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