uk.ac.roslin.ensembl.model.database

Interface Registry

All Known Implementing Classes:

DBRegistry

public interface Registry

Method Summary

Methods

Modifier and Type	Method and Description
boolean	addSessionAlias(Species sp, String alias)
boolean	addSessionAlias(String ensembl_genus_species_name, String alias)
String	findMybatisSchemaForSchemaVersion(DatabaseType type, String schema_version)
Set<? extends CollectionSpecies>	getBacterialSpeciesForAliasBeginning(String alias)
Set<? extends CollectionSpecies>	getBacterialSpeciesForAliasContaining(String alias)
StringBuilder	getBriefRegistryReport()
CollectionOfSpecies	getCollection(String name, String dbVersion)
Collection<? extends CollectionOfSpecies>	getCollectionRegistriesByName(String name)
List<? extends CollectionOfSpecies>	getCollections()
Collection<? extends CollectionOfSpecies>	getCollectionsByDBVersion(String dbVersion)
Collection<? extends CollectionSpecies>	getCollectionSpecies()
ComparisonDatabase	getComparaDatabase(EnsemblComparaDivision comparaDivision, String db_version)
Properties	getConfigProperties()
Database	getDatabase(String species_name_or_alias)
Database	getDatabase(String species_name_or_alias, DatabaseType database_type, String db_version)
Database	getDatabase(String species_name_or_alias, String db_version)
Database	getDatabaseForFullName(String fullname)
TreeSet<? extends Database>	getDatabasesByType(DatabaseType type)
DBConnection.DataSource	getDatasourceType()
TranscriptionEngine	getDefaultTranscriptionEngine()
String	getEnsemblNameForAlias(String alias)
Set<String>	getEnsemblNamesForAliasBeginning(String alias)
Set<String>	getEnsemblNamesForAliasContaining(String alias)
Set<String>	getGCAssemblyAccessionsForAliasBeginning(String alias)
Set<String>	getGCAssemblyAccessionsForAliasContaining(String alias)
int	getHighestEnsemblSchemaVersion()
int	getHighestReleaseVersion()
CollectionOfSpecies	getMostRecentCollection(String name)
String	getMostRecentEnsemblVersion()
Species	getMostRecentSpeciesByAlias(String alias_or_name)
Set<? extends CollectionSpecies>	getOldStyleBacterialSpeciesForAliasBeginning(String alias)
Set<? extends CollectionSpecies>	getOldStyleBacterialSpeciesForAliasContaining(String alias)
File	getRegistryReport()
HashMap<String,String>	getRenamedDBs()
Collection<? extends Species>	getSetOfEverySpeciesByAlias(String alias_or_name)
Collection<? extends Species>	getSetOfSpeciesByAlias(String alias_or_name)
Collection<? extends Species>	getSpecies()
Species	getSpeciesByAlias(String alias_or_name)
Species	getSpeciesByAlias(String alias_or_name, String version)
Species	getSpeciesByEnsemblName(String ensemblName)
Set<? extends Species>	getSpeciesForAliasBeginning(String alias)
Set<? extends Species>	getSpeciesForAliasContaining(String alias)
TranscriptionEngine	getTranscriptionEngine(Integer codonTable)
StringBuilder	getVersionReport() Reports the available database versions for this Registry.
boolean	isSpeciesInPanHomology(Species querySpecies, String dbVersion)
Database	makeDatabase(String db_name)
void	setSpeciesMetadata(CoreDatabase database)

Method Detail

getConfigProperties

Properties getConfigProperties()

getDatasourceType

DBConnection.DataSource getDatasourceType()

findMybatisSchemaForSchemaVersion

String findMybatisSchemaForSchemaVersion(DatabaseType type,
                                       String schema_version)

getMostRecentEnsemblVersion

String getMostRecentEnsemblVersion()

makeDatabase

Database makeDatabase(String db_name)
                      throws ConfigurationException

Throws:

ConfigurationException

getComparaDatabase

ComparisonDatabase getComparaDatabase(EnsemblComparaDivision comparaDivision,
                                    String db_version)

getDatabase

Database getDatabase(String species_name_or_alias)
                     throws NonUniqueException

Throws:

NonUniqueException

getDatabase

Database getDatabase(String species_name_or_alias,
                   String db_version)
                     throws NonUniqueException

Throws:

NonUniqueException

getDatabase

Database getDatabase(String species_name_or_alias,
                   DatabaseType database_type,
                   String db_version)
                     throws NonUniqueException

Throws:

NonUniqueException

getDatabaseForFullName

Database getDatabaseForFullName(String fullname)

getDatabasesByType

TreeSet<? extends Database> getDatabasesByType(DatabaseType type)

getSpeciesByAlias

Species getSpeciesByAlias(String alias_or_name)
                          throws NonUniqueException

Throws:

NonUniqueException

getSpeciesByAlias

Species getSpeciesByAlias(String alias_or_name,
                        String version)
                          throws NonUniqueException

Throws:

NonUniqueException

getMostRecentSpeciesByAlias

Species getMostRecentSpeciesByAlias(String alias_or_name)
                                    throws NonUniqueException

Throws:

NonUniqueException

getSetOfSpeciesByAlias

Collection<? extends Species> getSetOfSpeciesByAlias(String alias_or_name)

getSetOfEverySpeciesByAlias

Collection<? extends Species> getSetOfEverySpeciesByAlias(String alias_or_name)

getSpeciesByEnsemblName

Species getSpeciesByEnsemblName(String ensemblName)

getSpecies

Collection<? extends Species> getSpecies()

getCollectionSpecies

Collection<? extends CollectionSpecies> getCollectionSpecies()

getMostRecentCollection

CollectionOfSpecies getMostRecentCollection(String name)

getCollection

CollectionOfSpecies getCollection(String name,
                                String dbVersion)

getCollectionRegistriesByName

Collection<? extends CollectionOfSpecies> getCollectionRegistriesByName(String name)

getCollectionsByDBVersion

Collection<? extends CollectionOfSpecies> getCollectionsByDBVersion(String dbVersion)

getCollections

List<? extends CollectionOfSpecies> getCollections()

getHighestEnsemblSchemaVersion

int getHighestEnsemblSchemaVersion()
                                   throws DAOException,
                                          ConfigurationException

Throws:

DAOException

ConfigurationException

getHighestReleaseVersion

int getHighestReleaseVersion()
                             throws DAOException,
                                    ConfigurationException

Throws:

DAOException

ConfigurationException

getEnsemblNameForAlias

String getEnsemblNameForAlias(String alias)
                              throws NonUniqueException

Throws:

NonUniqueException

addSessionAlias

boolean addSessionAlias(String ensembl_genus_species_name,
                      String alias)
                        throws Exception

Throws:

Exception

addSessionAlias

boolean addSessionAlias(Species sp,
                      String alias)
                        throws Exception

Throws:

Exception

getRegistryReport

File getRegistryReport()
                       throws IOException

Throws:

IOException

getBriefRegistryReport

StringBuilder getBriefRegistryReport()

getVersionReport

StringBuilder getVersionReport()

Reports the available database versions for this Registry. Reports for both initialized or uninitialized Registries. since v74

Returns:

StringBuilder

setSpeciesMetadata

void setSpeciesMetadata(CoreDatabase database)
                        throws DAOException

Throws:

DAOException

getDefaultTranscriptionEngine

TranscriptionEngine getDefaultTranscriptionEngine()

getTranscriptionEngine

TranscriptionEngine getTranscriptionEngine(Integer codonTable)

getRenamedDBs

HashMap<String,String> getRenamedDBs()

isSpeciesInPanHomology

boolean isSpeciesInPanHomology(Species querySpecies,
                             String dbVersion)

getEnsemblNamesForAliasBeginning

Set<String> getEnsemblNamesForAliasBeginning(String alias)

getEnsemblNamesForAliasContaining

Set<String> getEnsemblNamesForAliasContaining(String alias)

getGCAssemblyAccessionsForAliasBeginning

Set<String> getGCAssemblyAccessionsForAliasBeginning(String alias)

getGCAssemblyAccessionsForAliasContaining

Set<String> getGCAssemblyAccessionsForAliasContaining(String alias)

getSpeciesForAliasBeginning

Set<? extends Species> getSpeciesForAliasBeginning(String alias)

getSpeciesForAliasContaining

Set<? extends Species> getSpeciesForAliasContaining(String alias)

getBacterialSpeciesForAliasBeginning

Set<? extends CollectionSpecies> getBacterialSpeciesForAliasBeginning(String alias)

getBacterialSpeciesForAliasContaining

Set<? extends CollectionSpecies> getBacterialSpeciesForAliasContaining(String alias)

getOldStyleBacterialSpeciesForAliasBeginning

Set<? extends CollectionSpecies> getOldStyleBacterialSpeciesForAliasBeginning(String alias)

getOldStyleBacterialSpeciesForAliasContaining

Set<? extends CollectionSpecies> getOldStyleBacterialSpeciesForAliasContaining(String alias)