blast_nucl_options.hpp
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- /*
- * ===========================================================================
- * 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 */
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