001    /**
002     * Copyright (C) 2010 The Roslin Institute <contact andy.law@roslin.ed.ac.uk>
003     *
004     * This file is part of the Ensembl Java API demonstration project developed by the
005     * Bioinformatics Group at The Roslin Institute, The Royal (Dick) School of
006     * Veterinary Studies, University of Edinburgh.
007     *
008     * This is free software: you can redistribute it and/or modify
009     * it under the terms of the GNU General Public License (version 3) as published by
010     * the Free Software Foundation.
011     *
012     * This software is distributed in the hope that it will be useful,
013     * but WITHOUT ANY WARRANTY; without even the implied warranty of
014     * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
015     * GNU General Public License for more details.
016     *
017     * You should have received a copy of the GNU General Public License
018     * in this software distribution. If not, see <http://www.gnu.org/licenses/gpl-3.0.html/>.
019     */
020    
021    package uk.ac.roslin.ensembl.dao.coreaccess;
022    
023    import java.util.List;
024    import uk.ac.roslin.ensembl.exception.DAOException;
025    import uk.ac.roslin.ensembl.model.Coordinate;
026    import uk.ac.roslin.ensembl.model.Mapping;
027    import uk.ac.roslin.ensembl.model.core.Gene;
028    import uk.ac.roslin.ensembl.model.core.DNASequence;
029    
030    public interface GeneDAO extends ReInitializationDAO  {
031    
032        public Gene getGeneByID(Integer id) throws DAOException;
033        public Gene addGeneByIDOnParent(Integer id, DNASequence parent) throws DAOException ;
034    
035        public Gene getGeneByStableID(String stableId) throws DAOException ;
036        public Gene addGeneByStableIDOnParent(String stableID, DNASequence parent) throws DAOException ;
037    
038        public List<? extends Mapping> getGeneMappingsOnRegion(DNASequence region, Coordinate coords) throws DAOException ;
039    
040    }