uk.ac.roslin.ensembl.dao.coreaccess

Interface GeneDAO

All Superinterfaces:

ReInitializationDAO

All Known Implementing Classes:

DBGeneDAO

public interface GeneDAO
extends ReInitializationDAO

Method Summary

Methods

Modifier and Type	Method and Description
Gene	addGeneByIDOnParent(Integer id, DNASequence parent)
Gene	addGeneByStableIDOnParent(String stableID, DNASequence parent)
String	getComparaDB()
Gene	getGeneByID(Integer id)
Gene	getGeneByStableID(String stableId)
List<? extends Mapping>	getGeneMappingsOnRegion(DNASequence region, Coordinate coords)
List<? extends Gene>	getGenesByExactName(String name)
List<? extends Gene>	getGenesByNameBeginning(String name)
List<? extends Gene>	getGenesForVegaID(String id)

Methods inherited from interface uk.ac.roslin.ensembl.dao.coreaccess.ReInitializationDAO

reInitialize

Method Detail

getGeneByID

Gene getGeneByID(Integer id)
                 throws DAOException

Throws:

DAOException

addGeneByIDOnParent

Gene addGeneByIDOnParent(Integer id,
                       DNASequence parent)
                         throws DAOException

Throws:

DAOException

getGeneByStableID

Gene getGeneByStableID(String stableId)
                       throws DAOException

Throws:

DAOException

addGeneByStableIDOnParent

Gene addGeneByStableIDOnParent(String stableID,
                             DNASequence parent)
                               throws DAOException

Throws:

DAOException

getGeneMappingsOnRegion

List<? extends Mapping> getGeneMappingsOnRegion(DNASequence region,
                                              Coordinate coords)
                                                throws DAOException

Throws:

DAOException

getGenesForVegaID

List<? extends Gene> getGenesForVegaID(String id)
                                       throws DAOException

Throws:

DAOException

getGenesByExactName

List<? extends Gene> getGenesByExactName(String name)
                                         throws DAOException

Throws:

DAOException

getGenesByNameBeginning

List<? extends Gene> getGenesByNameBeginning(String name)
                                             throws DAOException

Throws:

DAOException

getComparaDB

String getComparaDB()