uk.ac.roslin.ensembl.dao.database

Class DBSingleSpeciesVariationDatabase

java.lang.Object

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

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

uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesVariationDatabase

All Implemented Interfaces:

Comparable<Database>, Database, SingleSpeciesDatabase, SingleSpeciesVariationDatabase, VariationDatabase

public class DBSingleSpeciesVariationDatabase
extends DBSingleSpeciesDatabase
implements SingleSpeciesVariationDatabase

Author:

tpaterso

Field Summary

Fields inherited from class uk.ac.roslin.ensembl.dao.database.DBSingleSpeciesDatabase

dbSpeciesName, originalDBName, originalDBSpeciesName, species

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
DBSingleSpeciesCoreDatabase	getCoreDB()
Set<DACoordinateSystem>	getCSForFeature(ObjectType featureType)
List<FeatureType>	getFeaturesForCS(CoordinateSystem coordSys)
Integer	getMaxLengthForFeature(ObjectType featureType, CoordinateSystem cs)
DAOVariationFactory	getVariationFactory()
void	setCoreDB(SingleSpeciesCoreDatabase coreDB)

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

getdBName, getDbSpeciesName, getOriginalDBName, getOriginalDBSpeciesName, getRenamedDBName, getSpecies, isDBRenamed, setDbSpeciesName, setSpecies

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.SingleSpeciesDatabase

getDbSpeciesName, getSpecies, setDbSpeciesName, setSpecies

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

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

Methods inherited from interface java.lang.Comparable

compareTo

Constructor Detail

DBSingleSpeciesVariationDatabase

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

Throws:

ConfigurationException

Method Detail

getVariationFactory

public DAOVariationFactory getVariationFactory()

Specified by:

getVariationFactory in interface SingleSpeciesVariationDatabase

getCoreDB

public DBSingleSpeciesCoreDatabase getCoreDB()

setCoreDB

public void setCoreDB(SingleSpeciesCoreDatabase coreDB)

getCSForFeature

public Set<DACoordinateSystem> getCSForFeature(ObjectType featureType)
                                        throws DAOException

Throws:

DAOException

getFeaturesForCS

public List<FeatureType> getFeaturesForCS(CoordinateSystem coordSys)
                                   throws DAOException

Throws:

DAOException

getMaxLengthForFeature

public Integer getMaxLengthForFeature(ObjectType featureType,
                             CoordinateSystem cs)
                               throws DAOException

Throws:

DAOException