uk.ac.roslin.ensembl.dao.database

Class DBSingleSpeciesDatabase

java.lang.Object

uk.ac.roslin.ensembl.dao.database.DBDatabase

uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

All Implemented Interfaces:

Comparable<Database>, Database, SingleSpeciesDatabase

Direct Known Subclasses:

DBSingleSpeciesCoreDatabase, DBSingleSpeciesVariationDatabase

public class DBSingleSpeciesDatabase
extends DBDatabase
implements SingleSpeciesDatabase

Author:

tpaterso

Field Summary

Fields

Modifier and Type	Field and Description
protected String	dbSpeciesName
protected String	originalDBName
protected String	originalDBSpeciesName
protected DBSpecies	species

Constructor Summary

Constructors

Constructor and Description
DBSingleSpeciesDatabase(String db_name, EnsemblDBType type, Registry registry)

Method Summary

Methods

Modifier and Type	Method and Description
String	getdBName() Returns the real DBName as read from the getDatabases query.
String	getDbSpeciesName()
String	getOriginalDBName() Returns the original DBName as read from the getDatabases query.
String	getOriginalDBSpeciesName() Returns the original DBSpeciesName as parsed from the originalDName.
String	getRenamedDBName() Returns the renamed DBName if it was changed on instantiation due to a rewrite rule in the database configuration file.
DBSpecies	getSpecies()
boolean	isDBRenamed() Has the database been renamed due to a rule in the database configuration file.
void	setDbSpeciesName(String species)
void	setSpecies(Species species)

Methods inherited from class uk.ac.roslin.ensembl.dao.database.DBDatabase

compareTo, getBuild, getdBClassifier, getDBVersion, getIntDBVersion, getIntSchemaVersion, getNewSqlSession, getRegistry, getSchemaVersion, getSessionFactory, getType, setBuild, setdBName, setDBVersion, setIntDBVersion, setIntSchemaVersion, setRegistry, setSchemaVersion, setType, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface uk.ac.roslin.ensembl.model.database.Database

getBuild, getdBClassifier, getDBVersion, getIntDBVersion, getIntSchemaVersion, getNewSqlSession, getRegistry, getSchemaVersion, getType

Methods inherited from interface java.lang.Comparable

compareTo

Field Detail

species

protected DBSpecies species

dbSpeciesName

protected String dbSpeciesName

originalDBName

protected String originalDBName

originalDBSpeciesName

protected String originalDBSpeciesName

Constructor Detail

DBSingleSpeciesDatabase

public DBSingleSpeciesDatabase(String db_name,
                       EnsemblDBType type,
                       Registry registry)
                        throws ConfigurationException

Throws:

ConfigurationException

Method Detail

getDbSpeciesName

public String getDbSpeciesName()

Specified by:

getDbSpeciesName in interface SingleSpeciesDatabase

setDbSpeciesName

public void setDbSpeciesName(String species)

Specified by:

setDbSpeciesName in interface SingleSpeciesDatabase

setSpecies

public void setSpecies(Species species)

Specified by:

setSpecies in interface SingleSpeciesDatabase

getSpecies

public DBSpecies getSpecies()

Specified by:

getSpecies in interface SingleSpeciesDatabase

getOriginalDBName

public String getOriginalDBName()

Returns the original DBName as read from the getDatabases query. i.e. the real name of the database at the datasource without any renaming.

getdBName

public String getdBName()

Returns the real DBName as read from the getDatabases query. i.e. the real name of the database at the datasource without any renaming. Overwrites the method in the abstract parent cos if there has been renaming we want to return the original.

Specified by:

getdBName in interface Database

Overrides:

getdBName in class DBDatabase

getRenamedDBName

public String getRenamedDBName()

Returns the renamed DBName if it was changed on instantiation due to a rewrite rule in the database configuration file. i.e. if there has been a renaming this name cannot be used to access the database.

isDBRenamed

public boolean isDBRenamed()

Has the database been renamed due to a rule in the database configuration file.

getOriginalDBSpeciesName

public String getOriginalDBSpeciesName()

Returns the original DBSpeciesName as parsed from the originalDName. (i.e. from the real name of the database at the datasource without any renaming.) However if there has been renaming this name will now only be ab alia to the species not it db-style-name.