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 DBDNASequenceDAO

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.DBDNASequenceDAO
All Implemented Interfaces:
uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO

public class DBDNASequenceDAO
extends DBCoreObjectDAO
implements uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO

Author:
paterson

Nested Class Summary
 class DBDNASequenceDAO.SequenceRowHandler
           
 
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
DBDNASequenceDAO()
           
DBDNASequenceDAO(uk.ac.roslin.ensembl.dao.factory.DAOCollectionCoreFactory factory)
           
DBDNASequenceDAO(uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesCoreFactory factory)
           
 
Method Summary
 String getFullSequence(uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader reader)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence getSequenceByID(Integer id)
           
 String getSequenceByStartStop(uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader reader, Integer start, Integer stop)
           
 uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence getValidatedSequence(uk.ac.roslin.ensembl.model.core.DNASequence seq)
           
 List<? extends uk.ac.roslin.ensembl.model.core.DNASequence> getValidatedSequences(List<? extends uk.ac.roslin.ensembl.model.core.DNASequence> in_sequences)
           
 
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

DBDNASequenceDAO

public DBDNASequenceDAO()

DBDNASequenceDAO

public DBDNASequenceDAO(uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesCoreFactory factory)

DBDNASequenceDAO

public DBDNASequenceDAO(uk.ac.roslin.ensembl.dao.factory.DAOCollectionCoreFactory factory)
Method Detail

getSequenceByStartStop

public String getSequenceByStartStop(uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader reader,
                                     Integer start,
                                     Integer stop)
                              throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getSequenceByStartStop in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getFullSequence

public String getFullSequence(uk.ac.roslin.ensembl.biojava3.EnsemblDNASequenceReader reader)
                       throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getFullSequence in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getSequenceByID

public uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence getSequenceByID(Integer id)
                                                                        throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getSequenceByID in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getValidatedSequence

public uk.ac.roslin.ensembl.datasourceaware.core.DADNASequence getValidatedSequence(uk.ac.roslin.ensembl.model.core.DNASequence seq)
                                                                             throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getValidatedSequence in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
Throws:
uk.ac.roslin.ensembl.exception.DAOException

getValidatedSequences

public List<? extends uk.ac.roslin.ensembl.model.core.DNASequence> getValidatedSequences(List<? extends uk.ac.roslin.ensembl.model.core.DNASequence> in_sequences)
                                                                                  throws uk.ac.roslin.ensembl.exception.DAOException
Specified by:
getValidatedSequences in interface uk.ac.roslin.ensembl.dao.coreaccess.DNASequenceDAO
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