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.dao.database.coreaccess; 021 022 import java.util.ArrayList; 023 import uk.ac.roslin.ensembl.datasourceaware.core.DACoordinateSystem; 024 import java.util.HashMap; 025 import java.util.List; 026 import org.apache.ibatis.session.SqlSession; 027 import uk.ac.roslin.ensembl.dao.coreaccess.ChromosomeDAO; 028 import uk.ac.roslin.ensembl.datasourceaware.core.DAChromosome; 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.ChromosomeMapper; 034 import uk.ac.roslin.ensembl.exception.DAOException; 035 import uk.ac.roslin.ensembl.model.core.CoordinateSystem; 036 037 /** 038 * 039 * @author paterson 040 */ 041 public class DBChromosomeDAO extends DBCoreObjectDAO implements ChromosomeDAO { 042 043 public DBChromosomeDAO() { 044 super(); 045 } 046 047 public DBChromosomeDAO(DAOSingleSpeciesCoreFactory factory) { 048 super(factory); 049 } 050 051 public DBChromosomeDAO(DAOCollectionCoreFactory factory) { 052 super(factory); 053 } 054 055 @Override 056 public DAChromosome getChromosomeByName(String name) throws DAOException { 057 058 if (name==null || name.isEmpty()) { 059 return null; 060 } 061 062 DAChromosome out = null; 063 String chrName = name; 064 CoordinateSystem chrCS = null; 065 066 if (singleSpecies) { 067 chrCS = ssFactory.getDatabase().getChromosomeLevelCoordSystem(); 068 } else { 069 chrCS = collFactory.getDatabase().getChromosomeLevelCS(species); 070 } 071 072 if (chrCS==null || chrCS.getId()==null ) { 073 throw new DAOException("Failed to call to retrieve the CoordinateSystem for Chromosomes"); 074 } 075 076 Integer chrCSID = chrCS.getId(); 077 078 HashMap parameters = new HashMap(); 079 parameters.put("chrName",chrName); 080 parameters.put("coordSysID", chrCSID); 081 082 SqlSession session = null; 083 084 try { 085 session = this.getFactory().getNewSqlSession(); 086 ChromosomeMapper mapper = session.getMapper(ChromosomeMapper.class); 087 out = mapper.getChromosomeByName_CoordSysID(parameters); 088 } catch (Exception e) { 089 throw new DAOException("Failed to call getChromsomeByName_CoordSysID", e); 090 } finally { 091 if (session != null) { 092 session.close(); 093 } 094 } 095 096 if (out != null) { 097 out.setDaoFactory(daoFactory); 098 out.setCoordSystem(chrCS); 099 out.setSpecies(species); 100 } 101 102 return out; 103 } 104 105 @Override 106 public List<DAChromosome> getChromosomes() throws DAOException { 107 108 List<DAChromosome> out = new ArrayList<DAChromosome>(); 109 CoordinateSystem chrCS = null; 110 111 if (singleSpecies) { 112 chrCS = ssFactory.getDatabase().getChromosomeLevelCoordSystem(); 113 } else { 114 chrCS = collFactory.getDatabase().getChromosomeLevelCS(species); 115 } 116 117 if (chrCS==null || chrCS.getId()==null ) { 118 throw new DAOException("Failed to call to retrieve the CoordinateSystem for Chromosomes"); 119 } 120 121 Integer chrCSID = chrCS.getId(); 122 123 HashMap parameters = new HashMap(); 124 parameters.put("coordSysID", chrCSID); 125 126 SqlSession session = null; 127 128 try { 129 session = this.getFactory().getNewSqlSession(); 130 ChromosomeMapper mapper = session.getMapper(ChromosomeMapper.class); 131 out = mapper.getChromosomesByCoordSysID(parameters); 132 } catch (Exception e) { 133 throw new DAOException("Failed to call getChromsomes", e); 134 } finally { 135 if (session != null) { 136 session.close(); 137 } 138 } 139 for (DAChromosome c : out) { 140 c.setDaoFactory(daoFactory); 141 c.setCoordSystem(chrCS); 142 c.setSpecies(species); 143 } 144 145 return out; 146 } 147 } 148 149