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 package uk.ac.roslin.ensembl.datasourceaware.compara; 021 022 import java.util.ArrayList; 023 import java.util.List; 024 import java.util.TreeSet; 025 import uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory; 026 import uk.ac.roslin.ensembl.datasourceaware.DAObject; 027 import uk.ac.roslin.ensembl.datasourceaware.core.DAGene; 028 import uk.ac.roslin.ensembl.model.compara.HomologyRelationship; 029 import uk.ac.roslin.ensembl.model.compara.HomologyType; 030 import uk.ac.roslin.ensembl.model.core.Species; 031 import uk.ac.roslin.ensembl.model.relationship.RelationshipType; 032 033 034 public class DAHomologyRelationship extends DAObject implements HomologyRelationship<DAGene> { 035 036 public DAHomologyRelationship() { 037 super(); 038 } 039 040 // public DAHomologyRelationship(DAOComparaFactory factory) { 041 // //super(factory); 042 // } 043 044 private HomologyType type = null; 045 private String lastCommonAncestor = ""; 046 private TreeSet<DAGene> members = new TreeSet<DAGene>(DAObject.daComparator); 047 048 public TreeSet<DAGene> getMembers() { 049 return members; 050 } 051 052 public HomologyType getType() { 053 return this.type; 054 } 055 056 public void setType(HomologyType type) { 057 this.type = type; 058 } 059 060 public String getLastCommonAncestor() { 061 return this.lastCommonAncestor; 062 } 063 064 public List<Species> getSpecies() { 065 throw new UnsupportedOperationException("Not supported yet."); 066 } 067 068 public void setLastCommonAncestor(String lastCommonAncestor) { 069 this.lastCommonAncestor = lastCommonAncestor; 070 } 071 072 public HomologyType getRelationshipType() { 073 return this.type; 074 } 075 076 public void setRelationshipType(RelationshipType type) { 077 this.type = (HomologyType) type; 078 } 079 }