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.HomologyAlignmentProperties; 029 import uk.ac.roslin.ensembl.model.compara.HomologyPairRelationship; 030 import uk.ac.roslin.ensembl.model.core.Species; 031 032 public class DAHomologyPairRelationship extends DAHomologyRelationship 033 implements HomologyPairRelationship<DAGene> { 034 035 public DAHomologyPairRelationship() { 036 super(); 037 } 038 039 // public DAHomologyPairRelationship(DAOComparaFactory factory) { 040 // super(factory); 041 // } 042 043 DAGene source = null; 044 DAGene target = null; 045 046 /** 047 * Because a DAHomologyPairRelationship is tyeically instantiated from the 048 * compara databases - the target gene in particular is likely to not 049 * be a core-datasource aware object, and therefore species & and mapping details 050 * are only simple fields grabbed from compara: these are held in properties 051 * objects 052 */ 053 HomologyAlignmentProperties sourceProperties = null; 054 HomologyAlignmentProperties targetProperties = null; 055 056 @Override 057 public TreeSet<DAGene> getMembers() { 058 TreeSet<DAGene> genes = new TreeSet<DAGene>(DAObject.daComparator); 059 if (this.source != null ) { 060 genes.add(this.source); 061 } 062 if (this.target != null ) { 063 genes.add(this.target); 064 } 065 return genes; 066 } 067 068 @Override 069 public List<Species> getSpecies() { 070 List<Species> spp = new ArrayList<Species>( ); 071 if (this.source != null && this.source.getSpecies()!= null) { 072 spp.add(this.source.getSpecies()); 073 } 074 if (this.target != null && this.target.getSpecies() != null 075 && ! spp.contains(this.target.getSpecies()) 076 ) { 077 spp.add(this.target.getSpecies()); 078 } 079 return spp; 080 } 081 082 public HomologyAlignmentProperties getSourceProperties() { 083 return this.sourceProperties; 084 } 085 086 public HomologyAlignmentProperties getTargetProperties() { 087 return this.targetProperties; 088 } 089 090 public void setSourceProperties(HomologyAlignmentProperties sourceProperties) { 091 this.sourceProperties = sourceProperties; 092 } 093 094 public void setTargetProperties(HomologyAlignmentProperties targetProperties) { 095 this.targetProperties = targetProperties; 096 } 097 098 public void setSource(DAGene source) { 099 this.source = source; 100 } 101 102 public void setTarget(DAGene target) { 103 this.target = target; 104 } 105 106 public DAGene getSource() { 107 return this.source; 108 } 109 110 public DAGene getTarget() { 111 return this.target; 112 } 113 114 }