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