extension options *******************/

    /// Returns this mode, which mostly specifies whether composition of db
    /// sequence is taken into account when calculating expect values.
    ECompoAdjustModes GetCompositionBasedStats() const { 
        return m_Opts->GetCompositionBasedStats(); 
    }

    /// Sets this mode, which mostly specifies whether composition of db
    /// sequence is taken into account when calculating expect values.
    /// @param mode composition-based statistics mode [in]
    void SetCompositionBasedStats(ECompoAdjustModes mode)  { 
        m_Opts->SetCompositionBasedStats(mode); 
    }

    /// Returns this mode, specifying that smith waterman rather than the normal blast heuristic
    /// should be used for final extensions.
    /// into account when calculating expect values.
    bool GetSmithWatermanMode() const { return m_Opts->GetSmithWatermanMode(); }

    /// Sets this mode, specifying that smith waterman rather than the normal blast heuristic
    /// should be used for final extensions.
    /// @param m use smith-waterman if true [in]
    void SetSmithWatermanMode(bool m = false)  { m_Opts->SetSmithWatermanMode(m); }

protected:
    /// Overrides  SetGappedExtensionDefaults for advanced blastp options
    virtual void  SetGappedExtensionDefaults();

    /// Overrides SetQueryOptionDefaults for advanced blastp options to disable filtering
    virtual void SetQueryOptionDefaults();

private:
    /// Disallow copy constructor
    CBlastAdvancedProteinOptionsHandle(const CBlastAdvancedProteinOptionsHandle& rhs);
    /// Disallow assignment operator
    CBlastAdvancedProteinOptionsHandle& operator=(const CBlastAdvancedProteinOptionsHandle& rhs);
};

END_SCOPE(blast)
END_NCBI_SCOPE


/* @} */

#endif  /* ALGO_BLAST_API___ADVPROT_OPTIONS__HPP */
