NCBI C++ Toolkit Cross Reference

  C++/src/algo/blast/blastinput/rmblastn_args.cpp


/* $Id: rmblastn_args.cpp 62310 2014-04-01 15:13:51Z camacho $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * * =========================================================================== * * Author: Robert M. Hubley * Shameless based on the work of Christiam Camacho in * rmblastn_args.cpp * */ /** @file rmblastn_args.cpp * Implementation of the RMBLASTN command line arguments */ #ifndef SKIP_DOXYGEN_PROCESSING static char const rcsid[] = "$Id: rmblastn_args.cpp 62310 2014-04-01 15:13:51Z camacho $"; #endif #include <ncbi_pch.hpp> #include <algo/blast/blastinput/rmblastn_args.hpp> #include <algo/blast/api/disc_nucl_options.hpp> #include <algo/blast/api/blast_exception.hpp> #include <algo/blast/blastinput/blast_input_aux.hpp> BEGIN_NCBI_SCOPE BEGIN_SCOPE(blast) USING_SCOPE(objects); CRMBlastnAppArgs::CRMBlastnAppArgs() { CRef<IBlastCmdLineArgs> arg; // Something appears to be overriding this arg.Reset(new CProgramDescriptionArgs("rmblastn", "Nucleotide-Nucleotide BLAST with RepeatMasker Extensions")); const bool kQueryIsProtein = false; m_Args.push_back(arg); // Don't want the greedy megablast...no howdy doody static const string kDefaultTask = "rmblastn"; SetTask(kDefaultTask); set<string> tasks (CBlastOptionsFactory::GetTasks(CBlastOptionsFactory::eNuclNucl)); arg.Reset(new CTaskCmdLineArgs(tasks, kDefaultTask)); m_Args.push_back(arg); m_BlastDbArgs.Reset(new CBlastDatabaseArgs); arg.Reset(m_BlastDbArgs); m_Args.push_back(arg); m_StdCmdLineArgs.Reset(new CStdCmdLineArgs); arg.Reset(m_StdCmdLineArgs); m_Args.push_back(arg); arg.Reset(new CGenericSearchArgs(kQueryIsProtein, false, true)); m_Args.push_back(arg); arg.Reset(new CNuclArgs); m_Args.push_back(arg); arg.Reset(new CDiscontiguousMegablastArgs); m_Args.push_back(arg); arg.Reset(new CFilteringArgs(kQueryIsProtein)); m_Args.push_back(arg); // RMH: Wasn't previously an option in blastn arg.Reset(new CRMBlastNArg ); m_Args.push_back(arg); arg.Reset(new CGappedArgs); 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 CMbIndexArgs); m_Args.push_back(arg); m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein)); arg.Reset(m_QueryOptsArgs); 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); m_DebugArgs.Reset(new CDebugArgs); arg.Reset(m_DebugArgs); m_Args.push_back(arg); } CRef<CBlastOptionsHandle> CRMBlastnAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs& args) { CRef<CBlastOptionsHandle> retval = x_CreateOptionsHandleWithTask(locality, args[kTask].AsString()); return retval; } int CRMBlastnAppArgs::GetQueryBatchSize() const { return blast::GetQueryBatchSize(ProgramNameToEnum(GetTask())); } END_SCOPE(blast) END_NCBI_SCOPE

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