blast_options_handle.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: blast_options_handle.hpp,v $
 * PRODUCTION Revision 1000.1  2004/04/12 17:46:21  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.13
 * PRODUCTION
 * ===========================================================================
 */

#ifndef ALGO_BLAST_API___BLAST_OPTIONS_HANDLE__HPP
#define ALGO_BLAST_API___BLAST_OPTIONS_HANDLE__HPP

/*  $Id: blast_options_handle.hpp,v 1000.1 2004/04/12 17:46:21 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_options_handle.hpp
/// Declares the CBlastOptionsHandle and CBlastOptionsFactory classes.

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

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


BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)

class CBlastException;
class CBlastOptionsHandle;

/** 
* Creates BlastOptionsHandle objects with default values for the 
* programs/tasks requested.
*
* Concrete factory to create various properly configured BLAST options 
* objects with default values, given a program (or task). 
*
* Example:
* @code
* ...
* CRef<CBlastOptionsHandle> opts(CBlastOptionsFactory::Create(eBlastn));
* CBl2Seq blaster(query, subject, *opts);
* TSeqAlignVector results = blaster.Run();
* ...
* opts.Reset(CBlastOptionsFactory::Create(eMegablast));
* blaster.SetOptionsHandle() = *opts;
* results = blaster.Run();
* ...
* opts.Reset(CBlastOptionsFactory::Create(eDiscMegablast));
* blaster.SetOptionsHandle() = *opts;
* results = blaster.Run();
* ...
* @endcode
*/

class NCBI_XBLAST_EXPORT CBlastOptionsFactory
{
public:
    typedef CBlastOptions::EAPILocality EAPILocality;
    
    static CBlastOptionsHandle* Create(EProgram program, EAPILocality locality = CBlastOptions::eLocal)
        THROWS((CBlastException));

private:
    CBlastOptionsFactory();
};

/// Handle to the options to the BLAST algorithm.
///
/// This abstract base class only defines those options that are truly 
/// "universal" BLAST options (they apply to all flavors of BLAST).
/// Derived classes define options that are applicable only to those programs
/// whose options they manipulate.

class NCBI_XBLAST_EXPORT CBlastOptionsHandle : public CObject
{
public:
    typedef CBlastOptions::EAPILocality EAPILocality;
    
    CBlastOptionsHandle(EAPILocality locality);
    
    /// Return the object which this object is a handle for.
    ///
    /// Assumes user knows exactly how to set the individual options 
    /// correctly.
    const CBlastOptions& GetOptions() const { return *m_Opts; }
    CBlastOptions& SetOptions() { return *m_Opts; }
    
    /// Resets the state of the object to all default values.
    /// This is a template method (design pattern).
    virtual void SetDefaults();
    
    /// Returns true if this object needs default values set.
    void DoneDefaults() { m_Opts->DoneDefaults(); }
    
    /******************* Lookup table options ***********************/
    int GetAlphabetSize() const { return m_Opts->GetAlphabetSize(); }
    void SetAlphabetSize(int asz) { m_Opts->SetAlphabetSize(asz); }

    /******************* Query setup options ************************/
    const char* GetFilterString() const { return m_Opts->GetFilterString(); }
    void SetFilterString(const char* f) { m_Opts->SetFilterString(f); }

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

    double GetGapTrigger() const { return m_Opts->GetGapTrigger(); }
    void SetGapTrigger(double g) { m_Opts->SetGapTrigger(g); }

    /******************* Hit saving options *************************/
    int GetHitlistSize() const { return m_Opts->GetHitlistSize(); }
    void SetHitlistSize(int s) { m_Opts->SetHitlistSize(s); }
    int GetPrelimHitlistSize() const { return m_Opts->GetPrelimHitlistSize(); }
    void SetPrelimHitlistSize(int s) { m_Opts->SetPrelimHitlistSize(s); }

    int GetMaxNumHspPerSequence() const { 
        return m_Opts->GetMaxNumHspPerSequence();
    }
    void SetMaxNumHspPerSequence(int m) { m_Opts->SetMaxNumHspPerSequence(m); }

    // These 2 are never set in core... should they be removed?
    int GetTotalHspLimit() const { return m_Opts->GetTotalHspLimit(); }
    void SetTotalHspLimit(int l) { m_Opts->SetTotalHspLimit(l); }

    double GetEvalueThreshold() const { return m_Opts->GetEvalueThreshold(); }
    void SetEvalueThreshold(double eval) { m_Opts->SetEvalueThreshold(eval); } 
    int GetCutoffScore() const { return m_Opts->GetCutoffScore(); }
    void SetCutoffScore(int s) { m_Opts->SetCutoffScore(s); }

    double GetPercentIdentity() const { return m_Opts->GetPercentIdentity(); }
    void SetPercentIdentity(double p) { m_Opts->SetPercentIdentity(p); }

    bool GetGappedMode() const { return m_Opts->GetGappedMode(); }
    void SetGappedMode(bool m = true) { m_Opts->SetGappedMode(m); }

    /******************** Database (subject) options *******************/
    Int8 GetDbLength() const { return m_Opts->GetDbLength(); }
    void SetDbLength(Int8 len) { m_Opts->SetDbLength(len); }

    unsigned int GetDbSeqNum() const { return m_Opts->GetDbSeqNum(); }
    void SetDbSeqNum(unsigned int num) { m_Opts->SetDbSeqNum(num); }

protected:

    /// Data type this class controls access to
    CRef<CBlastOptions> m_Opts;

    // These methods make up the template method
    virtual void SetLookupTableDefaults() = 0;
    virtual void SetQueryOptionDefaults() = 0;
    virtual void SetInitialWordOptionsDefaults() = 0;
    virtual void SetGappedExtensionDefaults() = 0;
    virtual void SetScoringOptionsDefaults() = 0;
    virtual void SetHitSavingOptionsDefaults() = 0;
    virtual void SetEffectiveLengthsOptionsDefaults() = 0;
    virtual void SetSubjectSequenceOptionsDefaults() = 0;
};

END_SCOPE(blast)
END_NCBI_SCOPE


/* @} */


/*
 * ===========================================================================
 * $Log: blast_options_handle.hpp,v $
 * Revision 1000.1  2004/04/12 17:46:21  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.13
 *
 * Revision 1.13  2004/03/25 17:24:49  camacho
 * Minor change in sample code
 *
 * Revision 1.12  2004/03/25 17:18:44  camacho
 * Update documentation
 *
 * Revision 1.11  2004/03/19 18:56:04  camacho
 * Move to doxygen AlgoBlast group
 *
 * Revision 1.10  2004/03/19 14:53:24  camacho
 * Move to doxygen group AlgoBlast
 *
 * Revision 1.9  2004/03/10 14:54:39  madden
 * Remove methods for get/set matrix, matrix-path, gap-opening, gap-extension (moved up to next class)
 *
 * Revision 1.8  2004/02/18 23:47:56  dondosha
 * Uncommented [SG]etTotalHspLimit, as they will now be used
 *
 * Revision 1.7  2004/02/17 23:52:08  dondosha
 * Added methods to get/set preliminary hitlist size
 *
 * Revision 1.6  2004/02/03 21:30:20  camacho
 * Follow consistent use of doxygen tags
 *
 * Revision 1.5  2004/01/16 20:45:31  bealer
 * - Add locality flag and DoneDefaults() method.
 *
 * 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  2003/12/09 12:40:22  camacho
 * Added windows export specifiers
 *
 * Revision 1.2  2003/11/26 18:36:44  camacho
 * Renaming blast_option*pp -> blast_options*pp
 *
 * Revision 1.1  2003/11/26 18:22:15  camacho
 * +Blast Option Handle classes
 *
 * ===========================================================================
 */

#endif  /* ALGO_BLAST_API___BLAST_OPTIONS_HANDLE__HPP */