uk.ac.roslin.ensembl.dao.database.coreaccess

Class DBGeneDAO

java.lang.Object

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

uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO

All Implemented Interfaces:

GeneDAO, ReInitializationDAO

public class DBGeneDAO
extends DBCoreObjectDAO
implements GeneDAO

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	DBGeneDAO.GeneMappingRowHandler
class	DBGeneDAO.MappingRowHandler

Field Summary

Fields inherited from class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

collFactory, singleSpecies, species, ssFactory

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

configuration, daoFactory

Constructor Summary

Constructors

Constructor and Description
DBGeneDAO()
DBGeneDAO(DAOCollectionCoreFactory factory)
DBGeneDAO(DAOSingleSpeciesCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
DAGene	addGeneByIDOnParent(Integer id, DNASequence parent)
DAGene	addGeneByStableIDOnParent(String stableID, DNASequence parent) The gene returned has mapping to a sequence region - and the id for the coordinate system that this region belongs to
String	getComparaDB()
DAGene	getGeneByID(Integer id)
DAGene	getGeneByStableID(String stableID)
List<Mapping>	getGeneMappingsOnRegion(DNASequence region, Coordinate coords)
List<DAGene>	getGenesByExactName(String name)
List<DAGene>	getGenesByNameBeginning(String name)
List<DAGene>	getGenesForVegaID(String id) Returns a list of Ensembl Genes matching the query VegaID string.
void	reInitialize(IdentifiableObject object) Uses the stableid of an object to fill in missing data that would have been present if the the gene had intially been made by a call to getGeneByStableID or getGeneByID.

Methods inherited from class uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO

getDAOFactory, getSpecies, isSingleSpecies, setFactory, setFactory

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

DBGeneDAO

public DBGeneDAO()

DBGeneDAO

public DBGeneDAO(DAOSingleSpeciesCoreFactory factory)
          throws DAOException

Throws:

DAOException

DBGeneDAO

public DBGeneDAO(DAOCollectionCoreFactory factory)
          throws DAOException

Throws:

DAOException

Method Detail

reInitialize

public void reInitialize(IdentifiableObject object)
                  throws DAOException

Uses the stableid of an object to fill in missing data that would have been present if the the gene had intially been made by a call to getGeneByStableID or getGeneByID.

Specified by:

reInitialize in interface ReInitializationDAO

Parameters:

object -

Throws:

DAOException

getGeneByID

public DAGene getGeneByID(Integer id)
                   throws DAOException

Specified by:

getGeneByID in interface GeneDAO

Parameters:

id -

Throws:

DAOException

addGeneByIDOnParent

public DAGene addGeneByIDOnParent(Integer id,
                         DNASequence parent)
                           throws DAOException

Specified by:

addGeneByIDOnParent in interface GeneDAO

Throws:

DAOException

getGeneByStableID

public DAGene getGeneByStableID(String stableID)
                         throws DAOException

Specified by:

getGeneByStableID in interface GeneDAO

Parameters:

stableID -

Throws:

DAOException

addGeneByStableIDOnParent

public DAGene addGeneByStableIDOnParent(String stableID,
                               DNASequence parent)
                                 throws DAOException

The gene returned has mapping to a sequence region - and the id for the coordinate system that this region belongs to

Specified by:

addGeneByStableIDOnParent in interface GeneDAO

Parameters:

stableID -

parent -

Throws:

DAOException

getGeneMappingsOnRegion

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

Specified by:

getGeneMappingsOnRegion in interface GeneDAO

Throws:

DAOException

getGenesForVegaID

public List<DAGene> getGenesForVegaID(String id)
                               throws DAOException

Returns a list of Ensembl Genes matching the query VegaID string. Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default.

Specified by:

getGenesForVegaID in interface GeneDAO

Parameters:

id - a valid vega ID (these begin 'OTT...')

Throws:

DAOException

getGenesByExactName

public List<DAGene> getGenesByExactName(String name)
                                 throws DAOException

Specified by:

getGenesByExactName in interface GeneDAO

Throws:

DAOException

getGenesByNameBeginning

public List<DAGene> getGenesByNameBeginning(String name)
                                     throws DAOException

Specified by:

getGenesByNameBeginning in interface GeneDAO

Throws:

DAOException

getComparaDB

public String getComparaDB()

Specified by:

getComparaDB in interface GeneDAO