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.core; 021 022 import java.util.HashMap; 023 import uk.ac.roslin.ensembl.config.EnsemblComparaDivision; 024 import uk.ac.roslin.ensembl.config.EnsemblDBType; 025 import uk.ac.roslin.ensembl.dao.factory.DAOComparaFactory; 026 import uk.ac.roslin.ensembl.datasourceaware.DAObject; 027 import uk.ac.roslin.ensembl.dao.factory.DAOCoreFactory; 028 import uk.ac.roslin.ensembl.dao.factory.DAOSpeciesFactory; 029 import uk.ac.roslin.ensembl.model.core.CollectionSpecies; 030 import uk.ac.roslin.ensembl.model.core.CoreObject; 031 import uk.ac.roslin.ensembl.model.core.Species; 032 import uk.ac.roslin.ensembl.model.database.CollectionCoreDatabase; 033 import uk.ac.roslin.ensembl.model.database.CollectionDatabase; 034 import uk.ac.roslin.ensembl.model.database.SingleSpeciesCoreDatabase; 035 import uk.ac.roslin.ensembl.model.database.SingleSpeciesDatabase; 036 037 public abstract class DACoreObject extends DAObject implements CoreObject { 038 039 protected Species species = null; 040 // protected DAOComparaFactory instantiatingComparaFactory = null; 041 protected HashMap<EnsemblComparaDivision, DAOComparaFactory> comparaFactories = 042 new HashMap<EnsemblComparaDivision, DAOComparaFactory>(); 043 044 public DACoreObject() { 045 super(); 046 } 047 048 public DACoreObject(DAOCoreFactory factory) { 049 super(factory); 050 } 051 052 @Override 053 public DAOCoreFactory getDaoFactory() { 054 055 //@start of snip to instantiate a coreFactory from species +version info 056 //if their is no corefactory set : see matching change in DBHomologyDAO svn 132 057 058 //try and make a factory if there isn't one, but we do have set the db version and species 059 if (daoFactory == null && this.getDBVersion() != null 060 && this.getSpecies() != null) { 061 062 DAOCoreFactory f = null; 063 064 try { 065 //are we single or multispecies 066 if (this.getSpecies() instanceof CollectionSpecies) { 067 f = (DAOCoreFactory) ((CollectionCoreDatabase) ((CollectionSpecies) this.getSpecies()).getDatabaseByTypeAndVersion( 068 EnsemblDBType.collection_core, this.getDBVersion())).getCoreFactory(this.getSpecies()); 069 } else { 070 f = (DAOCoreFactory) ((SingleSpeciesCoreDatabase) this.getSpecies().getDatabaseByTypeAndVersion( 071 EnsemblDBType.core, this.getDBVersion())).getCoreFactory(); 072 } 073 } catch (Exception e) { 074 // LOGGER.warn("Failed to retrieve a Factory for new homologous gene object", e); 075 } 076 this.setDaoFactory(f); 077 078 } 079 //@end snip change svn 132 080 081 return (DAOCoreFactory) daoFactory; 082 } 083 084 public Species getSpecies() { 085 if (species == null && this.daoFactory != null && this.daoFactory instanceof DAOSpeciesFactory) { 086 species = ((DAOSpeciesFactory) this.daoFactory).getSpecies(); 087 } 088 return species; 089 } 090 091 public void setSpecies(Species species) { 092 this.species = species; 093 } 094 095 public DAOComparaFactory getComparaFactory(EnsemblComparaDivision comparaDivision) { 096 097 if (comparaFactories.containsKey(comparaDivision)) { 098 return comparaFactories.get(comparaDivision); 099 } else if (this.getDaoFactory() != null) { 100 DAOComparaFactory f = this.getDaoFactory().getComparaFactory(comparaDivision); 101 comparaFactories.put(comparaDivision, f); 102 return f; 103 } 104 return null; 105 } 106 107 public EnsemblComparaDivision getComparaDivision() { 108 if (this.getSpecies() != null) { 109 return this.getSpecies().getComparaDivision(); 110 } else return null; 111 } 112 113 public DAOComparaFactory getComparaFactory() { 114 115 return this.getComparaFactory(this.getComparaDivision()); 116 117 } 118 119 // public DAOComparaFactory getInstantiatingComparaFactory() { 120 // return instantiatingComparaFactory; 121 // } 122 123 // public void setInstantiatingComparaFactory(DAOComparaFactory instantiatingComparaFactory) { 124 // this.instantiatingComparaFactory = instantiatingComparaFactory; 125 // 126 // } 127 128 public void setDBVersion(String version) { 129 this.dbVersion = version; 130 } 131 132 public String getAssembly() { 133 134 if (this.getSpecies() == null || this.getDaoFactory() == null 135 || this.getDaoFactory().getDatabase() == null) { 136 return null; 137 } 138 139 try { 140 141 if (this.getSpecies() instanceof CollectionSpecies) { 142 return ((CollectionDatabase) this.getDaoFactory().getDatabase()).getAssembly( 143 (CollectionSpecies) this.getSpecies()); 144 145 } else { 146 return ((SingleSpeciesDatabase) this.getDaoFactory().getDatabase()).getAssembly(); 147 148 } 149 } catch (Exception e) { 150 return null; 151 } 152 153 } 154 155 }