src/jalview/io/DasSequenceFeatureFetcher.java

   1 /*\r
   2 * Jalview - A Sequence Alignment Editor and Viewer\r
   3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4 *\r
   5 * This program is free software; you can redistribute it and/or\r
   6 * modify it under the terms of the GNU General Public License\r
   7 * as published by the Free Software Foundation; either version 2\r
   8 * of the License, or (at your option) any later version.\r
   9 *\r
  10 * This program is distributed in the hope that it will be useful,\r
  11 * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13 * GNU General Public License for more details.\r
  14 *\r
  15 * You should have received a copy of the GNU General Public License\r
  16 * along with this program; if not, write to the Free Software\r
  17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18 */\r
  19 package jalview.io;\r
  20 \r
  21 import jalview.datamodel.*;\r
  22 \r
  23 import jalview.gui.*;\r
  24 \r
  25 import java.util.*;\r
  26 \r
  27 import java.net.URL;\r
  28 \r
  29 import org.biojava.dasobert.das.FeatureThread;\r
  30 import org.biojava.dasobert.dasregistry.Das1Source;\r
  31 import org.biojava.dasobert.eventmodel.FeatureEvent;\r
  32 import org.biojava.dasobert.eventmodel.FeatureListener;\r
  33 import org.biojava.services.das.registry.DasRegistryAxisClient;\r
  34 import org.biojava.services.das.registry.DasSource;\r
  35 \r
  36 \r
  37 import jalview.bin.Cache;\r
  38 \r
  39 \r
  40 /**\r
  41  * DOCUMENT ME!\r
  42  *\r
  43  * @author $author$\r
  44  * @version $Revision$\r
  45  */\r
  46 public class DasSequenceFeatureFetcher implements Runnable\r
  47 {\r
  48   final AlignmentI dataset;\r
  49   final AlignmentPanel ap;\r
  50   StringBuffer sbuffer = new StringBuffer();\r
  51 \r
  52 \r
  53 \r
  54   /**\r
  55    * Creates a new SequenceFeatureFetcher object.\r
  56    *\r
  57    * @param align DOCUMENT ME!\r
  58    * @param ap DOCUMENT ME!\r
  59    */\r
  60   public DasSequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
  61   {\r
  62     this.dataset = align.getDataset();\r
  63     this.ap = ap;\r
  64 \r
  65     Thread thread = new Thread(this);\r
  66     thread.start();\r
  67   }\r
  68   /**\r
  69    * creates a jalview sequence feature from a das feature document\r
  70    * @param dasfeature\r
  71    * @return sequence feature object created using dasfeature information\r
  72    */\r
  73   SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
  74   {\r
  75           try {\r
  76                 /**\r
  77            * Different qNames for a DAS Feature - are string keys to the HashMaps in features\r
  78            * "METHOD") ||\r
  79            qName.equals("TYPE") ||\r
  80            qName.equals("START") ||\r
  81            qName.equals("END") ||\r
  82            qName.equals("NOTE") ||\r
  83            qName.equals("LINK") ||\r
  84            qName.equals("SCORE")\r
  85            */\r
  86                   String desc = new String();\r
  87                   if (dasfeature.containsKey("NOTE"))\r
  88                                 desc+=(String) dasfeature.get("NOTE");\r
  89 \r
  90 \r
  91                   int start = 0, end = 0;\r
  92                   float score = 0f;\r
  93 \r
  94                   try{ start = Integer.parseInt( dasfeature.get("START").toString()); }\r
  95                   catch( Exception ex){}\r
  96                   try{ end = Integer.parseInt( dasfeature.get("END").toString()); }\r
  97                   catch (Exception ex){}\r
  98                   try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }\r
  99                   catch (Exception ex){}\r
 100 \r
 101 \r
 102                   SequenceFeature f = new SequenceFeature(\r
 103                                   (String) dasfeature.get("TYPE"),\r
 104                                   desc,\r
 105                                   start,\r
 106                                   end,\r
 107                                   score,\r
 108                                   nickname);\r
 109 \r
 110                   if (dasfeature.containsKey("LINK"))\r
 111                  {\r
 112                       f.addLink(f.getType()+" "+f.begin+"_"+f.end\r
 113                                 +"|"+ dasfeature.get("LINK"));\r
 114                   }\r
 115                   // (String) dasfeature.get("ID"),\r
 116                   ////  (String) dasfeature.get("METHOD"),\r
 117                                 //  (String) dasfeature.get("SCORE"),\r
 118                                 //  null\r
 119                         // );\r
 120 \r
 121                      // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
 122           return f;\r
 123           }\r
 124           catch (Exception e) {\r
 125             e.printStackTrace();\r
 126                   Cache.log.debug("Failed to parse "+dasfeature.toString(), e);\r
 127                   return null;\r
 128           }\r
 129   }\r
 130   /**\r
 131    * fetch and add das features to a sequence using the given source URL and Id to create a feature request\r
 132    * @param seq\r
 133    * @param SourceUrl\r
 134    * @param id\r
 135    */\r
 136   protected void createFeatureFetcher(final Sequence seq,\r
 137                                       final String sourceUrl,\r
 138                                       String id,\r
 139                                       String nickname)  {\r
 140           //////////////\r
 141           /// fetch DAS features\r
 142           final Das1Source source = new Das1Source();\r
 143           source.setUrl(sourceUrl);\r
 144           source.setNickname(nickname);\r
 145 \r
 146 \r
 147           Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
 148                           sourceUrl);\r
 149           if (id != null && id.length() > 0)\r
 150           {\r
 151             FeatureThread fetcher = new FeatureThread(id + ":" + seq.getStart() + "," +seq.getEnd()\r
 152                 , source);\r
 153 \r
 154             fetcher.addFeatureListener(new FeatureListener()\r
 155             {\r
 156               public void comeBackLater(FeatureEvent e)\r
 157               {\r
 158                 Cache.log.debug("das source " + e.getDasSource().getNickname() +\r
 159                                 " asked us to come back in " + e.getComeBackLater() +\r
 160                                 " secs.");\r
 161               }\r
 162 \r
 163               public void newFeatures(FeatureEvent e)\r
 164               {\r
 165                 Das1Source ds = e.getDasSource();\r
 166 \r
 167                 Map[] features = e.getFeatures();\r
 168                 // add features to sequence\r
 169                 Cache.log.debug("das source " + ds.getUrl() + " returned " +\r
 170                                 features.length + " features");\r
 171 \r
 172                 if (features.length > 0)\r
 173                 {\r
 174                   for (int i = 0; i < features.length; i++)\r
 175                   {\r
 176                     SequenceFeature f = newSequenceFeature(features[i],\r
 177                         source.getNickname());\r
 178 \r
 179                       System.out.println(source.getNickname()+" "+f.getType()+" "+\r
 180                                          f.begin+" "+f.end);\r
 181 \r
 182                       seq.addSequenceFeature(f);\r
 183                   }\r
 184                 }\r
 185               }\r
 186 \r
 187             }\r
 188 \r
 189             );\r
 190 \r
 191             //NOTE alignPanel listener will be called after the previous\r
 192             //anonymous listener!!!\r
 193             fetcher.addFeatureListener(ap);\r
 194 \r
 195             fetcher.start();\r
 196           }\r
 197   }\r
 198   /**\r
 199    * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset\r
 200    */\r
 201   public void run()\r
 202   {\r
 203     DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
 204 \r
 205     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");\r
 206     StringTokenizer st = new StringTokenizer(active, "\t");\r
 207     Vector selectedSources = new Vector();\r
 208     String token;\r
 209     while (st.hasMoreTokens())\r
 210     {\r
 211       token = st.nextToken();\r
 212       for(int i=0; i<sources.length; i++)\r
 213       {\r
 214         if(sources[i].getNickname().equals(token))\r
 215         {\r
 216           selectedSources.addElement(sources[i]);\r
 217           break;\r
 218         }\r
 219       }\r
 220     }\r
 221  // DasSource test = new DasSource();\r
 222  // test.setUrl("http://localhost:8080/das/gffdb/");\r
 223   //test.setNickname("Trixkid");\r
 224  // selectedSources.addElement(test);\r
 225 \r
 226 \r
 227     if(selectedSources == null || selectedSources.size()==0)\r
 228     {\r
 229       System.out.println("No DAS Sources active");\r
 230       return;\r
 231     }\r
 232 \r
 233     try\r
 234     {\r
 235       int seqIndex = 0;\r
 236       Vector sequences = dataset.getSequences();\r
 237       while (seqIndex < sequences.size())\r
 238       {\r
 239           Sequence sequence = (Sequence) sequences.get(seqIndex);\r
 240           Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),\r
 241               new String[]  {\r
 242               jalview.datamodel.DBRefSource.PDB,\r
 243               jalview.datamodel.DBRefSource.UNIPROT});\r
 244 \r
 245           for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)\r
 246           {\r
 247             DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);\r
 248 \r
 249             if (uprefs != null)\r
 250             {\r
 251               // we know the id for this entry, so don't note its ID in the unknownSequences list\r
 252               for (int j = 0, k = uprefs.size(); j < k; j++)\r
 253               {\r
 254                 // Will have to pass any mapping information to the fetcher - the start/end for the DBRefEntry may not be the same as the sequence's start/end\r
 255                 org.biojava.services.das.registry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
 256                 for (int l=0; l<cs.length; l++) {\r
 257                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)\r
 258                       uprefs.get(j)))\r
 259                   {\r
 260                     Cache.log.debug("Launched fetcher for coordinate system " +\r
 261                                     cs[l].getName());\r
 262                     createFeatureFetcher(sequence,\r
 263                                          dasSource.getUrl(),\r
 264                                          ( (DBRefEntry) uprefs.get(j)).\r
 265                                          getAccessionId(),\r
 266                                          dasSource.getNickname());\r
 267                   }\r
 268                 }\r
 269               }\r
 270             }\r
 271             else\r
 272             {\r
 273               String id = null;\r
 274               // try and use the name as the sequence id\r
 275               if (sequence.getName().indexOf("|") > -1)\r
 276               {\r
 277                 id = sequence.getName().substring(\r
 278                     sequence.getName().lastIndexOf("|") + 1);\r
 279               }\r
 280               else\r
 281               {\r
 282                 id = sequence.getName();\r
 283               }\r
 284               if (id != null)\r
 285               {\r
 286                 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references\r
 287                 createFeatureFetcher(sequence,\r
 288                                      dasSource.getUrl(),\r
 289                                      id,\r
 290                                      dasSource.getNickname());\r
 291               }\r
 292             }\r
 293           }\r
 294 \r
 295           seqIndex++;\r
 296     }\r
 297     }\r
 298     catch (Exception ex)\r
 299     {\r
 300       ex.printStackTrace();\r
 301     }\r
 302   }\r
 303 \r
 304 \r
 305  public static DasSource[] getDASSources()\r
 306   {\r
 307     try\r
 308     {\r
 309       String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
 310           "http://servlet.sanger.ac.uk/dasregistry/services/das_registry");\r
 311 \r
 312 \r
 313       URL url = new URL(registryURL);\r
 314 \r
 315       DasRegistryAxisClient client = new DasRegistryAxisClient(url);\r
 316 \r
 317       DasSource[] services = client.listServices();\r
 318 \r
 319       return services;\r
 320     }\r
 321     catch (Exception ex)\r
 322     {\r
 323       ex.printStackTrace();\r
 324     }\r
 325     return null;\r
 326 \r
 327   }\r
 328 }\r
 329 \r
 330 \r