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.coreaccess;
023
024import java.util.List;
025import uk.ac.roslin.ensembl.exception.DAOException;
026import uk.ac.roslin.ensembl.model.Coordinate;
027import uk.ac.roslin.ensembl.model.Mapping;
028import uk.ac.roslin.ensembl.model.core.DNASequence;
029import uk.ac.roslin.ensembl.model.core.Gene;
030
031public interface GeneDAO extends ReInitializationDAO  {
032
033    public Gene getGeneByID(Integer id) throws DAOException;
034    public Gene addGeneByIDOnParent(Integer id, DNASequence parent) throws DAOException ;
035
036    public Gene getGeneByStableID(String stableId) throws DAOException ;
037    public Gene addGeneByStableIDOnParent(String stableID, DNASequence parent) throws DAOException ;
038
039    public List<? extends Mapping> getGeneMappingsOnRegion(DNASequence region, Coordinate coords) throws DAOException ;
040    public List<? extends Gene> getGenesForVegaID(String id) throws DAOException; 
041    
042    public List<? extends Gene> getGenesByExactName(String name) throws DAOException; 
043    public List<? extends Gene> getGenesByNameBeginning(String name) throws DAOException; 
044
045    String getComparaDB();
046}