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NCBI C++ ToolKit: SDataLoaderConfig Struct Reference

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Configuration structure for the CBlastScopeSource. More...

#include <algo/blast/blastinput/blast_scope_src.hpp>

Configuration structure for the CBlastScopeSource.

Note
the choice of data loaders to use to configure the scope as well as the BLAST database(s) to search if the BLAST database data loader is used can be configured in the NCBI configuration file, BLAST section. For details, refer to the section 'Configuring BLAST' in the BLAST+ user manual

Definition at line 57 of file blast_scope_src.hpp.

◆ EConfigOpts

Configuration options for the BlastScopeSource.

Enumerator eUseBlastDbDataLoader 

Use the local BLAST database loader first, if this fails, use the remote BLAST database data loader.

eUseGenbankDataLoader 

Use the Genbank data loader.

eUseNoDataLoaders 

Do not add any data loaders.

eDefault 

Definition at line 65 of file blast_scope_src.hpp.

◆ SDataLoaderConfig() [1/2]

Constructor which relies on the configuration file to set the BLAST database to use.

Parameters
load_proteins is this object going to load/read proteins only [in] options configuration options [in]

Definition at line 81 of file blast_scope_src.hpp.

References kEmptyStr.

◆ SDataLoaderConfig() [2/2]

Constructor which allows the specification of a BLAST database to use to initialize the BLAST DB data loader, without the option to override this at runtime via the configuration file.

Parameters
dbname name of BLAST database [in] protein_data is this object going to load/read proteins only [in] options configuration options [in]

Definition at line 93 of file blast_scope_src.hpp.

References dbname().

◆ operator!=() ◆ operator==() ◆ OptimizeForWholeLargeSequenceRetrieval() void SDataLoaderConfig::OptimizeForWholeLargeSequenceRetrieval ( bool  value = true ) inline

Configures the BLAST database data loader to optimize the retrieval of *entire* large sequences.

Note
This option only has effect upon a BLAST database data loader's first initialization. If this setting should change on the same BLAST database, the data loader must be revoked from the object manager (this can be achieved with CBlastScopeSource::RevokeBlastDbDataLoader()).
Parameters
value TRUE to turn on, FALSE to turn off

Definition at line 106 of file blast_scope_src.hpp.

References rapidjson::value.

Referenced by BOOST_AUTO_TEST_CASE(), InitializeQueryDataLoaderConfiguration(), ReadSequencesToBlast(), CSeedTopApp::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CRMBlastnApp::Run(), CVecScreenApp::Run(), CVDBBlastnApp::Run(), CVDBTblastnApp::Run(), s_ImportQueries(), CBlastFormatterApp::x_ExtractQueries(), and CBlastFormatterVdbApp::x_ExtractQueries().

◆ UseDataLoaders() bool SDataLoaderConfig::UseDataLoaders ( ) const inline ◆ x_Init()

Initialization method.

Parameters
options configuration options [in] dbname name of BLAST database [in] load_proteins is this object going to load/read proteins only [in]
Note
the database can be overridden at runtime by the DATA_LOADERS entry in the BLAST section of the NCBI configuration file. Allowed values are blastdb, genbank, and none. If this is changed, please update the BLAST+ user manual

Definition at line 55 of file blast_scope_src.cpp.

References dbname(), CNcbiApplicationAPI::GetConfig(), CNcbiApplication::Instance(), and registry.

◆ x_LoadBlastDbDataLoaderConfig() ◆ x_LoadDataLoadersConfig() ◆ kDefaultNucleotideBlastDb const char * SDataLoaderConfig::kDefaultNucleotideBlastDb = "nt" static ◆ kDefaultProteinBlastDb const char * SDataLoaderConfig::kDefaultProteinBlastDb = "nr" static ◆ m_BlastDbName string SDataLoaderConfig::m_BlastDbName ◆ m_IsLoadingProteins bool SDataLoaderConfig::m_IsLoadingProteins ◆ m_UseBlastDbs bool SDataLoaderConfig::m_UseBlastDbs ◆ m_UseFixedSizeSlices bool SDataLoaderConfig::m_UseFixedSizeSlices ◆ m_UseGenbank bool SDataLoaderConfig::m_UseGenbank

The documentation for this struct was generated from the following files:

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