uk.ac.roslin.ensembl.dao.coreaccess

Interface TranscriptDAO

All Superinterfaces:

ReInitializationDAO

All Known Implementing Classes:

DBTranscriptDAO

public interface TranscriptDAO
extends ReInitializationDAO

Author:

tpaterso

Method Summary

Methods

Modifier and Type	Method and Description
Transcript	getTranscriptByID(Integer id)
Transcript	getTranscriptByStableID(String stableID)
List<? extends Transcript>	getTranscriptsForCcdsID(String id) Returns a list of Ensembl Transcripts matching the query CCDS ID string.
List<? extends Transcript>	getTranscriptsForGene(Gene gene)
List<? extends Transcript>	getTranscriptsForVegaID(String id) Returns a list of Ensembl Transcripts matching the query VegaID string.

Methods inherited from interface uk.ac.roslin.ensembl.dao.coreaccess.ReInitializationDAO

reInitialize

Method Detail

getTranscriptsForGene

List<? extends Transcript> getTranscriptsForGene(Gene gene)
                                                 throws DAOException

Throws:

DAOException

getTranscriptByStableID

Transcript getTranscriptByStableID(String stableID)
                                   throws DAOException

Throws:

DAOException

getTranscriptByID

Transcript getTranscriptByID(Integer id)
                             throws DAOException

Throws:

DAOException

getTranscriptsForVegaID

List<? extends Transcript> 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.

Parameters:

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

Returns:

List of (supertype of)Transcripts

Throws:

DAOException

getTranscriptsForCcdsID

List<? extends Transcript> 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.

Parameters:

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

Returns:

List of (supertype of)Transcripts

Throws:

DAOException