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.datasourceaware.core; 022 023 import java.util.ArrayList; 024 import java.util.List; 025 import org.apache.log4j.Logger; 026 import uk.ac.roslin.ensembl.config.EnsemblCoreObjectType; 027 import uk.ac.roslin.ensembl.exception.DAOException; 028 import uk.ac.roslin.ensembl.model.ObjectType; 029 import uk.ac.roslin.ensembl.model.core.ProteinFeature; 030 import uk.ac.roslin.ensembl.model.core.Translation; 031 032 /** 033 * 034 * @author tpaterso 035 */ 036 //just a demo class - very simplistic implementation 037 public class DATranslation extends DACoreObject implements Translation { 038 039 DATranscript transcript = null; 040 List<? extends ProteinFeature> proteinFeatures = null; 041 final static Logger LOGGER = Logger.getLogger(DATranslation.class); 042 043 public List<? extends ProteinFeature> getProteinFeatures() { 044 if (proteinFeatures == null) { 045 046 if (this.getId()==null) { 047 return null; 048 } 049 050 try { 051 proteinFeatures = this.getDaoFactory().getProteinFeatureDAO().getProteinFeaturesByTranslationID(this.id); 052 } catch (DAOException dex) { 053 LOGGER.info("failed to get Protein Features", dex); 054 } catch (Exception ex) { 055 LOGGER.info("failed to get Protein Features", ex); 056 } 057 058 } 059 return proteinFeatures; 060 } 061 062 public DATranscript getTranscript() { 063 return transcript; 064 } 065 066 public void setTranscript(DATranscript transcript) { 067 this.transcript = transcript; 068 } 069 070 public ObjectType getType() { 071 return EnsemblCoreObjectType.translation; 072 } 073 074 }