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.model.core; 022 023 import java.util.Collection; 024 import java.util.List; 025 import uk.ac.roslin.ensembl.config.EnsemblComparaDivision; 026 import uk.ac.roslin.ensembl.model.compara.HomologyPairRelationship; 027 028 029 public interface Gene extends Feature { 030 031 public String getDescription() ; 032 033 public Analysis getAnalysis() ; 034 035 public String getBiotype() ; 036 037 public Transcript getCanonicalTranscript() ; 038 039 public Translation getCanonicalTranslation() ; 040 041 public Collection<? extends Transcript> getTranscripts(); 042 043 public List<? extends HomologyPairRelationship> getHomologies() ; 044 045 public List<? extends HomologyPairRelationship> getHomologies(Species sp) ; 046 047 public List<? extends HomologyPairRelationship> getHomologies(EnsemblComparaDivision speciesGroup) ; 048 049 public List<? extends HomologyPairRelationship> getHomologies(EnsemblComparaDivision speciesGroup, Species sp) ; 050 051 //this shouldnt be in this interface - but in some view interface 052 //however we do need to be able to do this, for drawing application code 053 054 public List<? extends HomologyPairRelationship> getHomologiesWithoutLazyLoad(); 055 056 }