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Ensembl Data Access Module v1.09 |
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java.lang.Objectuk.ac.roslin.ensembl.dao.database.DBRegistry
public class DBRegistry
Constructor Summary | |
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DBRegistry()
Parameterless public constructor for DBRegistry object |
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DBRegistry(uk.ac.roslin.ensembl.config.DBConnection.DataSource type)
Public Constructor for default value DBRegistry object, using values in ensembl-config artifact. |
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DBRegistry(uk.ac.roslin.ensembl.config.RegistryConfiguration conf,
boolean initialize)
Public Constructor for default value DBRegistry object, using values in ensembl-config artifact. |
Method Summary | |
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boolean |
addSessionAlias(String ensembl_genus_species_name,
String alias)
Method for an adhoc alias to be added by the user in this session. |
void |
addSpecies(String dbStyleName,
uk.ac.roslin.ensembl.model.core.Species species)
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String |
findMybatisSchemaForSchemaVersion(uk.ac.roslin.ensembl.model.database.DatabaseType type,
String schema_version)
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HashMap<uk.ac.roslin.ensembl.model.core.CollectionSpecies,String> |
getAssemblies(uk.ac.roslin.ensembl.model.database.CollectionDatabase database)
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String |
getAssembly(uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase database)
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String |
getBriefRegistryReport()
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DBCollection |
getCollection(String name,
String dbVersion)
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Collection<DBCollection> |
getCollectionRegistriesByName(String name)
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List<DBCollection> |
getCollections()
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Collection<DBCollection> |
getCollectionsByDBVersion(String dbVersion)
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Collection<DBCollectionSpecies> |
getCollectionSpecies()
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uk.ac.roslin.ensembl.model.database.ComparisonDatabase |
getComparaDatabase(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision,
String db_version)
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Properties |
getConfigProperties()
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DBDatabase |
getDatabase(String species_name_or_alias)
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DBDatabase |
getDatabase(String speciesNameOrAlias_collectionName_comparaDivision,
uk.ac.roslin.ensembl.model.database.DatabaseType database_type,
String db_version)
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DBDatabase |
getDatabase(String species_name_or_alias,
String db_version)
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DBDatabase |
getDatabaseForFullName(String fullname)
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TreeSet<DBDatabase> |
getDatabasesByType(uk.ac.roslin.ensembl.model.database.DatabaseType type)
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uk.ac.roslin.ensembl.config.DBConnection.DataSource |
getDatasourceType()
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String |
getEnsemblNameForAlias(String alias)
Looks up the ensembl_genus_species_name for the given alias from the ensemblNameForAliasHash hash of aliases in this Registry. |
int |
getHighestDBVersion()
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int |
getHighestEnsemblSchemaVersion()
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TreeSet<Integer> |
getKnownSchemaVersions()
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String |
getMostRecentDBVersion()
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String |
getMostRecentEnsemblVersion()
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Collection<DBSpecies> |
getSpecies()
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DBSpecies |
getSpeciesByAlias(String alias_or_name)
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DBSpecies |
getSpeciesByEnsemblName(String ensemblName)
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void |
initialize()
private initialisation method for the registry which connects to ensembl via a DBDatasourceDAO and retreives details on all the current tables and creates database objects of the appropriate type for each. |
DBDatabase |
makeDatabase(String db_name)
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StringBuffer |
printRegistryReport()
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void |
setConfiguration(uk.ac.roslin.ensembl.config.DBConnection.DataSource type)
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void |
setConfiguration(uk.ac.roslin.ensembl.config.RegistryConfiguration conf)
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void |
setCoreDBBuildLevels(uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase database)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected org.apache.ibatis.session.SqlSessionFactory sqlMapper
protected Properties configProperties
protected uk.ac.roslin.ensembl.config.SchemaVersion schemaVersion
protected uk.ac.roslin.ensembl.config.DBConnection dbConnection
protected TreeSet<Integer> knownSchemaVersions
protected Reader reader
protected TreeMap<String,DBSpecies> speciesHash
protected TreeMap<String,DBCollectionSpecies> collectionspeciesHash
protected List<DBCollection> collections
protected TreeMap<String,TreeMap<String,DBCollection>> collectionNameDBVersionHash
protected TreeMap<String,String> ensemblNameForAliasHash
protected TreeSet<DBDatabase> allDatabases
protected TreeSet<DBSingleSpeciesDatabase> singleSpeciesDatabases
protected TreeSet<DBComparisonDatabase> comparisonDatabases
protected HashMap<uk.ac.roslin.ensembl.config.EnsemblComparaDivision,HashMap<String,DBComparisonDatabase>> comparaDBByDivision
protected TreeSet<DBCollectionDatabase> collectionDatabases
protected String newline
protected StringBuffer tooNewDB
protected StringBuffer unknownDB
protected uk.ac.roslin.ensembl.config.RegistryConfiguration regConfig
protected boolean alreadyInitialized
Constructor Detail |
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public DBRegistry()
public DBRegistry(uk.ac.roslin.ensembl.config.DBConnection.DataSource type) throws uk.ac.roslin.ensembl.exception.ConfigurationException, uk.ac.roslin.ensembl.exception.DAOException
type
- DBConnection.DataSource
uk.ac.roslin.ensembl.exception.ConfigurationException
uk.ac.roslin.ensembl.exception.DAOException
public DBRegistry(uk.ac.roslin.ensembl.config.RegistryConfiguration conf, boolean initialize) throws uk.ac.roslin.ensembl.exception.ConfigurationException, uk.ac.roslin.ensembl.exception.DAOException
type
- DBConnection.DataSourceinitialize
- boolean
uk.ac.roslin.ensembl.exception.ConfigurationException
uk.ac.roslin.ensembl.exception.DAOException
Method Detail |
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public void setConfiguration(uk.ac.roslin.ensembl.config.RegistryConfiguration conf) throws uk.ac.roslin.ensembl.exception.ConfigurationException, uk.ac.roslin.ensembl.exception.DAOException
uk.ac.roslin.ensembl.exception.ConfigurationException
uk.ac.roslin.ensembl.exception.DAOException
public void setConfiguration(uk.ac.roslin.ensembl.config.DBConnection.DataSource type) throws uk.ac.roslin.ensembl.exception.ConfigurationException, uk.ac.roslin.ensembl.exception.DAOException
uk.ac.roslin.ensembl.exception.ConfigurationException
uk.ac.roslin.ensembl.exception.DAOException
public void initialize() throws uk.ac.roslin.ensembl.exception.DAOException, uk.ac.roslin.ensembl.exception.ConfigurationException
DAOException,
- ConfigurationException
uk.ac.roslin.ensembl.exception.DAOException
uk.ac.roslin.ensembl.exception.ConfigurationException
public DBDatabase getDatabase(String species_name_or_alias)
getDatabase
in interface uk.ac.roslin.ensembl.model.database.Registry
public DBDatabase getDatabase(String species_name_or_alias, String db_version)
getDatabase
in interface uk.ac.roslin.ensembl.model.database.Registry
public DBDatabase getDatabase(String speciesNameOrAlias_collectionName_comparaDivision, uk.ac.roslin.ensembl.model.database.DatabaseType database_type, String db_version)
getDatabase
in interface uk.ac.roslin.ensembl.model.database.Registry
public uk.ac.roslin.ensembl.model.database.ComparisonDatabase getComparaDatabase(uk.ac.roslin.ensembl.config.EnsemblComparaDivision comparaDivision, String db_version)
getComparaDatabase
in interface uk.ac.roslin.ensembl.model.database.Registry
public DBDatabase getDatabaseForFullName(String fullname)
getDatabaseForFullName
in interface uk.ac.roslin.ensembl.model.database.Registry
public TreeSet<DBDatabase> getDatabasesByType(uk.ac.roslin.ensembl.model.database.DatabaseType type)
getDatabasesByType
in interface uk.ac.roslin.ensembl.model.database.Registry
public String findMybatisSchemaForSchemaVersion(uk.ac.roslin.ensembl.model.database.DatabaseType type, String schema_version)
findMybatisSchemaForSchemaVersion
in interface uk.ac.roslin.ensembl.model.database.Registry
public String getEnsemblNameForAlias(String alias)
getEnsemblNameForAlias
in interface uk.ac.roslin.ensembl.model.database.Registry
alias
- String
public boolean addSessionAlias(String ensembl_genus_species_name, String alias) throws Exception
addSessionAlias
in interface uk.ac.roslin.ensembl.model.database.Registry
ensembl_genus_species_name
- Ensmebl databse dbVersion of the name, e.g. 'homo_sapiens'alias
- any string the user wants to use an alias for this
Exception
- if update fails, with meaning full messagepublic Properties getConfigProperties()
getConfigProperties
in interface uk.ac.roslin.ensembl.model.database.Registry
public StringBuffer printRegistryReport()
printRegistryReport
in interface uk.ac.roslin.ensembl.model.database.Registry
public DBSpecies getSpeciesByAlias(String alias_or_name)
getSpeciesByAlias
in interface uk.ac.roslin.ensembl.model.database.Registry
public DBSpecies getSpeciesByEnsemblName(String ensemblName)
getSpeciesByEnsemblName
in interface uk.ac.roslin.ensembl.model.database.Registry
public String getMostRecentEnsemblVersion()
getMostRecentEnsemblVersion
in interface uk.ac.roslin.ensembl.model.database.Registry
public DBCollection getCollection(String name, String dbVersion)
getCollection
in interface uk.ac.roslin.ensembl.model.database.Registry
public Collection<DBCollection> getCollectionRegistriesByName(String name)
getCollectionRegistriesByName
in interface uk.ac.roslin.ensembl.model.database.Registry
public Collection<DBCollection> getCollectionsByDBVersion(String dbVersion)
getCollectionsByDBVersion
in interface uk.ac.roslin.ensembl.model.database.Registry
public List<DBCollection> getCollections()
getCollections
in interface uk.ac.roslin.ensembl.model.database.Registry
public Collection<DBSpecies> getSpecies()
getSpecies
in interface uk.ac.roslin.ensembl.model.database.Registry
public Collection<DBCollectionSpecies> getCollectionSpecies()
getCollectionSpecies
in interface uk.ac.roslin.ensembl.model.database.Registry
public void addSpecies(String dbStyleName, uk.ac.roslin.ensembl.model.core.Species species)
addSpecies
in interface uk.ac.roslin.ensembl.model.database.Registry
public String getMostRecentDBVersion()
getMostRecentDBVersion
in interface uk.ac.roslin.ensembl.model.database.Registry
public String getBriefRegistryReport()
public TreeSet<Integer> getKnownSchemaVersions()
public int getHighestEnsemblSchemaVersion()
getHighestEnsemblSchemaVersion
in interface uk.ac.roslin.ensembl.model.database.Registry
public int getHighestDBVersion()
getHighestDBVersion
in interface uk.ac.roslin.ensembl.model.database.Registry
public uk.ac.roslin.ensembl.config.DBConnection.DataSource getDatasourceType()
getDatasourceType
in interface uk.ac.roslin.ensembl.model.database.Registry
public DBDatabase makeDatabase(String db_name) throws uk.ac.roslin.ensembl.exception.ConfigurationException
makeDatabase
in interface uk.ac.roslin.ensembl.model.database.Registry
uk.ac.roslin.ensembl.exception.ConfigurationException
public void setCoreDBBuildLevels(uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase database) throws uk.ac.roslin.ensembl.exception.DAOException
setCoreDBBuildLevels
in interface uk.ac.roslin.ensembl.model.database.Registry
uk.ac.roslin.ensembl.exception.DAOException
public String getAssembly(uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase database) throws uk.ac.roslin.ensembl.exception.DAOException
getAssembly
in interface uk.ac.roslin.ensembl.model.database.Registry
uk.ac.roslin.ensembl.exception.DAOException
public HashMap<uk.ac.roslin.ensembl.model.core.CollectionSpecies,String> getAssemblies(uk.ac.roslin.ensembl.model.database.CollectionDatabase database) throws uk.ac.roslin.ensembl.exception.DAOException
getAssemblies
in interface uk.ac.roslin.ensembl.model.database.Registry
uk.ac.roslin.ensembl.exception.DAOException
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Ensembl Data Access Module v1.09 |
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PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |