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.dao.database.coreaccess; 022 023 import uk.ac.roslin.ensembl.exception.DAOException; 024 import java.util.ArrayList; 025 import java.util.List; 026 import org.apache.ibatis.session.SqlSession; 027 import uk.ac.roslin.ensembl.dao.coreaccess.ProteinFeatureDAO; 028 import uk.ac.roslin.ensembl.datasourceaware.core.DAProteinFeature; 029 import uk.ac.roslin.ensembl.dao.database.factory.DBDAOCollectionCoreFactory; 030 import uk.ac.roslin.ensembl.dao.database.factory.DBDAOSingleSpeciesCoreFactory; 031 import uk.ac.roslin.ensembl.dao.factory.DAOCollectionCoreFactory; 032 import uk.ac.roslin.ensembl.dao.factory.DAOSingleSpeciesCoreFactory; 033 import uk.ac.roslin.ensembl.mapper.core.ProteinFeatureMapper; 034 035 036 public class DBProteinFeatureDAO extends DBCoreObjectDAO implements ProteinFeatureDAO { 037 038 public DBProteinFeatureDAO() { 039 super(); 040 } 041 042 public DBProteinFeatureDAO(DAOSingleSpeciesCoreFactory factory) { 043 super(factory); 044 } 045 046 public DBProteinFeatureDAO(DAOCollectionCoreFactory factory) { 047 super(factory); 048 } 049 050 @Override 051 public List<DAProteinFeature> getProteinFeaturesByTranslationID(int translationID) throws DAOException { 052 053 List<DAProteinFeature> outList = new ArrayList<DAProteinFeature>(); 054 055 if ( translationID==0) { 056 return outList; 057 } 058 059 060 061 SqlSession session = null; 062 063 try { 064 session = this.getFactory().getNewSqlSession(); 065 ProteinFeatureMapper mapper = session.getMapper(ProteinFeatureMapper.class); 066 outList = mapper.getProteinFeaturesByTranslationID(translationID); 067 } catch (Exception e) { 068 throw new DAOException("Failed to call getProteinFeaturesByTranslationID", e); 069 } finally { 070 if (session != null) { 071 session.close(); 072 } 073 } 074 075 if (outList != null && ! outList.isEmpty()) { 076 for (DAProteinFeature pf : outList) { 077 pf.setDaoFactory(daoFactory); 078 } 079 } 080 return outList; 081 } 082 083 084 }