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.dasobert.dasregistry.DasSource;\r
  34 \r
  35 import org.biojava.dasobert.das2.io.DasSourceReaderImpl;\r
  36 import org.biojava.dasobert.dasregistry.Das1Source;\r
  37 import org.biojava.dasobert.dasregistry.DasSource;\r
  38 import org.biojava.dasobert.das2.Das2Source;\r
  39 import org.biojava.dasobert.das2.DasSourceConverter;\r
  40 \r
  41 \r
  42 import jalview.bin.Cache;\r
  43 \r
  44 \r
  45 /**\r
  46  * DOCUMENT ME!\r
  47  *\r
  48  * @author $author$\r
  49  * @version $Revision$\r
  50  */\r
  51 public class DasSequenceFeatureFetcher implements Runnable\r
  52 {\r
  53   final AlignmentI dataset;\r
  54   final AlignFrame af;\r
  55   StringBuffer sbuffer = new StringBuffer();\r
  56 \r
  57 \r
  58 \r
  59   /**\r
  60    * Creates a new SequenceFeatureFetcher object.\r
  61    *\r
  62    * @param align DOCUMENT ME!\r
  63    * @param ap DOCUMENT ME!\r
  64    */\r
  65   public DasSequenceFeatureFetcher(AlignmentI align,\r
  66                                    AlignFrame af)\r
  67   {\r
  68     this.dataset = align.getDataset();\r
  69     this.af = af;\r
  70 \r
  71     Thread thread = new Thread(this);\r
  72     thread.start();\r
  73   }\r
  74   /**\r
  75    * creates a jalview sequence feature from a das feature document\r
  76    * @param dasfeature\r
  77    * @return sequence feature object created using dasfeature information\r
  78    */\r
  79   SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
  80   {\r
  81           try {\r
  82                 /**\r
  83            * Different qNames for a DAS Feature - are string keys to the HashMaps in features\r
  84            * "METHOD") ||\r
  85            qName.equals("TYPE") ||\r
  86            qName.equals("START") ||\r
  87            qName.equals("END") ||\r
  88            qName.equals("NOTE") ||\r
  89            qName.equals("LINK") ||\r
  90            qName.equals("SCORE")\r
  91            */\r
  92                   String desc = new String();\r
  93                   if (dasfeature.containsKey("NOTE"))\r
  94                                 desc+=(String) dasfeature.get("NOTE");\r
  95 \r
  96 \r
  97                   int start = 0, end = 0;\r
  98                   float score = 0f;\r
  99 \r
 100                   try{ start = Integer.parseInt( dasfeature.get("START").toString()); }\r
 101                   catch( Exception ex){}\r
 102                   try{ end = Integer.parseInt( dasfeature.get("END").toString()); }\r
 103                   catch (Exception ex){}\r
 104                   try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }\r
 105                   catch (Exception ex){}\r
 106 \r
 107 \r
 108                   SequenceFeature f = new SequenceFeature(\r
 109                                   (String) dasfeature.get("TYPE"),\r
 110                                   desc,\r
 111                                   start,\r
 112                                   end,\r
 113                                   score,\r
 114                                   nickname);\r
 115 \r
 116                   if (dasfeature.containsKey("LINK"))\r
 117                  {\r
 118                       f.addLink(f.getType()+" "+f.begin+"_"+f.end\r
 119                                 +"|"+ dasfeature.get("LINK"));\r
 120                   }\r
 121                   // (String) dasfeature.get("ID"),\r
 122                   ////  (String) dasfeature.get("METHOD"),\r
 123                                 //  (String) dasfeature.get("SCORE"),\r
 124                                 //  null\r
 125                         // );\r
 126 \r
 127                      // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
 128           return f;\r
 129           }\r
 130           catch (Exception e) {\r
 131             e.printStackTrace();\r
 132                   Cache.log.debug("Failed to parse "+dasfeature.toString(), e);\r
 133                   return null;\r
 134           }\r
 135   }\r
 136   /**\r
 137    * fetch and add das features to a sequence using the given source URL and Id to create a feature request\r
 138    * @param seq\r
 139    * @param SourceUrl\r
 140    * @param id\r
 141    */\r
 142   protected void createFeatureFetcher(final Sequence seq,\r
 143                                       final String sourceUrl,\r
 144                                       String id,\r
 145                                       String nickname)  {\r
 146           //////////////\r
 147           /// fetch DAS features\r
 148           final Das1Source source = new Das1Source();\r
 149           source.setUrl(sourceUrl);\r
 150           source.setNickname(nickname);\r
 151 \r
 152 \r
 153           Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
 154                           sourceUrl);\r
 155           if (id != null && id.length() > 0)\r
 156           {\r
 157             FeatureThread fetcher = new FeatureThread(id\r
 158                +  ":" + seq.getStart() + "," +seq.getEnd()\r
 159                  , source);\r
 160 \r
 161             fetcher.addFeatureListener(new FeatureListener()\r
 162             {\r
 163               public void comeBackLater(FeatureEvent e)\r
 164               {\r
 165                 Cache.log.debug("das source " + e.getDasSource().getNickname() +\r
 166                                 " asked us to come back in " + e.getComeBackLater() +\r
 167                                 " secs.");\r
 168               }\r
 169 \r
 170               public void newFeatures(FeatureEvent e)\r
 171               {\r
 172                 Das1Source ds = e.getDasSource();\r
 173 \r
 174                 Map[] features = e.getFeatures();\r
 175                 // add features to sequence\r
 176                 Cache.log.debug("das source " + ds.getUrl() + " returned " +\r
 177                                 features.length + " features");\r
 178 \r
 179                 if (features.length > 0)\r
 180                 {\r
 181                   for (int i = 0; i < features.length; i++)\r
 182                   {\r
 183                       SequenceFeature f = newSequenceFeature(features[i],\r
 184                         source.getNickname());\r
 185 \r
 186                       seq.addSequenceFeature(f);\r
 187                   }\r
 188                 }\r
 189                 else\r
 190                 {\r
 191                   System.out.println("No features found for sequence " +seq.getName()\r
 192                                      +" from: "+ e.getDasSource().getNickname());\r
 193                 }\r
 194 \r
 195               }\r
 196             }\r
 197 \r
 198             );\r
 199 \r
 200             //NOTE alignPanel listener will be called after the previous\r
 201             //anonymous listener!!!\r
 202             fetcher.addFeatureListener(af);\r
 203 \r
 204             fetcher.start();\r
 205           }\r
 206   }\r
 207   /**\r
 208    * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset\r
 209    */\r
 210   public void run()\r
 211   {\r
 212     long startTime = System.currentTimeMillis();\r
 213     af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
 214 \r
 215     DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
 216 \r
 217     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");\r
 218     StringTokenizer st = new StringTokenizer(active, "\t");\r
 219     Vector selectedSources = new Vector();\r
 220     String token;\r
 221     while (st.hasMoreTokens())\r
 222     {\r
 223       token = st.nextToken();\r
 224       for(int i=0; i<sources.length; i++)\r
 225       {\r
 226         if(sources[i].getNickname().equals(token))\r
 227         {\r
 228           selectedSources.addElement(sources[i]);\r
 229           break;\r
 230         }\r
 231       }\r
 232     }\r
 233 \r
 234 \r
 235     if(selectedSources == null || selectedSources.size()==0)\r
 236     {\r
 237       System.out.println("No DAS Sources active");\r
 238       af.setProgressBar("No DAS Sources Active", startTime);\r
 239       return;\r
 240     }\r
 241 \r
 242     try\r
 243     {\r
 244       int seqIndex = 0;\r
 245       Vector sequences = dataset.getSequences();\r
 246       while (seqIndex < sequences.size())\r
 247       {\r
 248           Sequence sequence = (Sequence) sequences.get(seqIndex);\r
 249           Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),\r
 250               new String[]  {\r
 251               jalview.datamodel.DBRefSource.PDB,\r
 252               jalview.datamodel.DBRefSource.UNIPROT});\r
 253 \r
 254           for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)\r
 255           {\r
 256             DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);\r
 257 \r
 258             if (uprefs != null)\r
 259             {\r
 260               // we know the id for this entry, so don't note its ID in the unknownSequences list\r
 261               for (int j = 0;  j < uprefs.size(); j++)\r
 262               {\r
 263 \r
 264                 // 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
 265                 org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
 266                 for (int l=0; l<cs.length; l++)\r
 267                 {\r
 268                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)\r
 269                       uprefs.get(j)))\r
 270                   {\r
 271                     Cache.log.debug("Launched fetcher for coordinate system " +\r
 272                                     cs[l].getName());\r
 273 \r
 274 \r
 275                     createFeatureFetcher(sequence,\r
 276                                          dasSource.getUrl(),\r
 277                                          ( (DBRefEntry) uprefs.get(j)).\r
 278                                          getAccessionId(),\r
 279                                          dasSource.getNickname());\r
 280                   }\r
 281                 }\r
 282               }\r
 283             }\r
 284             else\r
 285             {\r
 286               String id = null;\r
 287               // try and use the name as the sequence id\r
 288               if (sequence.getName().indexOf("|") > -1)\r
 289               {\r
 290                 id = sequence.getName().substring(\r
 291                     sequence.getName().lastIndexOf("|") + 1);\r
 292               }\r
 293               else\r
 294               {\r
 295                 id = sequence.getName();\r
 296               }\r
 297               if (id != null)\r
 298               {\r
 299                 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references\r
 300                 createFeatureFetcher(sequence,\r
 301                                      dasSource.getUrl(),\r
 302                                      id,\r
 303                                      dasSource.getNickname());\r
 304               }\r
 305             }\r
 306           }\r
 307 \r
 308           seqIndex++;\r
 309     }\r
 310     }\r
 311     catch (Exception ex)\r
 312     {\r
 313       ex.printStackTrace();\r
 314     }\r
 315 \r
 316     af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
 317   }\r
 318 \r
 319 \r
 320   public static DasSource[] getDASSources()\r
 321   {\r
 322     DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
 323 \r
 324     String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
 325         "http://www.spice-3d.org/dasregistry/das1/sources"\r
 326       );\r
 327 \r
 328     try\r
 329     {\r
 330       URL url = new URL(registryURL);\r
 331 \r
 332       DasSource[] sources = reader.readDasSource(url);\r
 333 \r
 334       List das1sources = new ArrayList();\r
 335       for (int i = 0; i < sources.length; i++)\r
 336       {\r
 337         DasSource ds = sources[i];\r
 338         if (ds instanceof Das2Source)\r
 339         {\r
 340           Das2Source d2s = (Das2Source) ds;\r
 341           if (d2s.hasDas1Capabilities())\r
 342           {\r
 343             Das1Source d1s = DasSourceConverter.toDas1Source(d2s);\r
 344             das1sources.add(d1s);\r
 345           }\r
 346 \r
 347         }\r
 348         else if (ds instanceof Das1Source)\r
 349         {\r
 350           das1sources.add( (Das1Source) ds);\r
 351         }\r
 352       }\r
 353 \r
 354       return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);\r
 355     }\r
 356     catch (Exception ex)\r
 357     {\r
 358       ex.printStackTrace();\r
 359       return null;\r
 360     }\r
 361 \r
 362   }\r
 363 }\r
 364 \r
 365 \r