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 * Created on Aug 30, 2011 021 * Created by Andreas Prlic 022 * 023 * @since 3.0.2 024 */ 025package org.biojava.nbio.structure.scop; 026 027import org.biojava.nbio.structure.align.client.JFatCatClient; 028import org.biojava.nbio.structure.align.util.HTTPConnectionTools; 029import org.biojava.nbio.structure.scop.server.ScopDescriptions; 030import org.biojava.nbio.structure.scop.server.ScopDomains; 031import org.biojava.nbio.structure.scop.server.ScopNodes; 032import org.biojava.nbio.structure.scop.server.XMLUtil; 033 034import java.io.IOException; 035import java.io.InputStream; 036import java.net.URL; 037import java.util.List; 038 039 040/** A class that fetches information about SCOP from a remote data-source. It requires port 80 to open for HTTP connection. 041 * 042 * @author Andreas Prlic 043 * 044 */ 045public class RemoteScopInstallation implements ScopDatabase { 046 047 public static final String DEFAULT_SERVER = "http://source.rcsb.org/jfatcatserver/domains/"; 048 049 String server = DEFAULT_SERVER; 050 051 private String version = null; 052 053 public static void main(String[] args){ 054 055 ScopDatabase scop = new RemoteScopInstallation(); 056 ScopFactory.setScopDatabase(scop); 057 058 //System.out.println(scop.getByCategory(ScopCategory.Superfamily)); 059 060 System.out.println(scop.getDomainsForPDB("4HHB")); 061 } 062 063 064 public String getServer() { 065 return server; 066 } 067 068 public void setServer(String server) { 069 this.server = server; 070 } 071 072 @Override 073 public List<ScopDescription> getByCategory(ScopCategory category) { 074 List<ScopDescription> results = null; 075 try { 076 URL u = new URL(server + "getByCategory?category="+category+"&version="+getScopVersion()); 077 InputStream response = HTTPConnectionTools.getInputStream(u); 078 String xml = JFatCatClient.convertStreamToString(response); 079 080 if(! xml.trim().isEmpty()) { 081 ScopDescriptions container = ScopDescriptions.fromXML(xml); 082 results = container.getScopDescription(); 083 } 084 } catch (IOException e) { 085 throw new RuntimeException("Unable to reach "+ server + "getByCategory?category="+category+"&version="+getScopVersion(), e); 086 } 087 return results; 088 } 089 090 @Override 091 public List<ScopDescription> filterByClassificationId(String query) { 092 List<ScopDescription> results = null; 093 try { 094 URL u = new URL(server + "filterByClassificationId?query="+query+"&version="+getScopVersion()); 095 InputStream response = HTTPConnectionTools.getInputStream(u); 096 String xml = JFatCatClient.convertStreamToString(response); 097 098 if(! xml.trim().isEmpty()) { 099 ScopDescriptions container = ScopDescriptions.fromXML(xml); 100 results = container.getScopDescription(); 101 } 102 } catch (Exception e){ 103 throw new RuntimeException("Unable to reach "+ server + "filterByClassificationId?query="+query+"&version="+getScopVersion(), e); 104 } 105 return results; 106 } 107 108 @Override 109 public List<ScopNode> getTree(ScopDomain domain) { 110 List<ScopNode> results = null; 111 try { 112 URL u = new URL(server + "getTree?scopId="+domain.getScopId()+"&version="+getScopVersion()); 113 InputStream response = HTTPConnectionTools.getInputStream(u); 114 String xml = JFatCatClient.convertStreamToString(response); 115 116 if(! xml.trim().isEmpty()) { 117 ScopNodes container = ScopNodes.fromXML(xml); 118 results = container.getScopNode(); 119 } 120 } catch (Exception e){ 121 throw new RuntimeException("Unable to reach "+ server + "getTree?scopId="+domain.getScopId()+"&version="+getScopVersion(), e); 122 } 123 return results; 124 } 125 126 @Override 127 public List<ScopDomain> filterByDomainName(String query) { 128 query = query.trim(); 129 List<ScopDomain> results = null; 130 try { 131 URL u = new URL(server + "filterByDomainName?query="+query+"&version="+getScopVersion()); 132 //System.out.println(u); 133 InputStream response = HTTPConnectionTools.getInputStream(u); 134 String xml = JFatCatClient.convertStreamToString(response); 135 136 if(! xml.trim().isEmpty()) { 137 ScopDomains container = ScopDomains.fromXML(xml); 138 results = container.getScopDomain(); 139 } 140 } catch (Exception e){ 141 throw new RuntimeException("Unable to reach "+ server + "filterByDomainName?query="+query+"&version="+getScopVersion(), e); 142 } 143 return results; 144 } 145 146 @Override 147 public List<ScopDescription> filterByDescription(String query) { 148 List<ScopDescription> results = null; 149 try { 150 URL u = new URL(server + "filterByDescription?query="+query+"&version="+getScopVersion()); 151 InputStream response = HTTPConnectionTools.getInputStream(u); 152 String xml = JFatCatClient.convertStreamToString(response); 153 154 if(! xml.trim().isEmpty()) { 155 ScopDescriptions container = ScopDescriptions.fromXML(xml); 156 results = container.getScopDescription(); 157 } 158 } catch (Exception e){ 159 throw new RuntimeException("Unable to reach "+ server + "filterByDescription?query="+query+"&version="+getScopVersion(), e); 160 } 161 return results; 162 } 163 164 @Override 165 public ScopDescription getScopDescriptionBySunid(int sunid) { 166 167 ScopDescription desc = null; 168 169 170 try { 171 172 URL u = new URL(server + "getScopDescriptionBySunid?sunid="+sunid+"&version="+getScopVersion()); 173 InputStream response = HTTPConnectionTools.getInputStream(u); 174 String xml = JFatCatClient.convertStreamToString(response); 175 176 if(! xml.trim().isEmpty()) { 177 desc = XMLUtil.getScopDescriptionFromXML(xml); 178 } 179 180 } catch (Exception e){ 181 throw new RuntimeException("Unable to reach "+ server + "getScopDescriptionBySunid?sunid="+sunid+"&version="+getScopVersion(), e); 182 } 183 return desc; 184 } 185 186 @Override 187 public List<ScopDomain> getDomainsForPDB(String pdbId) { 188 List<ScopDomain> results = null; 189 try { 190 URL u = new URL(server + "getDomainsForPDB?pdbId="+pdbId+"&version="+getScopVersion()); 191 InputStream response = HTTPConnectionTools.getInputStream(u); 192 String xml = JFatCatClient.convertStreamToString(response); 193 194 if( !xml.trim().isEmpty()) { 195 ScopDomains container = ScopDomains.fromXML(xml); 196 results = container.getScopDomain(); 197 } 198 } catch (Exception e){ 199 throw new RuntimeException("Unable to reach "+ server + "getDomainsForPDB?pdbId="+pdbId+"&version="+getScopVersion(), e); 200 } 201 return results; 202 } 203 204 private ScopDomain requestRemoteDomainByScopID(String scopId) 205 throws IOException{ 206 scopId = scopId.trim(); 207 URL u = new URL(server + "getDomainByScopID?scopId="+scopId+"&version="+getScopVersion()); 208 InputStream response = HTTPConnectionTools.getInputStream(u); 209 String xml = JFatCatClient.convertStreamToString(response); 210 211 if( !xml.trim().isEmpty()) { 212 return XMLUtil.getScopDomainFromXML(xml); 213 } 214 return null; 215 } 216 217 @Override 218 public ScopDomain getDomainByScopID(String scopId) { 219 try { 220 return requestRemoteDomainByScopID(scopId); 221 } catch (Exception e){ 222 throw new RuntimeException("Unable to reach "+ server + "getDomainByScopID?scopId="+scopId+"&version="+getScopVersion(), e); 223 } 224 } 225 226 @Override 227 public ScopNode getScopNode(int sunid) { 228 ScopNode desc = null; 229 try { 230 URL u = new URL(server + "getScopNode?sunid="+sunid+"&version="+getScopVersion()); 231 InputStream response = HTTPConnectionTools.getInputStream(u); 232 String xml = JFatCatClient.convertStreamToString(response); 233 234 if( !xml.trim().isEmpty()) { 235 desc = XMLUtil.getScopNodeFromXML(xml); 236 } 237 } catch (Exception e){ 238 throw new RuntimeException("Unable to reach "+ server + "getScopNode?sunid="+sunid+"&version="+getScopVersion(), e); 239 } 240 return desc; 241 } 242 243 @Override 244 public String getScopVersion() { 245 // If no version is set, request the default version from the website 246 if( version == null) { 247 try { 248 URL u = new URL(server + "getScopVersion"); 249 InputStream response = HTTPConnectionTools.getInputStream(u); 250 version = JFatCatClient.convertStreamToString(response); 251 if( version != null) 252 version = version.trim(); 253 254 } catch (Exception e){ 255 throw new RuntimeException("Unable to reach "+ server + "getScopVersion", e); 256 } 257 } 258 return version; 259 } 260 261 @Override 262 public void setScopVersion(String version) { 263 this.version = version; 264 } 265 266 @Override 267 public List<ScopDomain> getScopDomainsBySunid(Integer sunid) { 268 List<ScopDomain> results = null; 269 try { 270 URL u = new URL(server + "getScopDomainsBySunid?sunid="+sunid+"&version="+getScopVersion()); 271 InputStream response = HTTPConnectionTools.getInputStream(u); 272 String xml = JFatCatClient.convertStreamToString(response); 273 274 if( !xml.trim().isEmpty()) { 275 ScopDomains container = ScopDomains.fromXML(xml); 276 results = container.getScopDomain(); 277 } 278 } catch (Exception e){ 279 throw new RuntimeException("Unable to reach "+ server + "getScopDomainsBySunid?sunid="+sunid+"&version="+getScopVersion(), e); 280 } 281 return results; 282 } 283 284 285 @Override 286 public List<String> getComments(int sunid) { 287 List<String> results = null; 288 try { 289 URL u = new URL(server + "getComments?sunid="+sunid+"&version="+getScopVersion()); 290 InputStream response = HTTPConnectionTools.getInputStream(u); 291 String xml = JFatCatClient.convertStreamToString(response); 292 293 if( !xml.trim().isEmpty()) { 294 results = XMLUtil.getCommentsFromXML(xml); 295 } 296 } catch (Exception e){ 297 throw new RuntimeException("Unable to reach "+ server + "getComments?sunid="+sunid+"&version="+getScopVersion(), e); 298 } 299 return results; 300 } 301 302}