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