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

Class DBTranscriptDAO

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.DBTranscriptDAO

All Implemented Interfaces:

ReInitializationDAO, TranscriptDAO

public class DBTranscriptDAO
extends DBCoreObjectDAO
implements TranscriptDAO

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	DBTranscriptDAO.TranscriptRowHandler

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
DBTranscriptDAO()
DBTranscriptDAO(DAOCollectionCoreFactory factory)
DBTranscriptDAO(DAOSingleSpeciesCoreFactory factory)

Method Summary

Methods

Modifier and Type	Method and Description
DATranscript	getTranscriptByID(Integer id)
DATranscript	getTranscriptByStableID(String stableID)
List<DATranscript>	getTranscriptsForCcdsID(String id) Returns a list of Ensembl Transcripts matching the query CCDS ID string.
List<DATranscript>	getTranscriptsForGene(Gene gene)
List<DATranscript>	getTranscriptsForVegaID(String id) Returns a list of Ensembl Transcripts matching the query VegaID string.
void	reInitialize(IdentifiableObject object) Uses the stableid of an object to fill in missing data

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

DBTranscriptDAO

public DBTranscriptDAO()

DBTranscriptDAO

public DBTranscriptDAO(DAOSingleSpeciesCoreFactory factory)
                throws DAOException

Throws:

DAOException

DBTranscriptDAO

public DBTranscriptDAO(DAOCollectionCoreFactory factory)
                throws DAOException

Throws:

DAOException

Method Detail

reInitialize

public void reInitialize(IdentifiableObject object)
                  throws DAOException

Uses the stableid of an object to fill in missing data

Specified by:

reInitialize in interface ReInitializationDAO

Parameters:

object -

Throws:

DAOException

getTranscriptByID

public DATranscript getTranscriptByID(Integer id)
                               throws DAOException

Specified by:

getTranscriptByID in interface TranscriptDAO

Parameters:

id -

Throws:

DAOException

getTranscriptByStableID

public DATranscript getTranscriptByStableID(String stableID)
                                     throws DAOException

Specified by:

getTranscriptByStableID in interface TranscriptDAO

Parameters:

stableID -

Throws:

DAOException

getTranscriptsForGene

public List<DATranscript> getTranscriptsForGene(Gene gene)
                                         throws DAOException

Specified by:

getTranscriptsForGene in interface TranscriptDAO

Throws:

DAOException

getTranscriptsForVegaID

public List<DATranscript> getTranscriptsForVegaID(String id)
                                           throws DAOException

Returns a list of Ensembl Transcripts 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:

getTranscriptsForVegaID in interface TranscriptDAO

Parameters:

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

Returns:

List of (supertype of)Transcripts

Throws:

DAOException

getTranscriptsForCcdsID

public List<DATranscript> getTranscriptsForCcdsID(String id)
                                           throws DAOException

Returns a list of Ensembl Transcripts matching the query CCDS ID string. CCDS currently curates consensus canonical transcripts for human and mouse. Calling this method on EnsemblGenomes (invertebrate) species will return an empty list by default.

Specified by:

getTranscriptsForCcdsID in interface TranscriptDAO

Parameters:

id - a valid CCDS accession or accession.version (these begin 'CCDS...')

Returns:

List of (supertype of)Transcripts

Throws:

DAOException