001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 */ 021package org.biojava.nbio.structure.scop; 022 023import org.slf4j.Logger; 024import org.slf4j.LoggerFactory; 025 026import java.util.HashMap; 027import java.util.Map; 028 029 030 031/** 032 * Controls the global ScopDatabase being used. 033 * 034 * <p>Defaults to a {@link RemoteScopInstallation}, which is fast for small numbers 035 * of queries. For many queries, using {@link #getSCOP(String, boolean) getSCOP(version,true)} 036 * may be faster, since it makes only one network request. 037 * 038 * <p>Example: Fetch the structure corresponding to an old version of scop 039 * 040 * <pre> 041 * ScopInstallation scop = new ScopInstallation(); 042 * scop.setScopVersion("1.69"); 043 * ScopFactory.setScopDatabase(scop); 044 * AtomCache cache = new AtomCache(); 045 * cache.setFetchFileEvenIfObsolete(true); //fetch older PDBs 046 * cache.setStrictSCOP(false); // correct simple errors in domain names 047 * Structure s = cache.getStructure("d3hbia_"); 048 * @author sbliven 049 * 050 */ 051public class ScopFactory { 052 053 private static final Logger logger = LoggerFactory.getLogger(ScopFactory.class); 054 055 // berkeley 2 056 public static final String VERSION_2_0_5 = "2.05"; 057 public static final String VERSION_2_0_4 = "2.04"; 058 public static final String VERSION_2_0_3 = "2.03"; 059 public static final String VERSION_2_0_2 = "2.02"; 060 public static final String VERSION_2_0_1 = "2.01"; 061 // berkeley 1 (aliases of above) 062 public static final String VERSION_1_75C = VERSION_2_0_3; 063 public static final String VERSION_1_75B = VERSION_2_0_2; 064 public static final String VERSION_1_75A = VERSION_2_0_1; 065 // original SCOP 066 // latest SCOP release from SCOP website = 1.75; 067 public static final String VERSION_1_75 = "1.75"; 068 // outdated stable versions 069 public static final String VERSION_1_73 = "1.73"; 070 public static final String VERSION_1_71 = "1.71"; 071 public static final String VERSION_1_69 = "1.69"; 072 public static final String VERSION_1_67 = "1.67"; 073 public static final String VERSION_1_65 = "1.65"; 074 public static final String VERSION_1_63 = "1.63"; 075 public static final String VERSION_1_61 = "1.61"; 076 public static final String VERSION_1_59 = "1.59"; 077 public static final String VERSION_1_57 = "1.57"; 078 public static final String VERSION_1_55 = "1.55"; 079 080 // The most recent version as of compilation time 081 public static final String LATEST_VERSION = VERSION_2_0_5; 082 083 // Hold one instance for each version 084 private static Map<String,ScopDatabase> versionedScopDBs = new HashMap<String, ScopDatabase>(); 085 private static String defaultVersion = LATEST_VERSION; 086 087 /** 088 * Get the current default instance for the default version 089 * @return 090 */ 091 public static ScopDatabase getSCOP(){ 092 return getSCOP(defaultVersion); 093 } 094 095 /** 096 * 097 * @param forceLocalData Whether to use a local installation or a remote installation 098 * @return 099 * @see #getSCOP(String, boolean) 100 */ 101 public static ScopDatabase getSCOP(boolean forceLocalData) { 102 return getSCOP(defaultVersion, forceLocalData); 103 } 104 105 /** 106 * requests a particular version of SCOP. 107 * 108 * Where possible, this will be the current default instance. 109 * Otherwise a new instance will be created. 110 * @param version 111 * @return 112 */ 113 public static ScopDatabase getSCOP(String version){ 114 // Default to a remote installation 115 return getSCOP(version,false); 116 } 117 118 /** 119 * Gets an instance of the specified scop version. 120 * 121 * <p> 122 * The particular implementation returned is influenced by the <tt>forceLocalData</tt> 123 * parameter. When false, the instance returned will generally be a 124 * {@link RemoteScopInstallation}, although this may be influenced by 125 * previous calls to this class. When true, the result is guaranteed to 126 * implement {@link LocalScopDatabase} (generally a {@link BerkeleyScopInstallation}). 127 * 128 * <p> 129 * Note that 130 * @param version A version number, such as {@link #VERSION_1_75A} 131 * @param forceLocalData Whether to use a local installation or a remote installation 132 * @return an 133 */ 134 public static ScopDatabase getSCOP(String version, boolean forceLocalData){ 135 if( version == null ) { 136 version = defaultVersion; 137 } 138 ScopDatabase scop = versionedScopDBs.get(version); 139 if ( forceLocalData) { 140 // Use a local installation 141 if( scop == null || !(scop instanceof LocalScopDatabase) ) { 142 logger.info("Creating new {}, version {}", BerkeleyScopInstallation.class.getSimpleName(), version); 143 BerkeleyScopInstallation berkeley = new BerkeleyScopInstallation(); 144 berkeley.setScopVersion(version); 145 versionedScopDBs.put(version,berkeley); 146 return berkeley; 147 } 148 return scop; 149 } else { 150 // Use a remote installation 151 if( scop == null ) { 152 logger.info("Creating new {}, version {}", RemoteScopInstallation.class.getSimpleName(), version); 153 scop = new RemoteScopInstallation(); 154 scop.setScopVersion(version); 155 versionedScopDBs.put(version,scop); 156 } 157 return scop; 158 } 159 } 160 161 162 /** 163 * Set the default scop version 164 * @param version A version number, such as {@link #VERSION_1_75A} 165 */ 166 public static void setScopDatabase(String version) { 167 getSCOP(version); 168 defaultVersion = version; 169 } 170 171 /** 172 * Set the default scop version 173 * @param version A version number, such as {@link #VERSION_1_75A} 174 * @param forceLocalData Whether to use a local installation or a remote installation 175 */ 176 public static void setScopDatabase(String version, boolean forceLocalData) { 177 logger.debug("ScopFactory: Setting ScopDatabase to version: {}, forced local: {}", version, forceLocalData); 178 getSCOP(version,forceLocalData); 179 defaultVersion = version; 180 } 181 182 /** 183 * Set the default scop version and instance 184 * @param scop 185 */ 186 public static void setScopDatabase(ScopDatabase scop){ 187 logger.debug("ScopFactory: Setting ScopDatabase to type: {}", scop.getClass().getName()); 188 defaultVersion = scop.getScopVersion(); 189 versionedScopDBs.put(defaultVersion,scop); 190 } 191}