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 /**\r
  42  * DOCUMENT ME!\r
  43  *\r
  44  * @author $author$\r
  45  * @version $Revision$\r
  46  */\r
  47 public class DasSequenceFeatureFetcher implements Runnable\r
  48 {\r
  49   final AlignmentI dataset;\r
  50   final AlignmentPanel ap;\r
  51   StringBuffer sbuffer = new StringBuffer();\r
  52 \r
  53 \r
  54 \r
  55   /**\r
  56    * Creates a new SequenceFeatureFetcher object.\r
  57    *\r
  58    * @param align DOCUMENT ME!\r
  59    * @param ap DOCUMENT ME!\r
  60    */\r
  61   public DasSequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
  62   {\r
  63     this.dataset = align.getDataset();\r
  64     this.ap = ap;\r
  65 \r
  66     Thread thread = new Thread(this);\r
  67     thread.start();\r
  68   }\r
  69   /**\r
  70    * creates a jalview sequence feature from a das feature document\r
  71    * @param dasfeature\r
  72    * @return sequence feature object created using dasfeature information\r
  73    */\r
  74   SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
  75   {\r
  76           try {\r
  77                 /**\r
  78            * Different qNames for a DAS Feature - are string keys to the HashMaps in features\r
  79            * "METHOD") ||\r
  80            qName.equals("TYPE") ||\r
  81            qName.equals("START") ||\r
  82            qName.equals("END") ||\r
  83            qName.equals("NOTE") ||\r
  84            qName.equals("LINK") ||\r
  85            qName.equals("SCORE")\r
  86            */\r
  87                   String desc = new String();\r
  88                   if (dasfeature.containsKey("NOTE"))\r
  89                                 desc+=(String) dasfeature.get("NOTE");\r
  90 \r
  91 \r
  92                   int start = 0, end = 0;\r
  93                   float score = 0f;\r
  94 \r
  95                   try{ start = Integer.parseInt( dasfeature.get("START").toString()); }\r
  96                   catch( Exception ex){}\r
  97                   try{ end = Integer.parseInt( dasfeature.get("END").toString()); }\r
  98                   catch (Exception ex){}\r
  99                   try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }\r
 100                   catch (Exception ex){}\r
 101 \r
 102 \r
 103                   SequenceFeature f = new SequenceFeature(\r
 104                                   (String) dasfeature.get("TYPE"),\r
 105                                   desc,\r
 106                                   start,\r
 107                                   end,\r
 108                                   score,\r
 109                                   nickname);\r
 110 \r
 111                   if (dasfeature.containsKey("LINK"))\r
 112                  {\r
 113                       f.addLink(f.getType()+" "+f.begin+"_"+f.end\r
 114                                 +"|"+ dasfeature.get("LINK"));\r
 115                   }\r
 116                   // (String) dasfeature.get("ID"),\r
 117                   ////  (String) dasfeature.get("METHOD"),\r
 118                                 //  (String) dasfeature.get("SCORE"),\r
 119                                 //  null\r
 120                         // );\r
 121 \r
 122                      // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
 123           return f;\r
 124           }\r
 125           catch (Exception e) {\r
 126             e.printStackTrace();\r
 127                   Cache.log.debug("Failed to parse "+dasfeature.toString(), e);\r
 128                   return null;\r
 129           }\r
 130   }\r
 131   /**\r
 132    * fetch and add das features to a sequence using the given source URL and Id to create a feature request\r
 133    * @param seq\r
 134    * @param SourceUrl\r
 135    * @param id\r
 136    */\r
 137   protected void createFeatureFetcher(final Sequence seq,\r
 138                                       final String sourceUrl,\r
 139                                       String id,\r
 140                                       String nickname)  {\r
 141           //////////////\r
 142           /// fetch DAS features\r
 143           final Das1Source source = new Das1Source();\r
 144           source.setUrl(sourceUrl);\r
 145           source.setNickname(nickname);\r
 146 \r
 147 \r
 148           Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
 149                           sourceUrl);\r
 150           if (id != null && id.length() > 0)\r
 151           {\r
 152             FeatureThread fetcher = new FeatureThread(id + ":" + seq.getStart() + "," +seq.getEnd()\r
 153                 , source);\r
 154 \r
 155             fetcher.addFeatureListener(new FeatureListener()\r
 156             {\r
 157               public void comeBackLater(FeatureEvent e)\r
 158               {\r
 159                 Cache.log.debug("das source " + e.getDasSource().getNickname() +\r
 160                                 " asked us to come back in " + e.getComeBackLater() +\r
 161                                 " secs.");\r
 162               }\r
 163 \r
 164               public void newFeatures(FeatureEvent e)\r
 165               {\r
 166                 Das1Source ds = e.getDasSource();\r
 167 \r
 168                 Map[] features = e.getFeatures();\r
 169                 // add features to sequence\r
 170                 Cache.log.debug("das source " + ds.getUrl() + " returned " +\r
 171                                 features.length + " features");\r
 172 \r
 173 \r
 174                 if (features.length > 0)\r
 175                 {\r
 176                   for (int i = 0; i < features.length; i++)\r
 177                   {\r
 178 \r
 179                     SequenceFeature f = newSequenceFeature(features[i],\r
 180                         source.getNickname());\r
 181 \r
 182                     if (seq.sequenceFeatures != null)\r
 183                     {\r
 184                       for (int j = 0; (f != null) && j < seq.sequenceFeatures.length;\r
 185                            j++)\r
 186                       {\r
 187                         if (seq.sequenceFeatures[j].equals(f))\r
 188                         {\r
 189                           f = null;\r
 190                         }\r
 191                       }\r
 192                     }\r
 193                     if (f != null)\r
 194                     {\r
 195                       seq.addSequenceFeature(f);\r
 196                     }\r
 197                   }\r
 198                 }\r
 199               }\r
 200 \r
 201             }\r
 202 \r
 203             );\r
 204 \r
 205             //NOTE alignPanel listener will be called after the previous\r
 206             //anonymous listener!!!\r
 207             fetcher.addFeatureListener(ap);\r
 208 \r
 209             fetcher.start();\r
 210           }\r
 211   }\r
 212   /**\r
 213    * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset\r
 214    */\r
 215   public void run()\r
 216   {\r
 217     DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
 218 \r
 219     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");\r
 220     StringTokenizer st = new StringTokenizer(active, "\t");\r
 221     Vector selectedSources = new Vector();\r
 222     String token;\r
 223     while (st.hasMoreTokens())\r
 224     {\r
 225       token = st.nextToken();\r
 226       for(int i=0; i<sources.length; i++)\r
 227       {\r
 228         if(sources[i].getNickname().equals(token))\r
 229         {\r
 230           selectedSources.addElement(sources[i]);\r
 231           break;\r
 232         }\r
 233       }\r
 234     }\r
 235  // DasSource test = new DasSource();\r
 236  // test.setUrl("http://localhost:8080/das/gffdb/");\r
 237   //test.setNickname("Trixkid");\r
 238  // selectedSources.addElement(test);\r
 239 \r
 240 \r
 241     if(selectedSources == null || selectedSources.size()==0)\r
 242     {\r
 243       System.out.println("No DAS Sources active");\r
 244       return;\r
 245     }\r
 246 \r
 247     try\r
 248     {\r
 249       int seqIndex = 0;\r
 250       Vector sequences = dataset.getSequences();\r
 251       while (seqIndex < sequences.size())\r
 252       {\r
 253           Sequence sequence = (Sequence) sequences.get(seqIndex);\r
 254           Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),\r
 255               new String[]  {\r
 256               jalview.datamodel.DBRefSource.PDB,\r
 257               jalview.datamodel.DBRefSource.UNIPROT});\r
 258 \r
 259           for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)\r
 260           {\r
 261             DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);\r
 262 \r
 263             if (uprefs != null)\r
 264             {\r
 265               // we know the id for this entry, so don't note its ID in the unknownSequences list\r
 266               for (int j = 0, k = uprefs.size(); j < k; j++)\r
 267               {\r
 268                 // 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
 269                 org.biojava.services.das.registry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
 270                 for (int l=0; l<cs.length; l++) {\r
 271                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)\r
 272                       uprefs.get(j)))\r
 273                   {\r
 274                     Cache.log.debug("Launched fetcher for coordinate system " +\r
 275                                     cs[l].getName());\r
 276                     createFeatureFetcher(sequence,\r
 277                                          dasSource.getUrl(),\r
 278                                          ( (DBRefEntry) uprefs.get(j)).\r
 279                                          getAccessionId(),\r
 280                                          dasSource.getNickname());\r
 281                   }\r
 282                 }\r
 283               }\r
 284             }\r
 285             else\r
 286             {\r
 287               String id = null;\r
 288               // try and use the name as the sequence id\r
 289               if (sequence.getName().indexOf("|") > -1)\r
 290               {\r
 291                 id = sequence.getName().substring(\r
 292                     sequence.getName().lastIndexOf("|") + 1);\r
 293               }\r
 294               else\r
 295               {\r
 296                 id = sequence.getName();\r
 297               }\r
 298               if (id != null)\r
 299               {\r
 300                 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references\r
 301                 createFeatureFetcher(sequence,\r
 302                                      dasSource.getUrl(),\r
 303                                      id,\r
 304                                      dasSource.getNickname());\r
 305               }\r
 306             }\r
 307           }\r
 308 \r
 309           seqIndex++;\r
 310     }\r
 311     }\r
 312     catch (Exception ex)\r
 313     {\r
 314       ex.printStackTrace();\r
 315     }\r
 316   }\r
 317 \r
 318 \r
 319  public static DasSource[] getDASSources()\r
 320   {\r
 321     try\r
 322     {\r
 323       String registryURL = jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
 324           "http://servlet.sanger.ac.uk/dasregistry/services/das_registry");\r
 325 \r
 326 \r
 327       URL url = new URL(registryURL);\r
 328 \r
 329       DasRegistryAxisClient client = new DasRegistryAxisClient(url);\r
 330 \r
 331       DasSource[] services = client.listServices();\r
 332 \r
 333       return services;\r
 334     }\r
 335     catch (Exception ex)\r
 336     {\r
 337       ex.printStackTrace();\r
 338     }\r
 339     return null;\r
 340 \r
 341   }\r
 342 \r
 343 }\r
 344 \r
 345 \r