Utility functions for BLAST VDB command line applications. More...
#include <ncbi_pch.hpp>#include "blast_vdb_app_util.hpp"#include <serial/serial.hpp>#include <serial/objostr.hpp>#include <algo/blast/vdb/vdb2blast_util.hpp>#include <algo/blast/vdb/vdbalias.hpp>
Include dependency graph for blast_vdb_app_util.cpp:
Go to the source code of this file.
Go to the SVN repository for this file.
Functions | |
| USING_SCOPE (objects) | |
| USING_SCOPE (blast) | |
| void | SortAndFetchSeqData (const blast::CSearchResultSet &results, CRef< CScope > scope, CScope::TBioseqHandles &handles) |
| static void | s_RegisterLocalDataLoader (list< string > &search_list, set< string > &local_paths, CRef< CObjectManager > &om, vector< string > &dl_local) |
| CRef< CScope > | GetVDBScope (string dbAllNames) |
Detailed Description
Utility functions for BLAST VDB command line applications.
Definition in file blast_vdb_app_util.cpp.
Function Documentation
◆ GetVDBScope()
Definition at line 106 of file blast_vdb_app_util.cpp.
References CScope::AddDataLoader(), set< Key, Compare >::begin(), CObjectManager::eDefault, CObjectManager::eNonDefault, NStr::fSplit_Tokenize, CObjectManager::GetInstance(), SRegisterLoaderInfo< TLoader >::GetLoader(), i, set< Key, Compare >::insert(), CVDBBlastUtil::IsSRA(), ITERATE, kEmptyStr, CObjectManager::kPriority_Loader, CObjectManager::kPriority_Local, CObjectManager::kPriority_Replace, local, names, NCBI_THROW, om, CCSRADataLoader::RegisterInObjectManager(), CWGSDataLoader::RegisterInObjectManager(), CGBDataLoader::RegisterInObjectManager(), s_RegisterLocalDataLoader(), and NStr::Split().
Referenced by CBlastFormatterVdbApp::PrintFormattedOutput(), CVDBBlastnApp::Run(), and CVDBTblastnApp::Run().
◆ s_RegisterLocalDataLoader()
|
static |
Definition at line 73 of file blast_vdb_app_util.cpp.
References set< Key, Compare >::begin(), CObjectManager::eDefault, set< Key, Compare >::end(), f, CVDBBlastUtil::IsSRA(), om, CCSRADataLoader::RegisterInObjectManager(), and CWGSDataLoader::RegisterInObjectManager().
Referenced by GetVDBScope().
◆ SortAndFetchSeqData()
| void SortAndFetchSeqData | ( | const blast::CSearchResultSet & | results, |
| CRef< CScope > | scope, | ||
| CScope::TBioseqHandles & | handles | ||
| ) |
Definition at line 50 of file blast_vdb_app_util.cpp.
References _ASSERT, CScope::GetBioseqHandles(), CSeq_id_Handle::GetHandle(), ITERATE, CRef< C, Locker >::NotEmpty(), result, and results.
Referenced by CVDBTblastnApp::Run().
◆ USING_SCOPE() [1/2]
| USING_SCOPE | ( | blast | ) |
◆ USING_SCOPE() [2/2]
| USING_SCOPE | ( | objects | ) |
