Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Model
v1.09

uk.ac.roslin.ensembl.model.database
Interface Registry


public interface Registry


Method Summary
 boolean addSessionAlias(String ensembl_genus_species_name, String alias)
           
 void addSpecies(String dbStyleName, Species species)
           
 String findMybatisSchemaForSchemaVersion(DatabaseType type, String schema_version)
           
 HashMap<CollectionSpecies,String> getAssemblies(CollectionDatabase database)
           
 String getAssembly(SingleSpeciesDatabase database)
           
 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()
           
 String getEnsemblNameForAlias(String alias)
           
 int getHighestDBVersion()
           
 int getHighestEnsemblSchemaVersion()
           
 String getMostRecentDBVersion()
           
 String getMostRecentEnsemblVersion()
           
 Collection<? extends Species> getSpecies()
           
 Species getSpeciesByAlias(String alias_or_name)
           
 Species getSpeciesByEnsemblName(String ensemblName)
           
 Database makeDatabase(String db_name)
           
 StringBuffer printRegistryReport()
           
 void setCoreDBBuildLevels(SingleSpeciesCoreDatabase 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)

getDatabase

Database getDatabase(String species_name_or_alias,
                     String db_version)

getDatabase

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

getDatabaseForFullName

Database getDatabaseForFullName(String fullname)

getDatabasesByType

TreeSet<? extends Database> getDatabasesByType(DatabaseType type)

getSpeciesByAlias

Species getSpeciesByAlias(String alias_or_name)

getSpeciesByEnsemblName

Species getSpeciesByEnsemblName(String ensemblName)

getSpecies

Collection<? extends Species> getSpecies()

getCollectionSpecies

Collection<? extends CollectionSpecies> getCollectionSpecies()

addSpecies

void addSpecies(String dbStyleName,
                Species species)

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()

getHighestDBVersion

int getHighestDBVersion()

getMostRecentDBVersion

String getMostRecentDBVersion()

getEnsemblNameForAlias

String getEnsemblNameForAlias(String alias)

addSessionAlias

boolean addSessionAlias(String ensembl_genus_species_name,
                        String alias)
                        throws Exception
Throws:
Exception

printRegistryReport

StringBuffer printRegistryReport()

getAssembly

String getAssembly(SingleSpeciesDatabase database)
                   throws DAOException
Throws:
DAOException

getAssemblies

HashMap<CollectionSpecies,String> getAssemblies(CollectionDatabase database)
                                                throws DAOException
Throws:
DAOException

setCoreDBBuildLevels

void setCoreDBBuildLevels(SingleSpeciesCoreDatabase database)
                          throws DAOException
Throws:
DAOException

Ensembl Model
v1.09

Ensembl Model v1.09
© Roslin Institute 2010. GNU General Public License, version3