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