NCBI C++ Toolkit Cross Reference


/* $Id: blastx_args.cpp 72378 2016-05-04 14:59:01Z camacho $ * =========================================================================== * * 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. * * =========================================================================== * * Author: Christiam Camacho * */ /** @file blastx_args.cpp * Implementation of the BLASTX command line arguments */ #include <ncbi_pch.hpp> #include <algo/blast/blastinput/blastx_args.hpp> #include <algo/blast/api/blastx_options.hpp> #include <algo/blast/blastinput/blast_input_aux.hpp> #include <algo/blast/api/version.hpp> BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) USING_SCOPE(objects); CBlastxAppArgs::CBlastxAppArgs() { CRef<IBlastCmdLineArgs> arg; static const string kProgram("blastx"); arg.Reset(new CProgramDescriptionArgs(kProgram, "Translated Query-Protein Subject BLAST")); const bool kQueryIsProtein = false; m_Args.push_back(arg); m_ClientId = kProgram + " " + CBlastVersion().Print(); static const char kDefaultTask[] = "blastx"; SetTask(kDefaultTask); set<string> tasks; tasks.insert(kDefaultTask); tasks.insert("blastx-fast"); arg.Reset(new CTaskCmdLineArgs(tasks, kDefaultTask)); m_Args.push_back(arg); m_BlastDbArgs.Reset(new CBlastDatabaseArgs); m_BlastDbArgs->SetDatabaseMaskingSupport(true); arg.Reset(m_BlastDbArgs); m_Args.push_back(arg); m_StdCmdLineArgs.Reset(new CStdCmdLineArgs); arg.Reset(m_StdCmdLineArgs); m_Args.push_back(arg); // N.B.: query is not protein because the options are applied on the // translated query arg.Reset(new CGenericSearchArgs( !kQueryIsProtein )); m_Args.push_back(arg); //Disable until OOF is supported in align manager //SB-1043 //arg.Reset(new CFrameShiftArgs); //m_Args.push_back(arg); arg.Reset(new CLargestIntronSizeArgs); m_Args.push_back(arg); // N.B.: query is not protein because the filtering is applied on the // translated query arg.Reset(new CFilteringArgs( !kQueryIsProtein )); m_Args.push_back(arg); arg.Reset(new CMatrixNameArg); m_Args.push_back(arg); arg.Reset(new CWordThresholdArg); m_Args.push_back(arg); m_HspFilteringArgs.Reset(new CHspFilteringArgs); arg.Reset(m_HspFilteringArgs); m_Args.push_back(arg); arg.Reset(new CWindowSizeArg); m_Args.push_back(arg); arg.Reset(new CGappedArgs); m_Args.push_back(arg); m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein)); arg.Reset(m_QueryOptsArgs); m_Args.push_back(arg); arg.Reset(new CGeneticCodeArgs(CGeneticCodeArgs::eQuery)); m_Args.push_back(arg); m_FormattingArgs.Reset(new CFormattingArgs); arg.Reset(m_FormattingArgs); m_Args.push_back(arg); m_MTArgs.Reset(new CMTArgs); arg.Reset(m_MTArgs); m_Args.push_back(arg); m_RemoteArgs.Reset(new CRemoteArgs); arg.Reset(m_RemoteArgs); m_Args.push_back(arg); arg.Reset(new CCompositionBasedStatsArgs); m_Args.push_back(arg); m_DebugArgs.Reset(new CDebugArgs); arg.Reset(m_DebugArgs); m_Args.push_back(arg); } CRef<CBlastOptionsHandle> CBlastxAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs& args) { _ASSERT(args.Exist(kTask)); _ASSERT(args[kTask].HasValue()); return x_CreateOptionsHandleWithTask(locality, args[kTask].AsString()); } int CBlastxAppArgs::GetQueryBatchSize() const { bool is_remote = (m_RemoteArgs.NotEmpty() && m_RemoteArgs->ExecuteRemotely()); return blast::GetQueryBatchSize(eBlastx, m_IsUngapped, is_remote); } END_SCOPE(blast) END_NCBI_SCOPE

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