English
- /*
- * ===========================================================================
- * PRODUCTION $Log: blast_rps_options.hpp,v $
- * PRODUCTION Revision 1000.2 2004/06/01 18:02:48 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef ALGO_BLAST_API___BLAST_RPS_OPTIONS__HPP
- #define ALGO_BLAST_API___BLAST_RPS_OPTIONS__HPP
- /* $Id: blast_rps_options.hpp,v 1000.2 2004/06/01 18:02:48 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: Tom Madden
- *
- */
- /// @file blast_rps_options.hpp
- /// Declares the CBlastRPSOptionsHandle class.
- #include <algo/blast/api/blast_prot_options.hpp>
- /** @addtogroup AlgoBlast
- *
- * @{
- */
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(blast)
- /// Handle to the rpsblast options to the BLAST algorithm.
- ///
- /// Adapter class for rpsblast BLAST comparisons.
- /// Exposes an interface to allow manipulation the options that are relevant to
- /// this type of search.
- class NCBI_XBLAST_EXPORT CBlastRPSOptionsHandle : public CBlastOptionsHandle
- {
- public:
- /// Creates object with default options set
- CBlastRPSOptionsHandle(EAPILocality locality = CBlastOptions::eLocal);
- ~CBlastRPSOptionsHandle() {}
- /******************* Lookup table options ***********************/
- int GetWordThreshold() const { return m_Opts->GetWordThreshold(); }
- short GetWordSize() const { return m_Opts->GetWordSize(); }
- /******************* Initial word options ***********************/
- int GetWindowSize() const { return m_Opts->GetWindowSize(); }
- void SetWindowSize(int ws) { m_Opts->SetWindowSize(ws); }
- 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); }
- /************************ Scoring options ************************/
- int GetGapOpeningCost() const { return m_Opts->GetGapOpeningCost(); }
- int GetGapExtensionCost() const { return m_Opts->GetGapExtensionCost(); }
- 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); }
- protected:
- virtual void SetLookupTableDefaults();
- virtual void SetQueryOptionDefaults();
- virtual void SetInitialWordOptionsDefaults();
- virtual void SetGappedExtensionDefaults();
- virtual void SetScoringOptionsDefaults();
- virtual void SetHitSavingOptionsDefaults();
- virtual void SetEffectiveLengthsOptionsDefaults();
- virtual void SetSubjectSequenceOptionsDefaults();
- private:
- CBlastRPSOptionsHandle(const CBlastRPSOptionsHandle& rhs);
- CBlastRPSOptionsHandle& operator=(const CBlastRPSOptionsHandle& rhs);
- };
- END_SCOPE(blast)
- END_NCBI_SCOPE
- /* @} */
- /*
- * ===========================================================================
- * $Log: blast_rps_options.hpp,v $
- * Revision 1000.2 2004/06/01 18:02:48 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
- *
- * Revision 1.5 2004/05/04 13:09:20 camacho
- * Made copy-ctor & assignment operator private
- *
- * Revision 1.4 2004/04/23 13:55:29 papadopo
- * derived BlastRPSOptionsHandle from BlastOptions (again)
- *
- * Revision 1.3 2004/04/16 14:31:49 papadopo
- * make this class a derived class of CBlastProteinOptionsHandle, that corresponds to the eRPSBlast program
- *
- * Revision 1.2 2004/03/19 14:53:24 camacho
- * Move to doxygen group AlgoBlast
- *
- * Revision 1.1 2004/03/10 14:52:34 madden
- * Options handle for RPSBlast searches
- *
- *
- * ===========================================================================
- */
- #endif /* ALGO_BLAST_API___BLAST_RPS_OPTIONS__HPP */
