src/jalview/io/vamsas/Sequencefeature.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
   3  * Copyright (C) 2009 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.vamsas;\r
  20 \r
  21 import java.util.Enumeration;\r
  22 import java.util.Vector;\r
  23 \r
  24 import uk.ac.vamsas.objects.core.DataSet;\r
  25 import uk.ac.vamsas.objects.core.DataSetAnnotations;\r
  26 import uk.ac.vamsas.objects.core.Link;\r
  27 import uk.ac.vamsas.objects.core.Property;\r
  28 import uk.ac.vamsas.objects.core.Provenance;\r
  29 import uk.ac.vamsas.objects.core.RangeAnnotation;\r
  30 import uk.ac.vamsas.objects.core.Score;\r
  31 import uk.ac.vamsas.objects.core.Seg;\r
  32 import uk.ac.vamsas.objects.core.Sequence;\r
  33 import uk.ac.vamsas.objects.utils.Properties;\r
  34 import jalview.bin.Cache;\r
  35 import jalview.datamodel.SequenceFeature;\r
  36 import jalview.datamodel.SequenceI;\r
  37 import jalview.io.VamsasAppDatastore;\r
  38 import jalview.util.UrlLink;\r
  39 \r
  40 /**\r
  41  * @author JimP\r
  42  * \r
  43  */\r
  44 public class Sequencefeature extends Rangetype\r
  45 {\r
  46 \r
  47   uk.ac.vamsas.objects.core.DataSet dataset;\r
  48 \r
  49   uk.ac.vamsas.objects.core.Sequence sequence;\r
  50 \r
  51   private SequenceI dsSeq;\r
  52 \r
  53   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,\r
  54           SequenceFeature sequenceFeature,\r
  55           uk.ac.vamsas.objects.core.DataSet dataset,\r
  56           uk.ac.vamsas.objects.core.Sequence sequence)\r
  57   {\r
  58     super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);\r
  59     this.dataset = dataset;\r
  60     this.sequence = sequence;\r
  61     doSync();\r
  62   }\r
  63 \r
  64   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,\r
  65           DataSetAnnotations dseta, SequenceI dsSeq)\r
  66   {\r
  67     super(vamsasAppDatastore, dseta, jalview.datamodel.SequenceFeature.class);\r
  68     this.dsSeq = dsSeq;\r
  69     doJvUpdate();\r
  70   }\r
  71 \r
  72   public void addToDocument()\r
  73   {\r
  74     DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
  75     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;\r
  76     dsa = (DataSetAnnotations) getDSAnnotationFromJalview(\r
  77             new DataSetAnnotations(), feature);\r
  78     if (dsa.getProvenance() == null)\r
  79     {\r
  80       dsa.setProvenance(new Provenance());\r
  81     }\r
  82     addProvenance(dsa.getProvenance(), "created"); // JBPNote - need\r
  83     // to update\r
  84     dsa.addSeqRef(sequence); // we have just created this annotation\r
  85     // - so safe to use this\r
  86     bindjvvobj(feature, dsa);\r
  87     dataset.addDataSetAnnotations(dsa);\r
  88   }\r
  89 \r
  90   public void addFromDocument()\r
  91   {\r
  92     DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
  93     if (dsa.getSeqRefCount()!=1)\r
  94     {\r
  95       Cache.log.warn("Not binding "+dsa.getVorbaId()+" to Sequence Feature - has multiple dataset sequence references.");\r
  96       return;\r
  97     }\r
  98     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;\r
  99     dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));\r
 100     jvobj = sf;\r
 101     bindjvvobj(sf, dsa);\r
 102   }\r
 103 \r
 104   public void conflict()\r
 105   {\r
 106     log.warn("Untested sequencefeature conflict code");\r
 107     DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
 108     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;\r
 109     jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);\r
 110     replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature to newly created feature\r
 111     dsSeq.addSequenceFeature(sf); // add new imported feature\r
 112     addToDocument(); // and create a new feature in the document        \r
 113   }\r
 114 \r
 115   public void updateToDoc()\r
 116   {\r
 117     DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
 118     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;\r
 119     if (dsa.getSeqRefCount() != 1)\r
 120     {\r
 121       replaceJvObjMapping(feature, null);\r
 122       Cache.log\r
 123               .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");\r
 124       doSync(); // re-verify bindings.\r
 125     }\r
 126     else\r
 127     {\r
 128       // Sync the features from Jalview\r
 129       long oldref = dsa.get__last_hash();\r
 130       getDSAnnotationFromJalview(dsa, feature);\r
 131       if (oldref != dsa.hashCode())\r
 132       {\r
 133         Cache.log\r
 134                 .debug("Updated dataset sequence annotation from feature.");\r
 135         addProvenance(dsa.getProvenance(), "modified");\r
 136       }\r
 137     }\r
 138 \r
 139   }\r
 140   public void updateFromDoc()\r
 141   {\r
 142     DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
 143     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;\r
 144     if (dsa.getSeqRefCount() != 1)\r
 145     {\r
 146       // conflicting update from document - we cannot map this feature anymore.\r
 147       replaceJvObjMapping(feature, null);\r
 148       Cache.log\r
 149               .warn("annotation ("+dsa.getVorbaId()+" bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");\r
 150        // - consider deleting the feature ?\r
 151       dsSeq.deleteFeature(feature);\r
 152       // doSync();\r
 153     }\r
 154     else\r
 155     {\r
 156       // Sync the features to Jalview - easiest to delete and add the feature again\r
 157       jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);\r
 158       dsSeq.deleteFeature(feature);\r
 159       replaceJvObjMapping(feature, newsf);\r
 160       dsSeq.addSequenceFeature(newsf);\r
 161       if (feature.otherDetails!=null) {\r
 162         // TODO later: leave this to finalise method ? \r
 163         feature.otherDetails.clear();\r
 164       }\r
 165     }\r
 166   }\r
 167 \r
 168   /**\r
 169    * correctly create/update a RangeAnnotation from a jalview sequence feature\r
 170    * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class\r
 171    * \r
 172    * @param dsa\r
 173    *                (typically DataSetAnnotations or\r
 174    *                AlignmentSequenceAnnotation)\r
 175    * @param feature\r
 176    *                (the feature to be mapped from)\r
 177    * @return\r
 178    */\r
 179   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,\r
 180           jalview.datamodel.SequenceFeature feature)\r
 181   {\r
 182     dsa.setType(feature.getType());\r
 183     Seg vSeg = new Seg();\r
 184     vSeg.setStart(feature.getBegin());\r
 185     vSeg.setEnd(feature.getEnd());\r
 186     vSeg.setInclusive(true);\r
 187     if (dsa.getSegCount() > 1)\r
 188     {\r
 189       Cache.log\r
 190               .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("\r
 191                       + dsa.getVorbaId() + ")");\r
 192     }\r
 193     dsa.setSeg(new Seg[]\r
 194     { vSeg });\r
 195     dsa.setDescription(feature.getDescription());\r
 196     dsa.setStatus(feature.getStatus());\r
 197     if (feature.links != null && feature.links.size() > 0)\r
 198     {\r
 199       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)\r
 200       {\r
 201         String link = (String) feature.links.elementAt(i);\r
 202         UrlLink ulink = new UrlLink(link);\r
 203         if (ulink.isValid())\r
 204         {\r
 205           // We only add static links to the document.\r
 206           Link vLink = new Link();\r
 207           vLink.setContent(ulink.getLabel());\r
 208           vLink.setHref(ulink.getTarget());\r
 209           dsa.addLink(vLink);\r
 210         }\r
 211       }\r
 212     }\r
 213     dsa.setGroup(feature.getFeatureGroup());\r
 214     if (feature.getScore() != Float.NaN)\r
 215     {\r
 216       Score fscore = new Score();\r
 217       dsa.setScore(new Score[]\r
 218       { fscore });\r
 219       fscore.setContent(feature.getScore());\r
 220       fscore.setName(feature.getType());\r
 221     }\r
 222     if (feature.otherDetails != null)\r
 223     {\r
 224       Enumeration iter = feature.otherDetails.keys();\r
 225       Vector props = dsa.getPropertyAsReference();\r
 226       while (iter.hasMoreElements())\r
 227       {\r
 228         String key = (String) iter.nextElement();\r
 229         if (!key.equalsIgnoreCase("score")\r
 230                 && !key.equalsIgnoreCase("status"))\r
 231         {\r
 232           Property nprop = new Property();\r
 233           nprop.setName(key);\r
 234           Object vlu = feature.getValue(key);\r
 235           nprop.setContent(feature.getValue(key).toString());\r
 236           boolean valid = false;\r
 237           if (vlu instanceof String)\r
 238           {\r
 239             nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);\r
 240             valid = true;\r
 241           }\r
 242           else if (vlu instanceof Integer)\r
 243           {\r
 244             valid = true;\r
 245             nprop\r
 246                     .setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);\r
 247           }\r
 248           else if (vlu instanceof Float)\r
 249           {\r
 250             nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);\r
 251             valid = true;\r
 252           }\r
 253           if (valid)\r
 254           {\r
 255             if (props != null)\r
 256             {\r
 257               uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,\r
 258                       nprop);\r
 259             }\r
 260             else\r
 261             {\r
 262               dsa.addProperty(nprop);\r
 263             }\r
 264           }\r
 265         }\r
 266       }\r
 267     }\r
 268     return dsa;\r
 269   }\r
 270   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)\r
 271   {\r
 272     int[] se = getBounds(dseta);\r
 273     SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta\r
 274             .getType(), dseta.getDescription(), dseta.getStatus(), se[0],\r
 275             se[1], dseta.getGroup());\r
 276     if (dseta.getLinkCount() > 0)\r
 277     {\r
 278       Link[] links = dseta.getLink();\r
 279       for (int i = 0; i < links.length; i++)\r
 280       { \r
 281         // TODO: use URLLink parsing/validation here.\r
 282         sf.addLink(links[i].getContent() + "|" + links[i].getHref());\r
 283       }\r
 284     }\r
 285     if (dseta.getScoreCount()>0)\r
 286     {\r
 287       Enumeration scr = dseta.enumerateScore();\r
 288       while (scr.hasMoreElements())\r
 289       {\r
 290         Score score = (Score) scr.nextElement();\r
 291         if (score.getName().equals(sf.getType()))\r
 292         {\r
 293           sf.setScore(score.getContent());\r
 294         } else {\r
 295           sf.setValue(score.getName(), ""+score.getContent());\r
 296         }\r
 297       }\r
 298     }\r
 299     // other details\r
 300     Enumeration props = dseta.enumerateProperty();\r
 301     while (props.hasMoreElements())\r
 302     {\r
 303       Property p = (Property) props.nextElement();\r
 304       Object val = null;\r
 305       if (Properties.isValid(p)) \r
 306       {\r
 307         if (Properties.isString(p))\r
 308         {\r
 309         val = p.getContent();\r
 310         }\r
 311         if (Properties.isBoolean(p))\r
 312         {\r
 313           try {\r
 314             val = new Boolean(p.getContent());\r
 315           } catch (Exception e) {}\r
 316         }\r
 317         if (Properties.isFloat(p))\r
 318         {\r
 319           try {\r
 320               val = new Float(p.getContent());\r
 321               \r
 322             } catch (Exception e)\r
 323             {\r
 324             }\r
 325           }\r
 326         if(Properties.isInteger(p))\r
 327         {\r
 328           try {\r
 329                 val = new Integer(p.getContent());\r
 330           } catch (Exception e)\r
 331           {\r
 332               } \r
 333         }\r
 334         if (val!=null)\r
 335         {\r
 336           sf.setValue(p.getName(), val);\r
 337         }\r
 338       }\r
 339     }\r
 340 \r
 341     return sf;\r
 342   }\r
 343 \r
 344 }\r