uk.ac.roslin.ensembl.dao.database.variation

Class DBVariationDAO

java.lang.Object

uk.ac.roslin.ensembl.dao.database.DBBaseDAO

uk.ac.roslin.ensembl.dao.database.variation.DBVariationDAO

All Implemented Interfaces:

VariationDAO

public class DBVariationDAO
extends DBBaseDAO
implements VariationDAO

Field Summary

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

configuration, daoFactory

Constructor Summary

Constructors

Constructor and Description
DBVariationDAO()
DBVariationDAO(DAOVariationFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
DAVariation	getUniquelyMappedVariation(String variationName)
List<DAVariation>	getUniquelyMappedVariations(List<String> variationNames)
List<VariationMapping>	getVariationMappingsOnRegion(DNASequence region, Coordinate coords)
List<DAVariation>	getVariationsOnRegion(DNASequence region, Coordinate coords)

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

getFactory, setConfiguration, setFactory

Methods inherited from class java.lang.Object

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

Constructor Detail

DBVariationDAO

public DBVariationDAO()

DBVariationDAO

public DBVariationDAO(DAOVariationFactory factory)
               throws DAOException

Throws:

DAOException

Method Detail

getVariationMappingsOnRegion

public List<VariationMapping> getVariationMappingsOnRegion(DNASequence region,
                                                  Coordinate coords)
                                                    throws DAOException

Specified by:

getVariationMappingsOnRegion in interface VariationDAO

Throws:

DAOException

getVariationsOnRegion

public List<DAVariation> getVariationsOnRegion(DNASequence region,
                                      Coordinate coords)
                                        throws DAOException

Specified by:

getVariationsOnRegion in interface VariationDAO

Throws:

DAOException

getUniquelyMappedVariation

public DAVariation getUniquelyMappedVariation(String variationName)
                                       throws DAOException

Specified by:

getUniquelyMappedVariation in interface VariationDAO

Throws:

DAOException

getUniquelyMappedVariations

public List<DAVariation> getUniquelyMappedVariations(List<String> variationNames)
                                              throws DAOException

Specified by:

getUniquelyMappedVariations in interface VariationDAO

Throws:

DAOException