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