Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
Ensembl Data Access Module
v1.09

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

java.lang.Object
  extended by uk.ac.roslin.ensembl.dao.database.DBBaseDAO
      extended by uk.ac.roslin.ensembl.dao.database.coreaccess.DBCoreObjectDAO
          extended by uk.ac.roslin.ensembl.dao.database.coreaccess.DBGeneDAO
All Implemented Interfaces:
uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO, uk.ac.roslin.ensembl.dao.coreaccess.ReInitializationDAO

public class DBGeneDAO
extends DBCoreObjectDAO
implements uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO


Nested Class Summary
 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
DBGeneDAO()
           
DBGeneDAO(uk.ac.roslin.ensembl.dao.factory.DAOCollectionCoreFactory factory)
           
DBGeneDAO(uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesCoreFactory factory)
           
 
Method Summary
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene addGeneByIDOnParent(Integer id, uk.ac.roslin.ensembl.model.core.DNASequence parent)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene addGeneByStableIDOnParent(String stableID, uk.ac.roslin.ensembl.model.core.DNASequence parent)
          The gene returned has mapping to a sequence region - and the id for the coordinate system that this region belongs to
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByID(Integer id)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByStableID(String stableID)
           
 List<uk.ac.roslin.ensembl.model.Mapping> getGeneMappingsOnRegion(uk.ac.roslin.ensembl.model.core.DNASequence region, uk.ac.roslin.ensembl.model.Coordinate coords)
           
 void reInitialize(uk.ac.roslin.ensembl.model.core.CoreObject 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
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(uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesCoreFactory factory)
          throws uk.ac.roslin.ensembl.exception.DAOException
Throws:
uk.ac.roslin.ensembl.exception.DAOException

DBGeneDAO

public DBGeneDAO(uk.ac.roslin.ensembl.dao.factory.DAOCollectionCoreFactory factory)
          throws uk.ac.roslin.ensembl.exception.DAOException
Throws:
uk.ac.roslin.ensembl.exception.DAOException
Method Detail

reInitialize

public void reInitialize(uk.ac.roslin.ensembl.model.core.CoreObject object)
                  throws uk.ac.roslin.ensembl.exception.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 uk.ac.roslin.ensembl.dao.coreaccess.ReInitializationDAO
Parameters:
object -
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getGeneByID

public uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByID(Integer id)
                                                             throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getGeneByID in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
Parameters:
id -
Returns:
Throws:
uk.ac.roslin.ensembl.exception.DAOException

addGeneByIDOnParent

public uk.ac.roslin.ensembl.datasourceaware.core.DAGene addGeneByIDOnParent(Integer id,
                                                                            uk.ac.roslin.ensembl.model.core.DNASequence parent)
                                                                     throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
addGeneByIDOnParent in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getGeneByStableID

public uk.ac.roslin.ensembl.datasourceaware.core.DAGene getGeneByStableID(String stableID)
                                                                   throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getGeneByStableID in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
Parameters:
stableID -
Returns:
Throws:
uk.ac.roslin.ensembl.exception.DAOException

addGeneByStableIDOnParent

public uk.ac.roslin.ensembl.datasourceaware.core.DAGene addGeneByStableIDOnParent(String stableID,
                                                                                  uk.ac.roslin.ensembl.model.core.DNASequence parent)
                                                                           throws uk.ac.roslin.ensembl.exception.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 uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
Parameters:
stableID -
parent -
Returns:
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getGeneMappingsOnRegion

public List<uk.ac.roslin.ensembl.model.Mapping> getGeneMappingsOnRegion(uk.ac.roslin.ensembl.model.core.DNASequence region,
                                                                        uk.ac.roslin.ensembl.model.Coordinate coords)
                                                                 throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getGeneMappingsOnRegion in interface uk.ac.roslin.ensembl.dao.coreaccess.GeneDAO
Throws:
uk.ac.roslin.ensembl.exception.DAOException

Ensembl Data Access Module
v1.09

Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3