1 /* $Id: blastx_options.cpp 368583 2012-07-10 12:20:47Z madden $ 2 * =========================================================================== 3 * 4 * PUBLIC DOMAIN NOTICE 5 * National Center for Biotechnology Information 6 * 7 * This software/database is a "United States Government Work" under the 8 * terms of the United States Copyright Act. It was written as part of 9 * the author's official duties as a United States Government employee and 10 * thus cannot be copyrighted. This software/database is freely available 11 * to the public for use. The National Library of Medicine and the U.S. 12 * Government have not placed any restriction on its use or reproduction. 13 * 14 * Although all reasonable efforts have been taken to ensure the accuracy 15 * and reliability of the software and data, the NLM and the U.S. 16 * Government do not and cannot warrant the performance or results that 17 * may be obtained by using this software or data. The NLM and the U.S. 18 * Government disclaim all warranties, express or implied, including 19 * warranties of performance, merchantability or fitness for any particular 20 * purpose. 21 * 22 * Please cite the author in any work or product based on this material. 23 * 24 * =========================================================================== 25 * 26 * Authors: Christiam Camacho 27 * 28 */ 29 30 /// @file blastx_options.cpp 31 /// Implements the CBlastxOptionsHandle class. 32 33 #include <ncbi_pch.hpp> 34 #include <algo/blast/api/blastx_options.hpp> 35 #include <objects/seqloc/Na_strand.hpp> 36 37 38 /** @addtogroup AlgoBlast 39 * 40 * @{ 41 */ 42 43 44 BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast)45BEGIN_SCOPE(blast) 46 47 CBlastxOptionsHandle::CBlastxOptionsHandle(EAPILocality locality) 48 : CBlastProteinOptionsHandle(locality) 49 { 50 SetDefaults(); 51 m_Opts->SetProgram(eBlastx); 52 } 53 54 void SetLookupTableDefaults()55CBlastxOptionsHandle::SetLookupTableDefaults() 56 { 57 CBlastProteinOptionsHandle::SetLookupTableDefaults(); 58 m_Opts->SetWordThreshold(BLAST_WORD_THRESHOLD_BLASTX); 59 } 60 61 void SetQueryOptionDefaults()62CBlastxOptionsHandle::SetQueryOptionDefaults() 63 { 64 CBlastProteinOptionsHandle::SetQueryOptionDefaults(); 65 m_Opts->SetStrandOption(objects::eNa_strand_both); 66 m_Opts->SetQueryGeneticCode(BLAST_GENETIC_CODE); 67 SetSegFiltering(false); // disable SEG filtering because of eCompositionMatrixAdjust mode 68 } 69 70 void SetGappedExtensionDefaults()71CBlastxOptionsHandle::SetGappedExtensionDefaults() 72 { 73 CBlastProteinOptionsHandle::SetGappedExtensionDefaults(); 74 m_Opts->SetCompositionBasedStats(eCompositionMatrixAdjust); 75 m_Opts->SetSmithWatermanMode(false); 76 _ASSERT(!m_Opts->GetSegFiltering()); 77 } 78 79 void SetScoringOptionsDefaults()80CBlastxOptionsHandle::SetScoringOptionsDefaults() 81 { 82 CBlastProteinOptionsHandle::SetScoringOptionsDefaults(); 83 } 84 85 void SetHitSavingOptionsDefaults()86CBlastxOptionsHandle::SetHitSavingOptionsDefaults() 87 { 88 CBlastProteinOptionsHandle::SetHitSavingOptionsDefaults(); 89 m_Opts->SetSumStatisticsMode(); 90 } 91 92 END_SCOPE(blast) 93 END_NCBI_SCOPE 94 95 96 /* @} */ 97