Uses of Class
org.opencb.cellbase.core.config.CellBaseConfiguration

Packages that use CellBaseConfiguration

Package	Description
org.opencb.cellbase.app.cli
org.opencb.cellbase.core.api
org.opencb.cellbase.core.config
org.opencb.cellbase.core.loader
org.opencb.cellbase.lib
org.opencb.cellbase.lib.download
org.opencb.cellbase.lib.impl
org.opencb.cellbase.lib.indexer
org.opencb.cellbase.lib.install
org.opencb.cellbase.lib.loader
org.opencb.cellbase.server.rest

Uses of CellBaseConfiguration in org.opencb.cellbase.app.cli

Fields in org.opencb.cellbase.app.cli declared as CellBaseConfiguration

Modifier and Type	Field and Description
protected CellBaseConfiguration	CommandExecutor.configuration

Uses of CellBaseConfiguration in org.opencb.cellbase.core.api

Fields in org.opencb.cellbase.core.api declared as CellBaseConfiguration

Modifier and Type	Field and Description
protected CellBaseConfiguration	DBAdaptorFactory.cellBaseConfiguration

Methods in org.opencb.cellbase.core.api that return CellBaseConfiguration

Modifier and Type	Method and Description
CellBaseConfiguration	DBAdaptorFactory.getCellBaseConfiguration()

Methods in org.opencb.cellbase.core.api with parameters of type CellBaseConfiguration

Modifier and Type	Method and Description
void	DBAdaptorFactory.setConfiguration(CellBaseConfiguration cellBaseConfiguration)

Constructors in org.opencb.cellbase.core.api with parameters of type CellBaseConfiguration

Constructor and Description
DBAdaptorFactory(CellBaseConfiguration cellBaseConfiguration)

Uses of CellBaseConfiguration in org.opencb.cellbase.core.config

Methods in org.opencb.cellbase.core.config that return CellBaseConfiguration

Modifier and Type	Method and Description
static CellBaseConfiguration	CellBaseConfiguration.load(InputStream configurationInputStream)
static CellBaseConfiguration	CellBaseConfiguration.load(InputStream configurationInputStream, CellBaseConfiguration.ConfigurationFileFormat format)
static CellBaseConfiguration	CellBaseConfiguration.load(Path configurationPath)
CellBaseConfiguration	CellBaseConfiguration.setDatabases(Databases databases)

Methods in org.opencb.cellbase.core.config with parameters of type CellBaseConfiguration

Modifier and Type	Method and Description
protected static void	CellBaseConfiguration.overwriteEnvVariables(CellBaseConfiguration configuration)
protected static void	CellBaseConfiguration.overwriteEnvVariables(CellBaseConfiguration configuration, Map<String,String> envVariables)

Uses of CellBaseConfiguration in org.opencb.cellbase.core.loader

Fields in org.opencb.cellbase.core.loader declared as CellBaseConfiguration

Modifier and Type	Field and Description
protected CellBaseConfiguration	CellBaseLoader.cellBaseConfiguration

Constructors in org.opencb.cellbase.core.loader with parameters of type CellBaseConfiguration

Constructor and Description
CellBaseLoader(BlockingQueue<List<String>> blockingQueue, String data, String database, String field, String[] innerFields, CellBaseConfiguration configuration)
LoadRunner(String loader, String database, int numThreads, CellBaseConfiguration cellBaseConfiguration)

Uses of CellBaseConfiguration in org.opencb.cellbase.lib

Methods in org.opencb.cellbase.lib with parameters of type CellBaseConfiguration

Modifier and Type	Method and Description
static Species	SpeciesUtils.getSpecies(CellBaseConfiguration configuration, String userProvidedSpecies, String userProvidedAssembly) Return species object based on species name and assembly.
static SpeciesConfiguration	SpeciesUtils.getSpeciesConfiguration(CellBaseConfiguration configuration, String species) Get configuration for the specified species.

Uses of CellBaseConfiguration in org.opencb.cellbase.lib.download

Constructors in org.opencb.cellbase.lib.download with parameters of type CellBaseConfiguration

Constructor and Description
DownloadManager(CellBaseConfiguration configuration, Path targetDirectory, SpeciesConfiguration speciesConfiguration, SpeciesConfiguration.Assembly assembly)

Uses of CellBaseConfiguration in org.opencb.cellbase.lib.impl

Constructors in org.opencb.cellbase.lib.impl with parameters of type CellBaseConfiguration

Constructor and Description
MongoDBAdaptorFactory(CellBaseConfiguration cellBaseConfiguration)

Uses of CellBaseConfiguration in org.opencb.cellbase.lib.indexer

Constructors in org.opencb.cellbase.lib.indexer with parameters of type CellBaseConfiguration

Constructor and Description
IndexManager(CellBaseConfiguration configuration)

Uses of CellBaseConfiguration in org.opencb.cellbase.lib.install

Methods in org.opencb.cellbase.lib.install with parameters of type CellBaseConfiguration

Modifier and Type	Method and Description
static void	MongoDBShardUtils.shard(org.opencb.commons.datastore.mongodb.MongoDataStore mongoDataStore, CellBaseConfiguration cellBaseConfiguration, Species species) Add shards.

Constructors in org.opencb.cellbase.lib.install with parameters of type CellBaseConfiguration

Constructor and Description
InstallManager(CellBaseConfiguration configuration)

Uses of CellBaseConfiguration in org.opencb.cellbase.lib.loader

Constructors in org.opencb.cellbase.lib.loader with parameters of type CellBaseConfiguration

Constructor and Description
MongoDBCellBaseLoader(BlockingQueue<List<String>> queue, String data, String database, String field, String[] innerFields, CellBaseConfiguration cellBaseConfiguration) Deprecated.

Uses of CellBaseConfiguration in org.opencb.cellbase.server.rest

Fields in org.opencb.cellbase.server.rest declared as CellBaseConfiguration

Modifier and Type	Field and Description
protected CellBaseConfiguration	GenericRestWSServer.cellBaseConfiguration Loading properties file just one time to be more efficient.