blast_nucl_options.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: blast_nucl_options.hpp,v $
 * PRODUCTION Revision 1000.2  2004/06/01 18:02:40  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.11
 * PRODUCTION
 * ===========================================================================
 */

#ifndef ALGO_BLAST_API___BLAST_NUCL_OPTIONS__HPP
#define ALGO_BLAST_API___BLAST_NUCL_OPTIONS__HPP

/*  $Id: blast_nucl_options.hpp,v 1000.2 2004/06/01 18:02:40 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
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Authors:  Christiam Camacho
 *
 */

/// @file blast_nucl_options.hpp
/// Declares the CBlastNucleotideOptionsHandle class.

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

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

BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)

/// Handle to the nucleotide-nucleotide options to the BLAST algorithm.
///
/// Adapter class for nucleotide-nucleotide BLAST comparisons.
/// Exposes an interface to allow manipulation the options that are relevant to
/// this type of search.
/// 
/// NB: By default, traditional megablast defaults are used. If blastn defaults
/// are desired, please call the appropriate member function:
///
///    void SetTraditionalBlastnDefaults();
///    void SetTraditionalMegablastDefaults();

class NCBI_XBLAST_EXPORT CBlastNucleotideOptionsHandle : 
                                            public CBlastOptionsHandle
{
public:

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

    virtual void SetDefaults();

    /******************* Lookup table options ***********************/
    int GetLookupTableType() const { return m_Opts->GetLookupTableType(); }
    void SetLookupTableType(int type) { m_Opts->SetLookupTableType(type); }

    unsigned char GetScanStep() const { return m_Opts->GetScanStep(); }
    void SetScanStep(unsigned char step) { m_Opts->SetScanStep(step); }

    short GetWordSize() const { return m_Opts->GetWordSize(); }
    void SetWordSize(short ws) { m_Opts->SetWordSize(ws); }

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

    /******************* Initial word options ***********************/
    int GetWindowSize() const { return m_Opts->GetWindowSize(); }
    void SetWindowSize(int ws) { m_Opts->SetWindowSize(ws); }

    SeedContainerType GetSeedContainerType() const {
        return m_Opts->GetSeedContainerType();
    }
    void SetSeedContainerType(SeedContainerType sct) {
        m_Opts->SetSeedContainerType(sct);
    }

    SeedExtensionMethod GetSeedExtensionMethod() const {
        return m_Opts->GetSeedExtensionMethod();
    }
    // Note that the scan step (or stride) is changed as a side effect of
    // calling this method because. This is because the scan step is best
    // calculated for the eRightAndLeft seed extension method and a fixed value
    // is used for the eRight seed extension method.
    void SetSeedExtensionMethod(SeedExtensionMethod sem) {
        switch (sem) {
        case eRight: 
            SetScanStep(COMPRESSION_RATIO);
            break;
        case eRightAndLeft:
        {
            unsigned int s = CalculateBestStride(GetWordSize(), 
                                                 GetVariableWordSize(), 
                                                 GetLookupTableType());
            SetScanStep(s);
            break;
        }
        default:
            abort();
        }
        m_Opts->SetSeedExtensionMethod(sem);
    }

    bool GetVariableWordSize() const { return m_Opts->GetVariableWordSize(); }
    void SetVariableWordSize(bool val = true) { 
        m_Opts->SetVariableWordSize(val); 
    }

    bool GetUngappedExtension() const { return m_Opts->GetUngappedExtension();}
    void SetUngappedExtension(bool val = true) { 
        m_Opts->SetUngappedExtension(val); 
    }

    double GetXDropoff() const { return m_Opts->GetXDropoff(); } 
    void SetXDropoff(double x) { m_Opts->SetXDropoff(x); }

    /******************* Gapped extension options *******************/
    double GetGapXDropoffFinal() const { 
        return m_Opts->GetGapXDropoffFinal(); 
    }
    void SetGapXDropoffFinal(double x) { m_Opts->SetGapXDropoffFinal(x); }

    EBlastPrelimGapExt GetGapExtnAlgorithm() const { return m_Opts->GetGapExtnAlgorithm(); }
    void SetGapExtnAlgorithm(EBlastPrelimGapExt algo) { m_Opts->SetGapExtnAlgorithm(algo); }

    EBlastTbackExt GetGapTracebackAlgorithm() const { return m_Opts->GetGapTracebackAlgorithm(); }
    void SetGapTracebackAlgorithm(EBlastTbackExt algo) { m_Opts->SetGapTracebackAlgorithm(algo); }

    /************************ Scoring options ************************/
    int GetMatchReward() const { return m_Opts->GetMatchReward(); }
    void SetMatchReward(int r) { m_Opts->SetMatchReward(r); }

    int GetMismatchPenalty() const { return m_Opts->GetMismatchPenalty(); }
    void SetMismatchPenalty(int p) { m_Opts->SetMismatchPenalty(p); }

    const char* GetMatrixName() const { return m_Opts->GetMatrixName(); }
    void SetMatrixName(const char* matrix) { m_Opts->SetMatrixName(matrix); }

    const char* GetMatrixPath() const { return m_Opts->GetMatrixPath(); }
    void SetMatrixPath(const char* path) { m_Opts->SetMatrixPath(path); }

    int GetGapOpeningCost() const { return m_Opts->GetGapOpeningCost(); }
    void SetGapOpeningCost(int g) { m_Opts->SetGapOpeningCost(g); }

    int GetGapExtensionCost() const { return m_Opts->GetGapExtensionCost(); }
    void SetGapExtensionCost(int e) { m_Opts->SetGapExtensionCost(e); }

    Int8 GetEffectiveSearchSpace() const { 
        return m_Opts->GetEffectiveSearchSpace(); 
    }
    void SetEffectiveSearchSpace(Int8 eff) {
        m_Opts->SetEffectiveSearchSpace(eff);
    }

    bool GetUseRealDbSize() const { return m_Opts->GetUseRealDbSize(); }
    void SetUseRealDbSize(bool u = true) { m_Opts->SetUseRealDbSize(u); }


    void SetTraditionalBlastnDefaults();
    void SetTraditionalMegablastDefaults();

protected:
    virtual void SetLookupTableDefaults();
    virtual void SetMBLookupTableDefaults();
    virtual void SetQueryOptionDefaults();
    virtual void SetInitialWordOptionsDefaults();
    virtual void SetMBInitialWordOptionsDefaults();
    virtual void SetGappedExtensionDefaults();
    virtual void SetMBGappedExtensionDefaults();
    virtual void SetScoringOptionsDefaults();
    virtual void SetMBScoringOptionsDefaults();
    virtual void SetHitSavingOptionsDefaults();
    virtual void SetEffectiveLengthsOptionsDefaults();
    virtual void SetSubjectSequenceOptionsDefaults();

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

END_SCOPE(blast)
END_NCBI_SCOPE


/* @} */


/*
 * ===========================================================================
 * $Log: blast_nucl_options.hpp,v $
 * Revision 1000.2  2004/06/01 18:02:40  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.11
 *
 * Revision 1.11  2004/05/18 12:48:24  madden
 * Add setter and getter for GapTracebackAlgorithm (EBlastTbackExt)
 *
 * Revision 1.10  2004/05/17 15:28:54  madden
 * Int algorithm_type replaced with enum EBlastPrelimGapExt
 *
 * Revision 1.9  2004/05/04 13:09:20  camacho
 * Made copy-ctor & assignment operator private
 *
 * Revision 1.8  2004/03/19 14:53:24  camacho
 * Move to doxygen group AlgoBlast
 *
 * Revision 1.7  2004/03/10 14:55:02  madden
 * Added methods for get/set matrix, matrix-path, gap-opening, gap-extension
 *
 * Revision 1.6  2004/02/10 19:48:07  dondosha
 * Added SetMBGappedExtensionDefaults method
 *
 * Revision 1.5  2004/01/16 20:42:59  bealer
 * - Add locality flag for blast options handle classes.
 *
 * Revision 1.4  2003/12/15 23:41:35  dondosha
 * Added [gs]etters of database (subject) length and number of sequences to general options handle
 *
 * Revision 1.3  2003/12/10 18:00:54  camacho
 * Added comment explaining defaults
 *
 * Revision 1.2  2003/12/09 12:40:22  camacho
 * Added windows export specifiers
 *
 * Revision 1.1  2003/11/26 18:22:14  camacho
 * +Blast Option Handle classes
 *
 * ===========================================================================
 */

#endif  /* ALGO_BLAST_API___BLAST_NUCL_OPTIONS__HPP */