Ensembl Data Access Module v1.09
© Roslin Institute 2010. GNU General Public License, version3
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:
- 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
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 java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
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
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
© Roslin Institute 2010. GNU General Public License, version3