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 import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
  44 \r
  45 import javax.swing.*;\r
  46 \r
  47 /**\r
  48  * DOCUMENT ME!\r
  49  *\r
  50  * @author $author$\r
  51  * @version $Revision$\r
  52  */\r
  53 public class DasSequenceFeatureFetcher implements Runnable\r
  54 {\r
  55   SequenceI [] sequences;\r
  56   AlignFrame af;\r
  57   StringBuffer sbuffer = new StringBuffer();\r
  58   Vector selectedSources;\r
  59 \r
  60   long startTime;\r
  61   int threadsRunning = 0;\r
  62 \r
  63 \r
  64   /**\r
  65    * Creates a new SequenceFeatureFetcher object.\r
  66    * Uses default\r
  67    *\r
  68    * @param align DOCUMENT ME!\r
  69    * @param ap DOCUMENT ME!\r
  70    */\r
  71   public DasSequenceFeatureFetcher(SequenceI [] sequences,\r
  72                                    final AlignFrame af,\r
  73                                    Vector selectedSources)\r
  74   {\r
  75     this.selectedSources = selectedSources;\r
  76     this.sequences = sequences;\r
  77     this.af = af;\r
  78 \r
  79     int uniprotCount = 0;\r
  80     for (int i = 0; i < selectedSources.size(); i++)\r
  81     {\r
  82       DasSource source = (DasSource) selectedSources.elementAt(i);\r
  83       DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
  84       for (int c = 0; c < coords.length; c++)\r
  85       {\r
  86         if (coords[c].getName().indexOf("UniProt")>-1)\r
  87         {\r
  88           uniprotCount++;\r
  89           break;\r
  90         }\r
  91       }\r
  92     }\r
  93 \r
  94     int refCount = 0;\r
  95     for(int i=0; i<sequences.length; i++)\r
  96     {\r
  97       DBRefEntry [] dbref = sequences[i].getDBRef();\r
  98       if(dbref!=null)\r
  99       {\r
 100         for(int j=0; j<dbref.length; j++)\r
 101         {\r
 102           if(dbref[j].getSource()\r
 103              .equals(jalview.datamodel.DBRefSource.UNIPROT))\r
 104           {\r
 105             refCount++;\r
 106             break;\r
 107           }\r
 108         }\r
 109       }\r
 110     }\r
 111 \r
 112     if(refCount<sequences.length && uniprotCount>0)\r
 113     {\r
 114 \r
 115      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 116           "Do you want Jalview to find\n"\r
 117          +"Uniprot Accession ids for given sequence names?",\r
 118          "Find Uniprot Accession Ids",\r
 119          JOptionPane.YES_NO_OPTION,\r
 120          JOptionPane.QUESTION_MESSAGE);\r
 121 \r
 122      if(reply == JOptionPane.YES_OPTION)\r
 123      {\r
 124        Thread thread = new Thread(new FetchDBRefs());\r
 125        thread.start();\r
 126      }\r
 127      else\r
 128       startFetching();\r
 129     }\r
 130     else\r
 131       startFetching();\r
 132 \r
 133   /* System.out.println("User selection is "   +\r
 134                        ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)\r
 135                       + " % Uniprot,  and "+refCount+" / " +sequences.length+" have uniprot accession");\r
 136 */\r
 137   }\r
 138 \r
 139   void startFetching()\r
 140   {\r
 141     Thread thread = new Thread(this);\r
 142     thread.start();\r
 143   }\r
 144 \r
 145   class FetchDBRefs implements Runnable\r
 146   {\r
 147     public void run()\r
 148     {\r
 149       new DBRefFetcher(\r
 150              af.getViewport().getAlignment(), af).fetchDBRefs(true);\r
 151       startFetching();\r
 152     }\r
 153   }\r
 154 \r
 155 \r
 156   /**\r
 157    * creates a jalview sequence feature from a das feature document\r
 158    * @param dasfeature\r
 159    * @return sequence feature object created using dasfeature information\r
 160    */\r
 161   SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
 162   {\r
 163           try {\r
 164                 /**\r
 165            * Different qNames for a DAS Feature - are string keys to the HashMaps in features\r
 166            * "METHOD") ||\r
 167            qName.equals("TYPE") ||\r
 168            qName.equals("START") ||\r
 169            qName.equals("END") ||\r
 170            qName.equals("NOTE") ||\r
 171            qName.equals("LINK") ||\r
 172            qName.equals("SCORE")\r
 173            */\r
 174                   String desc = new String();\r
 175                   if (dasfeature.containsKey("NOTE"))\r
 176                                 desc+=(String) dasfeature.get("NOTE");\r
 177 \r
 178 \r
 179                   int start = 0, end = 0;\r
 180                   float score = 0f;\r
 181 \r
 182                   try{ start = Integer.parseInt( dasfeature.get("START").toString()); }\r
 183                   catch( Exception ex){}\r
 184                   try{ end = Integer.parseInt( dasfeature.get("END").toString()); }\r
 185                   catch (Exception ex){}\r
 186                   try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }\r
 187                   catch (Exception ex){}\r
 188 \r
 189 \r
 190                   SequenceFeature f = new SequenceFeature(\r
 191                                   (String) dasfeature.get("TYPE"),\r
 192                                   desc,\r
 193                                   start,\r
 194                                   end,\r
 195                                   score,\r
 196                                   nickname);\r
 197 \r
 198                   if (dasfeature.containsKey("LINK"))\r
 199                  {\r
 200                       f.addLink(f.getType()+" "+f.begin+"_"+f.end\r
 201                                 +"|"+ dasfeature.get("LINK"));\r
 202                   }\r
 203                   // (String) dasfeature.get("ID"),\r
 204                   ////  (String) dasfeature.get("METHOD"),\r
 205                                 //  (String) dasfeature.get("SCORE"),\r
 206                                 //  null\r
 207                         // );\r
 208 \r
 209                      // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
 210           return f;\r
 211           }\r
 212           catch (Exception e) {\r
 213             e.printStackTrace();\r
 214                   Cache.log.debug("Failed to parse "+dasfeature.toString(), e);\r
 215                   return null;\r
 216           }\r
 217   }\r
 218   /**\r
 219    * fetch and add das features to a sequence using the given source URL and Id to create a feature request\r
 220    * @param seq\r
 221    * @param SourceUrl\r
 222    * @param id\r
 223    */\r
 224   protected void createFeatureFetcher(final SequenceI seq,\r
 225                                       final String sourceUrl,\r
 226                                       String id,\r
 227                                       String nickname)\r
 228   {\r
 229           //////////////\r
 230           /// fetch DAS features\r
 231           final Das1Source source = new Das1Source();\r
 232           source.setUrl(sourceUrl);\r
 233           source.setNickname(nickname);\r
 234 \r
 235 \r
 236           Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
 237                           sourceUrl);\r
 238 \r
 239           if (id != null && id.length() > 0)\r
 240           {\r
 241             setThreadsRunning(+1);\r
 242 \r
 243             int start=seq.getStart(), end = seq.getEnd();\r
 244 \r
 245             if(af.getViewport().getSelectionGroup()!=null)\r
 246             {\r
 247               SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());\r
 248               start = tmp.findPosition(\r
 249               af.getViewport().getSelectionGroup().getStartRes()\r
 250                   );\r
 251 \r
 252               end = tmp.findPosition(\r
 253                  af.getViewport().getSelectionGroup().getEndRes()\r
 254                  );\r
 255             }\r
 256 \r
 257             FeatureThread fetcher = new FeatureThread(id\r
 258                                                    //  +  ":" + start + "," + end,\r
 259                                                       , source);\r
 260 \r
 261 \r
 262             fetcher.addFeatureListener(new FeatureListener()\r
 263             {\r
 264               public void comeBackLater(FeatureEvent e)\r
 265               {\r
 266                 setThreadsRunning(-1);\r
 267                 Cache.log.debug("das source " + e.getDasSource().getNickname() +\r
 268                                 " asked us to come back in " + e.getComeBackLater() +\r
 269                                 " secs.");\r
 270               }\r
 271 \r
 272               public void newFeatures(FeatureEvent e)\r
 273               {\r
 274                 setThreadsRunning(-1);\r
 275                 Das1Source ds = e.getDasSource();\r
 276 \r
 277                 Map[] features = e.getFeatures();\r
 278                 // add features to sequence\r
 279                 Cache.log.debug("das source " + ds.getUrl() + " returned " +\r
 280                                 features.length + " features");\r
 281 \r
 282                 if (features.length > 0)\r
 283                 {\r
 284                   for (int i = 0; i < features.length; i++)\r
 285                   {\r
 286                       SequenceFeature f = newSequenceFeature(features[i],\r
 287                         source.getNickname());\r
 288 \r
 289                       seq.addSequenceFeature(f);\r
 290                   }\r
 291                 }\r
 292                 else\r
 293                 {\r
 294                   System.out.println("No features found for sequence " +seq.getName()\r
 295                                      +" from: "+ e.getDasSource().getNickname());\r
 296                 }\r
 297 \r
 298               }\r
 299             }\r
 300 \r
 301             );\r
 302 \r
 303             //NOTE alignPanel listener will be called after the previous\r
 304             //anonymous listener!!!\r
 305             fetcher.addFeatureListener(af);\r
 306 \r
 307             fetcher.start();\r
 308           }\r
 309   }\r
 310 \r
 311   synchronized void setThreadsRunning(int i)\r
 312   {\r
 313     threadsRunning += i;\r
 314     if(threadsRunning<1)\r
 315       af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
 316   }\r
 317 \r
 318   /**\r
 319    * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset\r
 320    */\r
 321   public void run()\r
 322   {\r
 323     startTime = System.currentTimeMillis();\r
 324     af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
 325 \r
 326     DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
 327 \r
 328     if(selectedSources==null || selectedSources.size()==0)\r
 329     {\r
 330       String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");\r
 331       StringTokenizer st = new StringTokenizer(active, "\t");\r
 332       Vector selectedSources = new Vector();\r
 333       String token;\r
 334       while (st.hasMoreTokens())\r
 335       {\r
 336         token = st.nextToken();\r
 337         for (int i = 0; i < sources.length; i++)\r
 338         {\r
 339           if (sources[i].getNickname().equals(token))\r
 340           {\r
 341             selectedSources.addElement(sources[i]);\r
 342             break;\r
 343           }\r
 344         }\r
 345       }\r
 346     }\r
 347 \r
 348     if(selectedSources == null || selectedSources.size()==0)\r
 349     {\r
 350       System.out.println("No DAS Sources active");\r
 351       af.setProgressBar("No DAS Sources Active", startTime);\r
 352       return;\r
 353     }\r
 354 \r
 355     try\r
 356     {\r
 357       int seqIndex = 0;\r
 358       while (seqIndex < sequences.length)\r
 359       {\r
 360           DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),\r
 361               new String[]  {\r
 362               jalview.datamodel.DBRefSource.PDB,\r
 363               jalview.datamodel.DBRefSource.UNIPROT});\r
 364 \r
 365           for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)\r
 366           {\r
 367             DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);\r
 368 \r
 369             if (uprefs != null)\r
 370             {\r
 371               // we know the id for this entry, so don't note its ID in the unknownSequences list\r
 372               for (int j = 0;  j < uprefs.length; j++)\r
 373               {\r
 374 \r
 375                 // 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
 376                 org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
 377                 for (int l=0; l<cs.length; l++)\r
 378                 {\r
 379                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))\r
 380                   {\r
 381                     Cache.log.debug("Launched fetcher for coordinate system " +\r
 382                                     cs[l].getName());\r
 383 \r
 384 \r
 385                     createFeatureFetcher(sequences[seqIndex],\r
 386                                          dasSource.getUrl(),\r
 387                                           uprefs[j].getAccessionId(),\r
 388                                          dasSource.getNickname());\r
 389                   }\r
 390                 }\r
 391               }\r
 392             }\r
 393             else\r
 394             {\r
 395               String id = null;\r
 396               // try and use the name as the sequence id\r
 397               if (sequences[seqIndex].getName().indexOf("|") > -1)\r
 398               {\r
 399                 id = sequences[seqIndex].getName().substring(\r
 400                     sequences[seqIndex].getName().lastIndexOf("|") + 1);\r
 401               }\r
 402               else\r
 403               {\r
 404                 id = sequences[seqIndex].getName();\r
 405               }\r
 406               if (id != null)\r
 407               {\r
 408                 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references\r
 409                 createFeatureFetcher(sequences[seqIndex],\r
 410                                      dasSource.getUrl(),\r
 411                                      id,\r
 412                                      dasSource.getNickname());\r
 413               }\r
 414             }\r
 415           }\r
 416 \r
 417           seqIndex++;\r
 418     }\r
 419     }\r
 420     catch (Exception ex)\r
 421     {\r
 422       ex.printStackTrace();\r
 423     }\r
 424   }\r
 425 \r
 426 \r
 427   public static DasSource[] getDASSources()\r
 428   {\r
 429     DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
 430 \r
 431     String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
 432         "http://das.sanger.ac.uk/registry/das1/sources/"\r
 433       );\r
 434 \r
 435     try\r
 436     {\r
 437       URL url = new URL(registryURL);\r
 438 \r
 439       DasSource[] sources = reader.readDasSource(url);\r
 440 \r
 441       List das1sources = new ArrayList();\r
 442       for (int i = 0; i < sources.length; i++)\r
 443       {\r
 444         DasSource ds = sources[i];\r
 445         if (ds instanceof Das2Source)\r
 446         {\r
 447           Das2Source d2s = (Das2Source) ds;\r
 448           if (d2s.hasDas1Capabilities())\r
 449           {\r
 450             Das1Source d1s = DasSourceConverter.toDas1Source(d2s);\r
 451             das1sources.add(d1s);\r
 452           }\r
 453 \r
 454         }\r
 455         else if (ds instanceof Das1Source)\r
 456         {\r
 457           das1sources.add( (Das1Source) ds);\r
 458         }\r
 459       }\r
 460 \r
 461       return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);\r
 462     }\r
 463     catch (Exception ex)\r
 464     {\r
 465       ex.printStackTrace();\r
 466       return null;\r
 467     }\r
 468 \r
 469   }\r
 470 }\r
 471 \r
 472 \r