NCBI C++ Toolkit Cross Reference

  C++/include/algo/blast/api/blast_nucl_options.hpp


#ifndef ALGO_BLAST_API___BLAST_NUCL_OPTIONS__HPP #define ALGO_BLAST_API___BLAST_NUCL_OPTIONS__HPP /* $Id: blast_nucl_options.hpp 58668 2013-06-26 13:46:36Z 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: 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); /// Create Options Handle from Existing CBlastOptions Object CBlastNucleotideOptionsHandle(CRef<CBlastOptions> opt); /// Sets Defaults virtual void SetDefaults(); /******************* Lookup table options ***********************/ /// Returns LookupTableType ELookupTableType GetLookupTableType() const { return m_Opts->GetLookupTableType(); } /// Sets LookupTableType /// @param type LookupTableType [in] void SetLookupTableType(ELookupTableType type) { m_Opts->SetLookupTableType(type); } /// Returns WordSize int GetWordSize() const { return m_Opts->GetWordSize(); } /// Sets WordSize /// @param ws WordSize [in] void SetWordSize(int ws) { m_Opts->SetWordSize(ws); } /******************* Query setup options ************************/ /// Returns StrandOption objects::ENa_strand GetStrandOption() const { return m_Opts->GetStrandOption(); } /// Sets StrandOption /// @param strand StrandOption [in] void SetStrandOption(objects::ENa_strand strand) { m_Opts->SetStrandOption(strand); } /// Is dust filtering enabled? bool GetDustFiltering() const { return m_Opts->GetDustFiltering(); } /// Enable dust filtering. /// @param val enable dust filtering [in] void SetDustFiltering(bool val) { m_Opts->SetDustFiltering(val); } /// Get level parameter for dust int GetDustFilteringLevel() const { return m_Opts->GetDustFilteringLevel(); } /// Set level parameter for dust. Acceptable values: 2 < level < 64 /// @param level dust filtering parameter level [in] void SetDustFilteringLevel(int level) { m_Opts->SetDustFilteringLevel(level); } /// Get window parameter for dust int GetDustFilteringWindow() const { return m_Opts->GetDustFilteringWindow(); } /// Set window parameter for dust. Acceptable values: 8 < windowsize < 64 /// @param window dust filtering parameter window [in] void SetDustFilteringWindow(int window) { m_Opts->SetDustFilteringWindow(window); } /// Get linker parameter for dust int GetDustFilteringLinker() const { return m_Opts->GetDustFilteringLinker(); } /// Set linker parameter for dust. Acceptable values: 1 < linker < 32 /// @param linker dust filtering parameter linker [in] void SetDustFilteringLinker(int linker) { m_Opts->SetDustFilteringLinker(linker); } /// Is repeat filtering enabled? bool GetRepeatFiltering() const { return m_Opts->GetRepeatFiltering(); } /// Enable repeat filtering. /// @param val enable repeat filtering [in] void SetRepeatFiltering(bool val) { m_Opts->SetRepeatFiltering(val); } /// Get the repeat filtering database const char* GetRepeatFilteringDB() const { return m_Opts->GetRepeatFilteringDB(); } /// Enable repeat filtering. /// @param db repeat filtering database [in] void SetRepeatFilteringDB(const char* db) { m_Opts->SetRepeatFilteringDB(db); } /// Get the window masker taxid (or 0 if not set). int GetWindowMaskerTaxId() const { return m_Opts->GetWindowMaskerTaxId(); } /// Enable window masker and select a taxid (or 0 to disable). /// @param taxid Select Window Masker filtering database for this taxid [in] void SetWindowMaskerTaxId(int taxid) { m_Opts->SetWindowMaskerTaxId(taxid); } /// Get the window masker database name (or NULL if not set). const char* GetWindowMaskerDatabase() const { return m_Opts->GetWindowMaskerDatabase(); } /// Enable window masker and select a database (or NULL to disable). /// @param taxid Select Window Masker filtering database by filename [in] void SetWindowMaskerDatabase(const char* db) { m_Opts->SetWindowMaskerDatabase(db); } /******************* Initial word options ***********************/ /// Returns XDropoff double GetXDropoff() const { return m_Opts->GetXDropoff(); } /// Sets XDropoff /// @param x XDropoff [in] void SetXDropoff(double x) { m_Opts->SetXDropoff(x); } /******************* Gapped extension options *******************/ /// Returns GapExtnAlgorithm EBlastPrelimGapExt GetGapExtnAlgorithm() const { return m_Opts->GetGapExtnAlgorithm(); } /// Sets GapExtnAlgorithm /// @param algo GapExtnAlgorithm [in] void SetGapExtnAlgorithm(EBlastPrelimGapExt algo) {m_Opts->SetGapExtnAlgorithm(algo);} /// Returns GapTracebackAlgorithm EBlastTbackExt GetGapTracebackAlgorithm() const { return m_Opts->GetGapTracebackAlgorithm(); } /// Sets GapTracebackAlgorithm /// @param algo GapTracebackAlgorithm [in] void SetGapTracebackAlgorithm(EBlastTbackExt algo) {m_Opts->SetGapTracebackAlgorithm(algo); } /************************ Scoring options ************************/ /// Returns MatchReward int GetMatchReward() const { return m_Opts->GetMatchReward(); } /// Sets MatchReward /// @param r MatchReward [in] void SetMatchReward(int r) { m_Opts->SetMatchReward(r); } /// Returns MismatchPenalty int GetMismatchPenalty() const { return m_Opts->GetMismatchPenalty(); } /// Sets MismatchPenalty /// @param p MismatchPenalty [in] void SetMismatchPenalty(int p) { m_Opts->SetMismatchPenalty(p); } /// Returns MatrixName const char* GetMatrixName() const { return m_Opts->GetMatrixName(); } /// Sets MatrixName /// @param matrix MatrixName [in] void SetMatrixName(const char* matrix) { m_Opts->SetMatrixName(matrix); } /// Returns GapOpeningCost int GetGapOpeningCost() const { return m_Opts->GetGapOpeningCost(); } /// Sets GapOpeningCost /// @param g GapOpeningCost [in] void SetGapOpeningCost(int g) { m_Opts->SetGapOpeningCost(g); } /// Returns GapExtensionCost int GetGapExtensionCost() const { return m_Opts->GetGapExtensionCost(); } /// Sets GapExtensionCost /// @param e GapExtensionCost [in] void SetGapExtensionCost(int e) { m_Opts->SetGapExtensionCost(e); } /// Sets TraditionalBlastnDefaults void SetTraditionalBlastnDefaults(); /// Sets TraditionalMegablastDefaults void SetTraditionalMegablastDefaults(); /// Sets default options for VecScreen void SetVecScreenDefaults(); protected: /// Set the program and service name for remote blast. virtual void SetRemoteProgramAndService_Blast3() { m_Opts->SetRemoteProgramAndService_Blast3("blastn", "megablast"); } /// Overrides LookupTableDefaults for nucleotide options virtual void SetLookupTableDefaults(); /// Overrides MBLookupTableDefaults for nucleotide options virtual void SetMBLookupTableDefaults(); /// Overrides QueryOptionDefaults for nucleotide options virtual void SetQueryOptionDefaults(); /// Overrides InitialWordOptionsDefaults for nucleotide options virtual void SetInitialWordOptionsDefaults(); /// Overrides MBInitialWordOptionsDefaults for nucleotide options virtual void SetMBInitialWordOptionsDefaults(); /// Overrides GappedExtensionDefaults for nucleotide options virtual void SetGappedExtensionDefaults(); /// Overrides MBGappedExtensionDefaults for nucleotide options virtual void SetMBGappedExtensionDefaults(); /// Overrides ScoringOptionsDefaults for nucleotide options virtual void SetScoringOptionsDefaults(); /// Overrides MBScoringOptionsDefaults for nucleotide options virtual void SetMBScoringOptionsDefaults(); /// Overrides HitSavingOptionsDefaults for nucleotide options virtual void SetHitSavingOptionsDefaults(); /// Overrides MBHitSavingOptionsDefaults for nucleotide options virtual void SetMBHitSavingOptionsDefaults(); /// Overrides EffectiveLengthsOptionsDefaults for nucleotide options virtual void SetEffectiveLengthsOptionsDefaults(); /// Overrides SubjectSequenceOptionsDefaults for nucleotide options virtual void SetSubjectSequenceOptionsDefaults(); private: /// Disallow copy constructor CBlastNucleotideOptionsHandle(const CBlastNucleotideOptionsHandle& rhs); /// Disallow assignment operator CBlastNucleotideOptionsHandle& operator=(const CBlastNucleotideOptionsHandle& rhs); }; END_SCOPE(blast) END_NCBI_SCOPE /* @} */ #endif /* ALGO_BLAST_API___BLAST_NUCL_OPTIONS__HPP */

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