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

Packages that use SpeciesConfiguration

Package	Description
org.opencb.cellbase.core.api
org.opencb.cellbase.core.config
org.opencb.cellbase.lib
org.opencb.cellbase.lib.builders
org.opencb.cellbase.lib.download

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

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

Modifier and Type	Method and Description
protected SpeciesConfiguration	DBAdaptorFactory.getSpecies(String speciesName)

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

Modifier and Type	Method and Description
protected String	DBAdaptorFactory.getAssembly(SpeciesConfiguration speciesConfiguration, String assemblyName)

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

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

Modifier and Type	Method and Description
SpeciesConfiguration	CellBaseConfiguration.getSpeciesConfig(String id) get the config for this species.
SpeciesConfiguration	SpeciesConfiguration.setShards(List<SpeciesConfiguration.ShardConfig> shards)

Methods in org.opencb.cellbase.core.config that return types with arguments of type SpeciesConfiguration

Modifier and Type	Method and Description
List<SpeciesConfiguration>	CellBaseConfiguration.getAllSpecies()
List<SpeciesConfiguration>	SpeciesProperties.getBacteria()
List<SpeciesConfiguration>	SpeciesProperties.getFungi()
List<SpeciesConfiguration>	SpeciesProperties.getMetazoa()
List<SpeciesConfiguration>	SpeciesProperties.getPlants()
List<SpeciesConfiguration>	SpeciesProperties.getProtist()
List<SpeciesConfiguration>	SpeciesProperties.getVertebrates()
List<SpeciesConfiguration>	SpeciesProperties.getVirus()

Method parameters in org.opencb.cellbase.core.config with type arguments of type SpeciesConfiguration

Modifier and Type	Method and Description
void	SpeciesProperties.setBacteria(List<SpeciesConfiguration> bacteria)
void	SpeciesProperties.setFungi(List<SpeciesConfiguration> fungi)
void	SpeciesProperties.setMetazoa(List<SpeciesConfiguration> metazoa)
void	SpeciesProperties.setPlants(List<SpeciesConfiguration> plants)
void	SpeciesProperties.setProtist(List<SpeciesConfiguration> protist)
void	SpeciesProperties.setVertebrates(List<SpeciesConfiguration> vertebrates)
void	SpeciesProperties.setVirus(List<SpeciesConfiguration> virus)

Constructor parameters in org.opencb.cellbase.core.config with type arguments of type SpeciesConfiguration

Constructor and Description
SpeciesProperties(List<SpeciesConfiguration> vertebrates, List<SpeciesConfiguration> metazoa, List<SpeciesConfiguration> fungi, List<SpeciesConfiguration> protist, List<SpeciesConfiguration> plants, List<SpeciesConfiguration> virus, List<SpeciesConfiguration> bacteria)
SpeciesProperties(List<SpeciesConfiguration> vertebrates, List<SpeciesConfiguration> metazoa, List<SpeciesConfiguration> fungi, List<SpeciesConfiguration> protist, List<SpeciesConfiguration> plants, List<SpeciesConfiguration> virus, List<SpeciesConfiguration> bacteria)
SpeciesProperties(List<SpeciesConfiguration> vertebrates, List<SpeciesConfiguration> metazoa, List<SpeciesConfiguration> fungi, List<SpeciesConfiguration> protist, List<SpeciesConfiguration> plants, List<SpeciesConfiguration> virus, List<SpeciesConfiguration> bacteria)
SpeciesProperties(List<SpeciesConfiguration> vertebrates, List<SpeciesConfiguration> metazoa, List<SpeciesConfiguration> fungi, List<SpeciesConfiguration> protist, List<SpeciesConfiguration> plants, List<SpeciesConfiguration> virus, List<SpeciesConfiguration> bacteria)
SpeciesProperties(List<SpeciesConfiguration> vertebrates, List<SpeciesConfiguration> metazoa, List<SpeciesConfiguration> fungi, List<SpeciesConfiguration> protist, List<SpeciesConfiguration> plants, List<SpeciesConfiguration> virus, List<SpeciesConfiguration> bacteria)
SpeciesProperties(List<SpeciesConfiguration> vertebrates, List<SpeciesConfiguration> metazoa, List<SpeciesConfiguration> fungi, List<SpeciesConfiguration> protist, List<SpeciesConfiguration> plants, List<SpeciesConfiguration> virus, List<SpeciesConfiguration> bacteria)
SpeciesProperties(List<SpeciesConfiguration> vertebrates, List<SpeciesConfiguration> metazoa, List<SpeciesConfiguration> fungi, List<SpeciesConfiguration> protist, List<SpeciesConfiguration> plants, List<SpeciesConfiguration> virus, List<SpeciesConfiguration> bacteria)

Uses of SpeciesConfiguration in org.opencb.cellbase.lib

Methods in org.opencb.cellbase.lib that return SpeciesConfiguration

Modifier and Type	Method and Description
static SpeciesConfiguration	SpeciesUtils.getSpeciesConfiguration(CellBaseConfiguration configuration, String species) Get configuration for the specified species.

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

Modifier and Type	Method and Description
static SpeciesConfiguration.Assembly	SpeciesUtils.getAssembly(SpeciesConfiguration speciesConfiguration, String assemblyString) Check given assembly is valid, case insensitve.
static SpeciesConfiguration.Assembly	SpeciesUtils.getDefaultAssembly(SpeciesConfiguration speciesConfiguration) Get the default assembly for species.
static String	SpeciesUtils.getSpeciesShortname(SpeciesConfiguration speciesConfiguration) Formats the species name, e.g.

Uses of SpeciesConfiguration in org.opencb.cellbase.lib.builders

Constructors in org.opencb.cellbase.lib.builders with parameters of type SpeciesConfiguration

Constructor and Description
GeneParser(Path gtfFile, Path geneDescriptionFile, Path xrefsFile, Path uniprotIdMappingFile, Path tfbsFile, Path geneExpressionFile, Path geneDrugFile, Path hpoFile, Path disgenetFile, Path gnomadFile, Path genomeSequenceFilePath, SpeciesConfiguration speciesConfiguration, boolean flexibleGTFParsing, CellBaseSerializer serializer)
GeneParser(Path geneDirectoryPath, Path genomeSequenceFastaFile, SpeciesConfiguration speciesConfiguration, boolean flexibleGTFParsing, CellBaseSerializer serializer)
GeneParser(Path geneDirectoryPath, Path genomeSequenceFastaFile, SpeciesConfiguration speciesConfiguration, CellBaseSerializer serializer)

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

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

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