Search Toolkit Book for SDataLoaderConfig

Configuration structure for the CBlastScopeSource. More...

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

Public Types
enum	EConfigOpts { eUseBlastDbDataLoader = (0x1 << 0) , eUseGenbankDataLoader = (0x1 << 1) , eUseNoDataLoaders = (0x1 << 2) , eDefault = (eUseBlastDbDataLoader \| eUseGenbankDataLoader) }
	Configuration options for the BlastScopeSource. More...

Public Member Functions
	SDataLoaderConfig (bool load_proteins, EConfigOpts options=eDefault)
	Constructor which relies on the configuration file to set the BLAST database to use. More...

	SDataLoaderConfig (const string &dbname, bool protein_data, EConfigOpts options=eDefault)
	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. More...

void	OptimizeForWholeLargeSequenceRetrieval (bool value=true)
	Configures the BLAST database data loader to optimize the retrieval of entire large sequences. More...

bool	UseDataLoaders () const
	Determine whether either of the data loaders should be used. More...

bool	operator== (const SDataLoaderConfig &rhs) const
	Equality operator. More...

bool	operator!= (const SDataLoaderConfig &rhs) const
	Inequality operator. More...

Public Attributes
bool	m_UseBlastDbs
	Use the BLAST database data loaders. More...

string	m_BlastDbName
	Name of the BLAST database to use (non-empty if m_UseBlastDbs is true) More...

bool	m_IsLoadingProteins
	Is this intended to load protein sequences. More...

bool	m_UseGenbank
	Use the Genbank data loader. More...

bool	m_UseFixedSizeSlices
	Argument to configure BLAST database data loader. More...

Static Public Attributes
static const char *	kDefaultProteinBlastDb = "nr"
	Default protein BLAST database to use for the BLAST DB data loaders. More...

static const char *	kDefaultNucleotideBlastDb = "nt"
	Default nucleotide BLAST database to use for the BLAST DB data loaders. More...

Private Member Functions
void	x_Init (EConfigOpts options, const string &dbname, bool load_proteins)
	Initialization method. More...

void	x_LoadDataLoadersConfig (const CNcbiRegistry &registry)
	Load the DATA_LOADERS configuration value from the config file. More...

void	x_LoadBlastDbDataLoaderConfig (const CNcbiRegistry &registry)
	Load the BLAST database configured to search for the blastdb DATA_LOADERS option from the config file. More...

Detailed Description

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.

Member Enumeration Documentation

◆ EConfigOpts

enum SDataLoaderConfig::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.

Constructor & Destructor Documentation

◆ SDataLoaderConfig() [1/2]

SDataLoaderConfig::SDataLoaderConfig	(	bool	load_proteins,
		EConfigOpts	options = `eDefault`
	)

inline

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]

SDataLoaderConfig::SDataLoaderConfig	(	const string &	dbname,
		bool	protein_data,
		EConfigOpts	options = `eDefault`
	)

inline

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().

Member Function Documentation

◆ operator!=()

bool SDataLoaderConfig::operator!= ( const SDataLoaderConfig & rhs ) const

Inequality operator.

Definition at line 354 of file blast_scope_src.cpp.

◆ operator==()

bool SDataLoaderConfig::operator== ( const SDataLoaderConfig & rhs ) const

Equality operator.

Definition at line 333 of file blast_scope_src.cpp.

References m_BlastDbName, m_IsLoadingProteins, m_UseBlastDbs, and m_UseGenbank.

◆ 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

Determine whether either of the data loaders should be used.

Definition at line 111 of file blast_scope_src.hpp.

Referenced by CBlastFastaInputSource::x_InitInputReader().

◆ x_Init()

void SDataLoaderConfig::x_Init	(	SDataLoaderConfig::EConfigOpts	options,
		const string &	dbname,
		bool	load_proteins
	)

private

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()

void SDataLoaderConfig::x_LoadBlastDbDataLoaderConfig ( const CNcbiRegistry & registry )

private

Load the BLAST database configured to search for the blastdb DATA_LOADERS option from the config file.

Definition at line 98 of file blast_scope_src.cpp.

References _ASSERT, IRegistry::Get(), IRegistry::HasEntry(), kDefaultNucleotideBlastDb, kDefaultProteinBlastDb, m_BlastDbName, m_IsLoadingProteins, m_UseBlastDbs, and registry.

◆ x_LoadDataLoadersConfig()

void SDataLoaderConfig::x_LoadDataLoadersConfig ( const CNcbiRegistry & registry )

private

Load the DATA_LOADERS configuration value from the config file.

Definition at line 76 of file blast_scope_src.cpp.

References _TRACE, NStr::FindNoCase(), IRegistry::Get(), IRegistry::HasEntry(), m_UseBlastDbs, m_UseGenbank, NPOS, and registry.

Member Data Documentation

◆ kDefaultNucleotideBlastDb

const char * SDataLoaderConfig::kDefaultNucleotideBlastDb = "nt"

static

Default nucleotide BLAST database to use for the BLAST DB data loaders.

Definition at line 62 of file blast_scope_src.hpp.

Referenced by x_LoadBlastDbDataLoaderConfig().

◆ kDefaultProteinBlastDb

const char * SDataLoaderConfig::kDefaultProteinBlastDb = "nr"

static

Default protein BLAST database to use for the BLAST DB data loaders.

Definition at line 60 of file blast_scope_src.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), and x_LoadBlastDbDataLoaderConfig().

◆ m_BlastDbName

string SDataLoaderConfig::m_BlastDbName

Name of the BLAST database to use (non-empty if m_UseBlastDbs is true)

Definition at line 116 of file blast_scope_src.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CBlastScopeSource::CBlastScopeSource(), InitializeQueryDataLoaderConfiguration(), operator==(), s_RetrieveSequenceLength(), and x_LoadBlastDbDataLoaderConfig().

◆ m_IsLoadingProteins

bool SDataLoaderConfig::m_IsLoadingProteins

Is this intended to load protein sequences.

Definition at line 119 of file blast_scope_src.hpp.

Referenced by CBlastScopeSource::CBlastScopeSource(), operator==(), and x_LoadBlastDbDataLoaderConfig().

◆ m_UseBlastDbs

bool SDataLoaderConfig::m_UseBlastDbs

Use the BLAST database data loaders.

Definition at line 114 of file blast_scope_src.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), InitializeQueryDataLoaderConfiguration(), operator==(), s_RetrieveSequenceLength(), CBlastScopeSource::x_InitBlastDatabaseDataLoader(), x_LoadBlastDbDataLoaderConfig(), and x_LoadDataLoadersConfig().

◆ m_UseFixedSizeSlices

bool SDataLoaderConfig::m_UseFixedSizeSlices

Argument to configure BLAST database data loader.

Definition at line 130 of file blast_scope_src.hpp.

Referenced by CBlastScopeSource::x_InitBlastDatabaseDataLoader().

◆ m_UseGenbank

bool SDataLoaderConfig::m_UseGenbank

Use the Genbank data loader.

Definition at line 122 of file blast_scope_src.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), InitializeQueryDataLoaderConfiguration(), operator==(), s_RetrieveSequenceLength(), CBlastScopeSource::x_InitGenbankDataLoader(), and x_LoadDataLoadersConfig().

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

include/algo/blast/blastinput/blast_scope_src.hpp
src/algo/blast/blastinput/blast_scope_src.cpp

Public Types

Public Member Functions

Public Attributes

Static Public Attributes

Private Member Functions

Detailed Description

Member Enumeration Documentation

◆ EConfigOpts

Constructor & Destructor Documentation

◆ SDataLoaderConfig() [1/2]

◆ SDataLoaderConfig() [2/2]

Member Function Documentation

◆ operator!=()

◆ operator==()

◆ OptimizeForWholeLargeSequenceRetrieval()

◆ UseDataLoaders()

◆ x_Init()

◆ x_LoadBlastDbDataLoaderConfig()

◆ x_LoadDataLoadersConfig()

Member Data Documentation

◆ kDefaultNucleotideBlastDb

◆ kDefaultProteinBlastDb

◆ m_BlastDbName

◆ m_IsLoadingProteins

◆ m_UseBlastDbs

◆ m_UseFixedSizeSlices

◆ m_UseGenbank