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.eventmodel.FeatureEvent;\r
  31 import org.biojava.dasobert.eventmodel.FeatureListener;\r
  32 import org.biojava.dasobert.dasregistry.DasSource;\r
  33 \r
  34 import org.biojava.dasobert.das2.io.DasSourceReaderImpl;\r
  35 import org.biojava.dasobert.dasregistry.Das1Source;\r
  36 import org.biojava.dasobert.dasregistry.DasSource;\r
  37 import org.biojava.dasobert.das2.Das2Source;\r
  38 import org.biojava.dasobert.das2.DasSourceConverter;\r
  39 \r
  40 \r
  41 import jalview.bin.Cache;\r
  42 import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
  43 \r
  44 import javax.swing.*;\r
  45 \r
  46 /**\r
  47  * DOCUMENT ME!\r
  48  *\r
  49  * @author $author$\r
  50  * @version $Revision$\r
  51  */\r
  52 public class DasSequenceFeatureFetcher implements Runnable\r
  53 {\r
  54   SequenceI [] sequences;\r
  55   AlignFrame af;\r
  56   StringBuffer sbuffer = new StringBuffer();\r
  57   Vector selectedSources;\r
  58 \r
  59   long startTime;\r
  60   int threadsRunning = 0;\r
  61 \r
  62 \r
  63   /**\r
  64    * Creates a new SequenceFeatureFetcher object.\r
  65    * Uses default\r
  66    *\r
  67    * @param align DOCUMENT ME!\r
  68    * @param ap DOCUMENT ME!\r
  69    */\r
  70   public DasSequenceFeatureFetcher(SequenceI [] sequences,\r
  71                                    final AlignFrame af,\r
  72                                    Vector selectedSources)\r
  73   {\r
  74     this.selectedSources = selectedSources;\r
  75     this.sequences = sequences;\r
  76     this.af = af;\r
  77 \r
  78     int uniprotCount = 0;\r
  79     for (int i = 0; i < selectedSources.size(); i++)\r
  80     {\r
  81       DasSource source = (DasSource) selectedSources.elementAt(i);\r
  82       DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
  83       for (int c = 0; c < coords.length; c++)\r
  84       {\r
  85         if (coords[c].getName().indexOf("UniProt")>-1)\r
  86         {\r
  87           uniprotCount++;\r
  88           break;\r
  89         }\r
  90       }\r
  91     }\r
  92 \r
  93     int refCount = 0;\r
  94     for(int i=0; i<sequences.length; i++)\r
  95     {\r
  96       DBRefEntry [] dbref = sequences[i].getDBRef();\r
  97       if(dbref!=null)\r
  98       {\r
  99         for(int j=0; j<dbref.length; j++)\r
 100         {\r
 101           if(dbref[j].getSource()\r
 102              .equals(jalview.datamodel.DBRefSource.UNIPROT))\r
 103           {\r
 104             refCount++;\r
 105             break;\r
 106           }\r
 107         }\r
 108       }\r
 109     }\r
 110 \r
 111     if(refCount<sequences.length && uniprotCount>0)\r
 112     {\r
 113 \r
 114      int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
 115           "Do you want Jalview to find\n"\r
 116          +"Uniprot Accession ids for given sequence names?",\r
 117          "Find Uniprot Accession Ids",\r
 118          JOptionPane.YES_NO_OPTION,\r
 119          JOptionPane.QUESTION_MESSAGE);\r
 120 \r
 121      if(reply == JOptionPane.YES_OPTION)\r
 122      {\r
 123        Thread thread = new Thread(new FetchDBRefs());\r
 124        thread.start();\r
 125      }\r
 126      else\r
 127       startFetching();\r
 128     }\r
 129     else\r
 130       startFetching();\r
 131 \r
 132   /* System.out.println("User selection is "   +\r
 133                        ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)\r
 134                       + " % Uniprot,  and "+refCount+" / " +sequences.length+" have uniprot accession");\r
 135 */\r
 136   }\r
 137 \r
 138   void startFetching()\r
 139   {\r
 140     Thread thread = new Thread(this);\r
 141     thread.start();\r
 142   }\r
 143 \r
 144   class FetchDBRefs implements Runnable\r
 145   {\r
 146     public void run()\r
 147     {\r
 148       new DBRefFetcher(\r
 149              af.getViewport().getAlignment(), af).fetchDBRefs(true);\r
 150       startFetching();\r
 151     }\r
 152   }\r
 153 \r
 154 \r
 155   /**\r
 156    * creates a jalview sequence feature from a das feature document\r
 157    * @param dasfeature\r
 158    * @return sequence feature object created using dasfeature information\r
 159    */\r
 160   SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
 161   {\r
 162           try {\r
 163                 /**\r
 164            * Different qNames for a DAS Feature - are string keys to the HashMaps in features\r
 165            * "METHOD") ||\r
 166            qName.equals("TYPE") ||\r
 167            qName.equals("START") ||\r
 168            qName.equals("END") ||\r
 169            qName.equals("NOTE") ||\r
 170            qName.equals("LINK") ||\r
 171            qName.equals("SCORE")\r
 172            */\r
 173                   String desc = new String();\r
 174                   if (dasfeature.containsKey("NOTE"))\r
 175                                 desc+=(String) dasfeature.get("NOTE");\r
 176 \r
 177 \r
 178                   int start = 0, end = 0;\r
 179                   float score = 0f;\r
 180 \r
 181                   try{ start = Integer.parseInt( dasfeature.get("START").toString()); }\r
 182                   catch( Exception ex){}\r
 183                   try{ end = Integer.parseInt( dasfeature.get("END").toString()); }\r
 184                   catch (Exception ex){}\r
 185                   try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }\r
 186                   catch (Exception ex){}\r
 187 \r
 188 \r
 189                   SequenceFeature f = new SequenceFeature(\r
 190                                   (String) dasfeature.get("TYPE"),\r
 191                                   desc,\r
 192                                   start,\r
 193                                   end,\r
 194                                   score,\r
 195                                   nickname);\r
 196 \r
 197                   if (dasfeature.containsKey("LINK"))\r
 198                  {\r
 199                       f.addLink(f.getType()+" "+f.begin+"_"+f.end\r
 200                                 +"|"+ dasfeature.get("LINK"));\r
 201                   }\r
 202                   // (String) dasfeature.get("ID"),\r
 203                   ////  (String) dasfeature.get("METHOD"),\r
 204                                 //  (String) dasfeature.get("SCORE"),\r
 205                                 //  null\r
 206                         // );\r
 207 \r
 208                      // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
 209           return f;\r
 210           }\r
 211           catch (Exception e) {\r
 212             e.printStackTrace();\r
 213                   Cache.log.debug("Failed to parse "+dasfeature.toString(), e);\r
 214                   return null;\r
 215           }\r
 216   }\r
 217   /**\r
 218    * fetch and add das features to a sequence using the given source URL and Id to create a feature request\r
 219    * @param seq\r
 220    * @param SourceUrl\r
 221    * @param id\r
 222    */\r
 223   protected void createFeatureFetcher(final SequenceI seq,\r
 224                                       final String sourceUrl,\r
 225                                       String id,\r
 226                                       String nickname)\r
 227   {\r
 228           //////////////\r
 229           /// fetch DAS features\r
 230           final Das1Source source = new Das1Source();\r
 231           source.setUrl(sourceUrl);\r
 232           source.setNickname(nickname);\r
 233 \r
 234 \r
 235           Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
 236                           sourceUrl);\r
 237 \r
 238           if (id != null && id.length() > 0)\r
 239           {\r
 240             setThreadsRunning(+1);\r
 241 \r
 242             int start=seq.getStart(), end = seq.getEnd();\r
 243 \r
 244             if(af.getViewport().getSelectionGroup()!=null)\r
 245             {\r
 246               SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());\r
 247               start = tmp.findPosition(\r
 248               af.getViewport().getSelectionGroup().getStartRes()\r
 249                   );\r
 250 \r
 251               end = tmp.findPosition(\r
 252                  af.getViewport().getSelectionGroup().getEndRes()\r
 253                  );\r
 254             }\r
 255 \r
 256             FeatureThread fetcher = new FeatureThread(id\r
 257                                                    //  +  ":" + start + "," + end,\r
 258                                                       , source);\r
 259 \r
 260 \r
 261             fetcher.addFeatureListener(new FeatureListener()\r
 262             {\r
 263               public void comeBackLater(FeatureEvent e)\r
 264               {\r
 265                 setThreadsRunning(-1);\r
 266                 Cache.log.debug("das source " + e.getDasSource().getNickname() +\r
 267                                 " asked us to come back in " + e.getComeBackLater() +\r
 268                                 " secs.");\r
 269               }\r
 270 \r
 271               public void newFeatures(FeatureEvent e)\r
 272               {\r
 273                 setThreadsRunning(-1);\r
 274                 Das1Source ds = e.getDasSource();\r
 275 \r
 276                 Map[] features = e.getFeatures();\r
 277                 // add features to sequence\r
 278                 Cache.log.debug("das source " + ds.getUrl() + " returned " +\r
 279                                 features.length + " features");\r
 280 \r
 281                 if (features.length > 0)\r
 282                 {\r
 283                   for (int i = 0; i < features.length; i++)\r
 284                   {\r
 285                       SequenceFeature f = newSequenceFeature(features[i],\r
 286                         source.getNickname());\r
 287 \r
 288                       seq.addSequenceFeature(f);\r
 289                   }\r
 290                 }\r
 291                 else\r
 292                 {\r
 293                   System.out.println("No features found for sequence " +seq.getName()\r
 294                                      +" from: "+ e.getDasSource().getNickname());\r
 295                 }\r
 296 \r
 297               }\r
 298             }\r
 299 \r
 300             );\r
 301 \r
 302             //NOTE alignPanel listener will be called after the previous\r
 303             //anonymous listener!!!\r
 304             fetcher.addFeatureListener(af);\r
 305 \r
 306             fetcher.start();\r
 307           }\r
 308   }\r
 309 \r
 310   synchronized void setThreadsRunning(int i)\r
 311   {\r
 312     threadsRunning += i;\r
 313     if(threadsRunning<1)\r
 314       af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
 315   }\r
 316 \r
 317   /**\r
 318    * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset\r
 319    */\r
 320   public void run()\r
 321   {\r
 322     startTime = System.currentTimeMillis();\r
 323     af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
 324 \r
 325     DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
 326 \r
 327     if(selectedSources==null || selectedSources.size()==0)\r
 328     {\r
 329       String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");\r
 330       StringTokenizer st = new StringTokenizer(active, "\t");\r
 331       Vector selectedSources = new Vector();\r
 332       String token;\r
 333       while (st.hasMoreTokens())\r
 334       {\r
 335         token = st.nextToken();\r
 336         for (int i = 0; i < sources.length; i++)\r
 337         {\r
 338           if (sources[i].getNickname().equals(token))\r
 339           {\r
 340             selectedSources.addElement(sources[i]);\r
 341             break;\r
 342           }\r
 343         }\r
 344       }\r
 345     }\r
 346 \r
 347     if(selectedSources == null || selectedSources.size()==0)\r
 348     {\r
 349       System.out.println("No DAS Sources active");\r
 350       af.setProgressBar("No DAS Sources Active", startTime);\r
 351       return;\r
 352     }\r
 353 \r
 354     try\r
 355     {\r
 356       int seqIndex = 0;\r
 357       while (seqIndex < sequences.length)\r
 358       {\r
 359           DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),\r
 360               new String[]  {\r
 361               jalview.datamodel.DBRefSource.PDB,\r
 362               jalview.datamodel.DBRefSource.UNIPROT});\r
 363 \r
 364           for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)\r
 365           {\r
 366             DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);\r
 367 \r
 368             if (uprefs != null)\r
 369             {\r
 370               // we know the id for this entry, so don't note its ID in the unknownSequences list\r
 371               for (int j = 0;  j < uprefs.length; j++)\r
 372               {\r
 373 \r
 374                 // 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
 375                 DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
 376                 for (int l=0; l<cs.length; l++)\r
 377                 {\r
 378                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), uprefs[j]))\r
 379                   {\r
 380                     Cache.log.debug("Launched fetcher for coordinate system " +\r
 381                                     cs[l].getName());\r
 382 \r
 383 \r
 384                     createFeatureFetcher(sequences[seqIndex],\r
 385                                          dasSource.getUrl(),\r
 386                                           uprefs[j].getAccessionId(),\r
 387                                          dasSource.getNickname());\r
 388                   }\r
 389                 }\r
 390               }\r
 391             }\r
 392             else\r
 393             {\r
 394               String id = null;\r
 395               // try and use the name as the sequence id\r
 396               if (sequences[seqIndex].getName().indexOf("|") > -1)\r
 397               {\r
 398                 id = sequences[seqIndex].getName().substring(\r
 399                     sequences[seqIndex].getName().lastIndexOf("|") + 1);\r
 400               }\r
 401               else\r
 402               {\r
 403                 id = sequences[seqIndex].getName();\r
 404               }\r
 405               if (id != null)\r
 406               {\r
 407                 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references\r
 408                 createFeatureFetcher(sequences[seqIndex],\r
 409                                      dasSource.getUrl(),\r
 410                                      id,\r
 411                                      dasSource.getNickname());\r
 412               }\r
 413             }\r
 414           }\r
 415 \r
 416           seqIndex++;\r
 417     }\r
 418     }\r
 419     catch (Exception ex)\r
 420     {\r
 421       ex.printStackTrace();\r
 422     }\r
 423   }\r
 424 \r
 425 \r
 426   public static DasSource[] getDASSources()\r
 427   {\r
 428     DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
 429 \r
 430     String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
 431         "http://das.sanger.ac.uk/registry/das1/sources/"\r
 432       );\r
 433 \r
 434     try\r
 435     {\r
 436       URL url = new URL(registryURL);\r
 437 \r
 438       DasSource[] sources = reader.readDasSource(url);\r
 439 \r
 440       List das1sources = new ArrayList();\r
 441       for (int i = 0; i < sources.length; i++)\r
 442       {\r
 443         DasSource ds = sources[i];\r
 444         if (ds instanceof Das2Source)\r
 445         {\r
 446           Das2Source d2s = (Das2Source) ds;\r
 447           if (d2s.hasDas1Capabilities())\r
 448           {\r
 449             Das1Source d1s = DasSourceConverter.toDas1Source(d2s);\r
 450             das1sources.add(d1s);\r
 451           }\r
 452 \r
 453         }\r
 454         else if (ds instanceof Das1Source)\r
 455         {\r
 456           das1sources.add( (Das1Source) ds);\r
 457         }\r
 458       }\r
 459 \r
 460       return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);\r
 461     }\r
 462     catch (Exception ex)\r
 463     {\r
 464       ex.printStackTrace();\r
 465       return null;\r
 466     }\r
 467 \r
 468   }\r
 469 }\r
 470 \r
 471 \r