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 \r
  44 \r
  45 /**\r
  46  * DOCUMENT ME!\r
  47  *\r
  48  * @author $author$\r
  49  * @version $Revision$\r
  50  */\r
  51 public class DasSequenceFeatureFetcher implements Runnable\r
  52 {\r
  53   final AlignmentI dataset;\r
  54   final AlignFrame af;\r
  55   StringBuffer sbuffer = new StringBuffer();\r
  56 \r
  57 \r
  58 \r
  59   /**\r
  60    * Creates a new SequenceFeatureFetcher object.\r
  61    *\r
  62    * @param align DOCUMENT ME!\r
  63    * @param ap DOCUMENT ME!\r
  64    */\r
  65   public DasSequenceFeatureFetcher(AlignmentI align,\r
  66                                    AlignFrame af)\r
  67   {\r
  68     this.dataset = align.getDataset();\r
  69     this.af = af;\r
  70 \r
  71     Thread thread = new Thread(this);\r
  72     thread.start();\r
  73   }\r
  74   /**\r
  75    * creates a jalview sequence feature from a das feature document\r
  76    * @param dasfeature\r
  77    * @return sequence feature object created using dasfeature information\r
  78    */\r
  79   SequenceFeature newSequenceFeature(Map dasfeature, String nickname)\r
  80   {\r
  81           try {\r
  82                 /**\r
  83            * Different qNames for a DAS Feature - are string keys to the HashMaps in features\r
  84            * "METHOD") ||\r
  85            qName.equals("TYPE") ||\r
  86            qName.equals("START") ||\r
  87            qName.equals("END") ||\r
  88            qName.equals("NOTE") ||\r
  89            qName.equals("LINK") ||\r
  90            qName.equals("SCORE")\r
  91            */\r
  92                   String desc = new String();\r
  93                   if (dasfeature.containsKey("NOTE"))\r
  94                                 desc+=(String) dasfeature.get("NOTE");\r
  95 \r
  96 \r
  97                   int start = 0, end = 0;\r
  98                   float score = 0f;\r
  99 \r
 100                   try{ start = Integer.parseInt( dasfeature.get("START").toString()); }\r
 101                   catch( Exception ex){}\r
 102                   try{ end = Integer.parseInt( dasfeature.get("END").toString()); }\r
 103                   catch (Exception ex){}\r
 104                   try{ score = Integer.parseInt( dasfeature.get("SCORE").toString()); }\r
 105                   catch (Exception ex){}\r
 106 \r
 107 \r
 108                   SequenceFeature f = new SequenceFeature(\r
 109                                   (String) dasfeature.get("TYPE"),\r
 110                                   desc,\r
 111                                   start,\r
 112                                   end,\r
 113                                   score,\r
 114                                   nickname);\r
 115 \r
 116                   if (dasfeature.containsKey("LINK"))\r
 117                  {\r
 118                       f.addLink(f.getType()+" "+f.begin+"_"+f.end\r
 119                                 +"|"+ dasfeature.get("LINK"));\r
 120                   }\r
 121                   // (String) dasfeature.get("ID"),\r
 122                   ////  (String) dasfeature.get("METHOD"),\r
 123                                 //  (String) dasfeature.get("SCORE"),\r
 124                                 //  null\r
 125                         // );\r
 126 \r
 127                      // System.out.println(nickname+" "+f.getType()+" "+f.begin+" "+f.end);\r
 128           return f;\r
 129           }\r
 130           catch (Exception e) {\r
 131             e.printStackTrace();\r
 132                   Cache.log.debug("Failed to parse "+dasfeature.toString(), e);\r
 133                   return null;\r
 134           }\r
 135   }\r
 136   /**\r
 137    * fetch and add das features to a sequence using the given source URL and Id to create a feature request\r
 138    * @param seq\r
 139    * @param SourceUrl\r
 140    * @param id\r
 141    */\r
 142   protected void createFeatureFetcher(final Sequence seq,\r
 143                                       final String sourceUrl,\r
 144                                       String id,\r
 145                                       String nickname)  {\r
 146           //////////////\r
 147           /// fetch DAS features\r
 148           final Das1Source source = new Das1Source();\r
 149           source.setUrl(sourceUrl);\r
 150           source.setNickname(nickname);\r
 151 \r
 152 \r
 153           Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
 154                           sourceUrl);\r
 155           if (id != null && id.length() > 0)\r
 156           {\r
 157             FeatureThread fetcher = new FeatureThread(id\r
 158             //   +  ":" + seq.getStart() + "," +seq.getEnd()\r
 159                  , source);\r
 160 \r
 161             fetcher.addFeatureListener(new FeatureListener()\r
 162             {\r
 163               public void comeBackLater(FeatureEvent e)\r
 164               {\r
 165                 Cache.log.debug("das source " + e.getDasSource().getNickname() +\r
 166                                 " asked us to come back in " + e.getComeBackLater() +\r
 167                                 " secs.");\r
 168               }\r
 169 \r
 170               public void newFeatures(FeatureEvent e)\r
 171               {\r
 172                 Das1Source ds = e.getDasSource();\r
 173 \r
 174                 Map[] features = e.getFeatures();\r
 175                 // add features to sequence\r
 176                 Cache.log.debug("das source " + ds.getUrl() + " returned " +\r
 177                                 features.length + " features");\r
 178 \r
 179                 if (features.length > 0)\r
 180                 {\r
 181                   for (int i = 0; i < features.length; i++)\r
 182                   {\r
 183                       SequenceFeature f = newSequenceFeature(features[i],\r
 184                         source.getNickname());\r
 185 \r
 186                       seq.addSequenceFeature(f);\r
 187                   }\r
 188                 }\r
 189               }\r
 190             }\r
 191 \r
 192             );\r
 193 \r
 194             //NOTE alignPanel listener will be called after the previous\r
 195             //anonymous listener!!!\r
 196             fetcher.addFeatureListener(af);\r
 197 \r
 198             fetcher.start();\r
 199           }\r
 200   }\r
 201   /**\r
 202    * Spawns a number of dasobert Fetcher threads to add features to sequences in the dataset\r
 203    */\r
 204   public void run()\r
 205   {\r
 206     long startTime = System.currentTimeMillis();\r
 207     af.setProgressBar("Fetching DAS Sequence Features", startTime);\r
 208 \r
 209     DasSource [] sources = new jalview.gui.DasSourceBrowser().getDASSource();\r
 210 \r
 211     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");\r
 212     StringTokenizer st = new StringTokenizer(active, "\t");\r
 213     Vector selectedSources = new Vector();\r
 214     String token;\r
 215     while (st.hasMoreTokens())\r
 216     {\r
 217       token = st.nextToken();\r
 218       for(int i=0; i<sources.length; i++)\r
 219       {\r
 220         if(sources[i].getNickname().equals(token))\r
 221         {\r
 222           selectedSources.addElement(sources[i]);\r
 223           break;\r
 224         }\r
 225       }\r
 226     }\r
 227 \r
 228 \r
 229     if(selectedSources == null || selectedSources.size()==0)\r
 230     {\r
 231       System.out.println("No DAS Sources active");\r
 232       af.setProgressBar("No DAS Sources Active", startTime);\r
 233       return;\r
 234     }\r
 235 \r
 236     try\r
 237     {\r
 238       int seqIndex = 0;\r
 239       Vector sequences = dataset.getSequences();\r
 240       while (seqIndex < sequences.size())\r
 241       {\r
 242           Sequence sequence = (Sequence) sequences.get(seqIndex);\r
 243           Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),\r
 244               new String[]  {\r
 245               jalview.datamodel.DBRefSource.PDB,\r
 246               jalview.datamodel.DBRefSource.UNIPROT});\r
 247 \r
 248           for(int sourceIndex=0; sourceIndex<selectedSources.size(); sourceIndex++)\r
 249           {\r
 250             DasSource dasSource = (DasSource)selectedSources.elementAt(sourceIndex);\r
 251 \r
 252             if (uprefs != null)\r
 253             {\r
 254               // we know the id for this entry, so don't note its ID in the unknownSequences list\r
 255               for (int j = 0;  j < uprefs.size(); j++)\r
 256               {\r
 257 \r
 258                 // 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
 259                 org.biojava.dasobert.dasregistry.DasCoordinateSystem cs[] = dasSource.getCoordinateSystem();\r
 260                 for (int l=0; l<cs.length; l++)\r
 261                 {\r
 262                   if (jalview.util.DBRefUtils.isDasCoordinateSystem(cs[l].getName(), (DBRefEntry)\r
 263                       uprefs.get(j)))\r
 264                   {\r
 265                     Cache.log.debug("Launched fetcher for coordinate system " +\r
 266                                     cs[l].getName());\r
 267 \r
 268 \r
 269                     createFeatureFetcher(sequence,\r
 270                                          dasSource.getUrl(),\r
 271                                          ( (DBRefEntry) uprefs.get(j)).\r
 272                                          getAccessionId(),\r
 273                                          dasSource.getNickname());\r
 274                   }\r
 275                 }\r
 276               }\r
 277             }\r
 278             else\r
 279             {\r
 280               String id = null;\r
 281               // try and use the name as the sequence id\r
 282               if (sequence.getName().indexOf("|") > -1)\r
 283               {\r
 284                 id = sequence.getName().substring(\r
 285                     sequence.getName().lastIndexOf("|") + 1);\r
 286               }\r
 287               else\r
 288               {\r
 289                 id = sequence.getName();\r
 290               }\r
 291               if (id != null)\r
 292               {\r
 293                 // Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references\r
 294                 createFeatureFetcher(sequence,\r
 295                                      dasSource.getUrl(),\r
 296                                      id,\r
 297                                      dasSource.getNickname());\r
 298               }\r
 299             }\r
 300           }\r
 301 \r
 302           seqIndex++;\r
 303     }\r
 304     }\r
 305     catch (Exception ex)\r
 306     {\r
 307       ex.printStackTrace();\r
 308     }\r
 309 \r
 310     af.setProgressBar("DAS Feature Fetching Complete", startTime);\r
 311   }\r
 312 \r
 313 \r
 314   public static DasSource[] getDASSources()\r
 315   {\r
 316     DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
 317 \r
 318     String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
 319         "http://www.spice-3d.org/dasregistry/das1/sources"\r
 320       );\r
 321 \r
 322     try\r
 323     {\r
 324       URL url = new URL(registryURL);\r
 325 \r
 326       DasSource[] sources = reader.readDasSource(url);\r
 327 \r
 328       List das1sources = new ArrayList();\r
 329       for (int i = 0; i < sources.length; i++)\r
 330       {\r
 331         DasSource ds = sources[i];\r
 332         if (ds instanceof Das2Source)\r
 333         {\r
 334           Das2Source d2s = (Das2Source) ds;\r
 335           if (d2s.hasDas1Capabilities())\r
 336           {\r
 337             Das1Source d1s = DasSourceConverter.toDas1Source(d2s);\r
 338             das1sources.add(d1s);\r
 339           }\r
 340 \r
 341         }\r
 342         else if (ds instanceof Das1Source)\r
 343         {\r
 344           das1sources.add( (Das1Source) ds);\r
 345         }\r
 346       }\r
 347 \r
 348       return (Das1Source[]) das1sources.toArray(new Das1Source[das1sources.size()]);\r
 349     }\r
 350     catch (Exception ex)\r
 351     {\r
 352       ex.printStackTrace();\r
 353       return null;\r
 354     }\r
 355 \r
 356   }\r
 357 }\r
 358 \r
 359 \r