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

Class DBTranslationDAO

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.DBTranslationDAO

All Implemented Interfaces:

ReInitializationDAO, TranslationDAO

public class DBTranslationDAO
extends DBCoreObjectDAO
implements TranslationDAO

Author:

tpaterso

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
DBTranslationDAO()
DBTranslationDAO(DAOCollectionCoreFactory factory)
DBTranslationDAO(DAOSingleSpeciesCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
DATranslation	getTranslationByID(Integer id)
DATranslation	getTranslationByStableID(String stableID)
List<DATranslation>	getTranslationsForTranscript(Transcript transcript)
List<DATranslation>	getTranslationsForVegaID(String id) Returns a list of Ensembl Translations matching the query VegaID string.
void	reInitialize(IdentifiableObject object)

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

DBTranslationDAO

public DBTranslationDAO()

DBTranslationDAO

public DBTranslationDAO(DAOSingleSpeciesCoreFactory factory)

DBTranslationDAO

public DBTranslationDAO(DAOCollectionCoreFactory factory)

Method Detail

getTranslationByID

public DATranslation getTranslationByID(Integer id)
                                 throws DAOException

Specified by:

getTranslationByID in interface TranslationDAO

Throws:

DAOException

getTranslationByStableID

public DATranslation getTranslationByStableID(String stableID)
                                       throws DAOException

Specified by:

getTranslationByStableID in interface TranslationDAO

Throws:

DAOException

getTranslationsForTranscript

public List<DATranslation> getTranslationsForTranscript(Transcript transcript)
                                                 throws DAOException

Specified by:

getTranslationsForTranscript in interface TranslationDAO

Throws:

DAOException

reInitialize

public void reInitialize(IdentifiableObject object)
                  throws DAOException

Specified by:

reInitialize in interface ReInitializationDAO

Throws:

DAOException

getTranslationsForVegaID

public List<DATranslation> getTranslationsForVegaID(String id)
                                             throws DAOException

Returns a list of Ensembl Translations matching the query VegaID string. Vega currently curates gene, transcript and protein annotations for a human and and a few key regions of other vertebrate species. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default.

Specified by:

getTranslationsForVegaID in interface TranslationDAO

Parameters:

id - a valid vega ID (these begin 'OTT...')

Throws:

DAOException