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.model.core;
023
024import java.util.Collection;
025import java.util.List;
026import uk.ac.roslin.ensembl.config.EnsemblComparaDivision;
027import uk.ac.roslin.ensembl.model.compara.HomologyPairRelationship;
028
029
030public interface Gene  extends Feature, Analyzed, WithDisplayXRef {
031
032    public String getDescription() ;
033
034    public String getBiotype() ;
035
036    public Transcript getCanonicalTranscript() ;
037
038    public Translation getCanonicalTranslation() ;
039
040    public Collection<? extends Transcript> getTranscripts();
041
042    public List<? extends HomologyPairRelationship> getHomologies() ;
043
044    public List<? extends HomologyPairRelationship> getHomologies(Species sp) ;
045
046    public List<? extends HomologyPairRelationship> getHomologies(EnsemblComparaDivision speciesGroup) ;
047
048    public List<? extends HomologyPairRelationship> getHomologies(EnsemblComparaDivision speciesGroup, Species sp) ;
049
050    //this shouldnt be in this interface - but in some view interface
051    //however we do need to be able to do this, for drawing application code
052
053    public List<? extends HomologyPairRelationship> getHomologiesWithoutLazyLoad();
054
055}