001/**
002 * Copyright (C) 2010-2015 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
003 *
004 * This file is part of JEnsembl: a Java API to Ensembl data sources developed by the
005 * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
006 * Veterinary Studies, University of Edinburgh.
007 *
008 * Project hosted at: http://jensembl.sourceforge.net
009 *
010 * This is free software: you can redistribute it and/or modify
011 * it under the terms of the GNU General Public License (version 3) as published by
012 * the Free Software Foundation.
013 *
014 * This software is distributed in the hope that it will be useful,
015 * but WITHOUT ANY WARRANTY; without even the implied warranty of
016 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
017 * GNU General Public License for more details.
018 *
019 * You should have received a copy of the GNU General Public License
020 * in this software distribution. If not, see: http://opensource.org/licenses/gpl-3.0.html
021 */
022package uk.ac.roslin.ensembl.dao.factory;
023
024import uk.ac.roslin.ensembl.config.EnsemblComparaDivision;
025import uk.ac.roslin.ensembl.dao.XRefDAO;
026import uk.ac.roslin.ensembl.dao.coreaccess.*;
027import uk.ac.roslin.ensembl.exception.DAOException;
028import uk.ac.roslin.ensembl.model.database.CoreDatabase;
029
030public interface DAOCoreFactory extends DAOFactoryWithAnalyses  {
031
032    @Override
033    public CoreDatabase getDatabase();
034    
035    public GeneDAO getGeneDAO() throws DAOException;
036    public ProteinFeatureDAO getProteinFeatureDAO() throws DAOException;
037    public ChromosomeDAO getChromosomeDAO() throws DAOException;
038    public CoordinateSystemDAO getCoordinateSystemDAO() throws DAOException;
039    public AssemblyDAO getAssemblyDAO() throws DAOException;
040    public DNASequenceDAO getSequenceDAO() throws DAOException;
041    public TranslationDAO getTranslationDAO() throws DAOException;
042    public TranscriptDAO getTranscriptDAO()  throws DAOException;
043    public ExonDAO getExonDAO()  throws DAOException;
044    public DAOComparaFactory getComparaFactory(EnsemblComparaDivision comparaDivision);
045    public XRefDAO getXRefDAO()  throws DAOException;  
046    public DAOVariationFactory getVariationFactory();
047    public boolean hasVariationFactory();
048
049}