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 DBExonDAO

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.DBExonDAO
All Implemented Interfaces:
uk.ac.roslin.ensembl.dao.coreaccess.ExonDAO, uk.ac.roslin.ensembl.dao.coreaccess.ReInitializationDAO

public class DBExonDAO
extends DBCoreObjectDAO
implements uk.ac.roslin.ensembl.dao.coreaccess.ExonDAO


Nested Class Summary
 class DBExonDAO.ExonRowHandler
           
 
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
DBExonDAO()
           
DBExonDAO(uk.ac.roslin.ensembl.dao.factory.DAOCollectionCoreFactory factory)
           
DBExonDAO(uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesCoreFactory factory)
           
 
Method Summary
 uk.ac.roslin.ensembl.datasourceaware.core.DAExon getExonByID(Integer id)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DAExon getExonByStableID(String stableID)
           
 List<uk.ac.roslin.ensembl.datasourceaware.core.DAExon> getExonsForTranscript(uk.ac.roslin.ensembl.model.core.Transcript transcript)
           
 void reInitialize(uk.ac.roslin.ensembl.model.core.CoreObject object)
          Uses the stableid of an object to fill in missing data
 
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

DBExonDAO

public DBExonDAO()

DBExonDAO

public DBExonDAO(uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesCoreFactory factory)
          throws uk.ac.roslin.ensembl.exception.DAOException
Throws:
uk.ac.roslin.ensembl.exception.DAOException

DBExonDAO

public DBExonDAO(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

Specified by:
reInitialize in interface uk.ac.roslin.ensembl.dao.coreaccess.ReInitializationDAO
Parameters:
object -
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getExonByID

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

getExonByStableID

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

getExonsForTranscript

public List<uk.ac.roslin.ensembl.datasourceaware.core.DAExon> getExonsForTranscript(uk.ac.roslin.ensembl.model.core.Transcript transcript)
                                                                             throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getExonsForTranscript in interface uk.ac.roslin.ensembl.dao.coreaccess.ExonDAO
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