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

Class DBDNASequenceDAO

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.DBDNASequenceDAO

All Implemented Interfaces:

DNASequenceDAO

public class DBDNASequenceDAO
extends DBCoreObjectDAO
implements DNASequenceDAO

Author:

paterson

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
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

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
String	getFullSequence(EnsemblDNASequenceReader reader)
DADNASequence	getSequenceByID(Integer id)
String	getSequenceByStartStop(EnsemblDNASequenceReader reader, Integer start, Integer stop)
DADNASequence	getValidatedSequence(DNASequence seq)
List<? extends DNASequence>	getValidatedSequences(List<? extends DNASequence> in_sequences)

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

DBDNASequenceDAO

public DBDNASequenceDAO()

DBDNASequenceDAO

public DBDNASequenceDAO(DAOSingleSpeciesCoreFactory factory)

DBDNASequenceDAO

public DBDNASequenceDAO(DAOCollectionCoreFactory factory)

Method Detail

getSequenceByStartStop

public String getSequenceByStartStop(EnsemblDNASequenceReader reader,
                            Integer start,
                            Integer stop)
                              throws DAOException

Specified by:

getSequenceByStartStop in interface DNASequenceDAO

Throws:

DAOException

getFullSequence

public String getFullSequence(EnsemblDNASequenceReader reader)
                       throws DAOException

Specified by:

getFullSequence in interface DNASequenceDAO

Throws:

DAOException

getSequenceByID

public DADNASequence getSequenceByID(Integer id)
                              throws DAOException

Specified by:

getSequenceByID in interface DNASequenceDAO

Throws:

DAOException

getValidatedSequence

public DADNASequence getValidatedSequence(DNASequence seq)
                                   throws DAOException

Specified by:

getValidatedSequence in interface DNASequenceDAO

Throws:

DAOException

getValidatedSequences

public List<? extends DNASequence> getValidatedSequences(List<? extends DNASequence> in_sequences)
                                                  throws DAOException

Specified by:

getValidatedSequences in interface DNASequenceDAO

Throws:

DAOException