src/jalview/io/vamsas/Sequencefeature.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
   4  * \r
   5  * This file is part of Jalview.\r
   6  * \r
   7  * Jalview is free software: you can redistribute it and/or\r
   8  * modify it under the terms of the GNU General Public License \r
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  10  * \r
  11  * Jalview is distributed in the hope that it will be useful, but \r
  12  * WITHOUT ANY WARRANTY; without even the implied warranty \r
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
  14  * PURPOSE.  See the GNU General Public License for more details.\r
  15  * \r
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  17  */\r
  18 package jalview.io.vamsas;\r
  19 \r
  20 import java.util.Enumeration;\r
  21 import java.util.Vector;\r
  22 \r
  23 import uk.ac.vamsas.objects.core.DataSet;\r
  24 import uk.ac.vamsas.objects.core.DataSetAnnotations;\r
  25 import uk.ac.vamsas.objects.core.Link;\r
  26 import uk.ac.vamsas.objects.core.Property;\r
  27 import uk.ac.vamsas.objects.core.Provenance;\r
  28 import uk.ac.vamsas.objects.core.RangeAnnotation;\r
  29 import uk.ac.vamsas.objects.core.Score;\r
  30 import uk.ac.vamsas.objects.core.Seg;\r
  31 import uk.ac.vamsas.objects.core.Sequence;\r
  32 import uk.ac.vamsas.objects.utils.Properties;\r
  33 import jalview.bin.Cache;\r
  34 import jalview.datamodel.SequenceFeature;\r
  35 import jalview.datamodel.SequenceI;\r
  36 import jalview.io.VamsasAppDatastore;\r
  37 import jalview.util.UrlLink;\r
  38 \r
  39 /**\r
  40  * @author JimP\r
  41  * \r
  42  */\r
  43 public class Sequencefeature extends Rangetype\r
  44 {\r
  45 \r
  46   uk.ac.vamsas.objects.core.DataSet dataset;\r
  47 \r
  48   uk.ac.vamsas.objects.core.Sequence sequence;\r
  49 \r
  50   private SequenceI dsSeq;\r
  51 \r
  52   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,\r
  53           SequenceFeature sequenceFeature,\r
  54           uk.ac.vamsas.objects.core.DataSet dataset,\r
  55           uk.ac.vamsas.objects.core.Sequence sequence)\r
  56   {\r
  57     super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);\r
  58     this.dataset = dataset;\r
  59     this.sequence = sequence;\r
  60     doSync();\r
  61   }\r
  62 \r
  63   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,\r
  64           DataSetAnnotations dseta, SequenceI dsSeq)\r
  65   {\r
  66     super(vamsasAppDatastore, dseta,\r
  67             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\r
  96               .warn("Not binding "\r
  97                       + dsa.getVorbaId()\r
  98                       + " to Sequence Feature - has multiple dataset sequence references.");\r
  99       return;\r
 100     }\r
 101     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;\r
 102     dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));\r
 103     jvobj = sf;\r
 104     bindjvvobj(sf, dsa);\r
 105   }\r
 106 \r
 107   public void conflict()\r
 108   {\r
 109     log.warn("Untested sequencefeature conflict code");\r
 110     DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
 111     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;\r
 112     jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);\r
 113     replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature\r
 114                                       // to newly created feature\r
 115     dsSeq.addSequenceFeature(sf); // add new imported feature\r
 116     addToDocument(); // and create a new feature in the document\r
 117   }\r
 118 \r
 119   public void updateToDoc()\r
 120   {\r
 121     DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
 122     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;\r
 123     if (dsa.getSeqRefCount() != 1)\r
 124     {\r
 125       replaceJvObjMapping(feature, null);\r
 126       Cache.log\r
 127               .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");\r
 128       doSync(); // re-verify bindings.\r
 129     }\r
 130     else\r
 131     {\r
 132       // Sync the features from Jalview\r
 133       long oldref = dsa.get__last_hash();\r
 134       getDSAnnotationFromJalview(dsa, feature);\r
 135       if (oldref != dsa.hashCode())\r
 136       {\r
 137         Cache.log\r
 138                 .debug("Updated dataset sequence annotation from feature.");\r
 139         addProvenance(dsa.getProvenance(), "modified");\r
 140       }\r
 141     }\r
 142 \r
 143   }\r
 144 \r
 145   public void updateFromDoc()\r
 146   {\r
 147     DataSetAnnotations dsa = (DataSetAnnotations) vobj;\r
 148     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;\r
 149     if (dsa.getSeqRefCount() != 1)\r
 150     {\r
 151       // conflicting update from document - we cannot map this feature anymore.\r
 152       replaceJvObjMapping(feature, null);\r
 153       Cache.log\r
 154               .warn("annotation ("\r
 155                       + dsa.getVorbaId()\r
 156                       + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");\r
 157       // - consider deleting the feature ?\r
 158       dsSeq.deleteFeature(feature);\r
 159       // doSync();\r
 160     }\r
 161     else\r
 162     {\r
 163       // Sync the features to Jalview - easiest to delete and add the feature\r
 164       // again\r
 165       jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);\r
 166       dsSeq.deleteFeature(feature);\r
 167       replaceJvObjMapping(feature, newsf);\r
 168       dsSeq.addSequenceFeature(newsf);\r
 169       if (feature.otherDetails != null)\r
 170       {\r
 171         // TODO later: leave this to finalise method ?\r
 172         feature.otherDetails.clear();\r
 173       }\r
 174     }\r
 175   }\r
 176 \r
 177   /**\r
 178    * correctly create/update a RangeAnnotation from a jalview sequence feature\r
 179    * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class\r
 180    * \r
 181    * @param dsa\r
 182    *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)\r
 183    * @param feature\r
 184    *          (the feature to be mapped from)\r
 185    * @return\r
 186    */\r
 187   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,\r
 188           jalview.datamodel.SequenceFeature feature)\r
 189   {\r
 190     dsa.setType(feature.getType());\r
 191     Seg vSeg = new Seg();\r
 192     vSeg.setStart(feature.getBegin());\r
 193     vSeg.setEnd(feature.getEnd());\r
 194     vSeg.setInclusive(true);\r
 195     if (dsa.getSegCount() > 1)\r
 196     {\r
 197       Cache.log\r
 198               .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("\r
 199                       + dsa.getVorbaId() + ")");\r
 200     }\r
 201     dsa.setSeg(new Seg[]\r
 202     { vSeg });\r
 203     dsa.setDescription(feature.getDescription());\r
 204     dsa.setStatus(feature.getStatus());\r
 205     if (feature.links != null && feature.links.size() > 0)\r
 206     {\r
 207       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)\r
 208       {\r
 209         String link = (String) feature.links.elementAt(i);\r
 210         UrlLink ulink = new UrlLink(link);\r
 211         if (ulink.isValid())\r
 212         {\r
 213           // We only add static links to the document.\r
 214           Link vLink = new Link();\r
 215           vLink.setContent(ulink.getLabel());\r
 216           vLink.setHref(ulink.getTarget());\r
 217           dsa.addLink(vLink);\r
 218         }\r
 219       }\r
 220     }\r
 221     dsa.setGroup(feature.getFeatureGroup());\r
 222     if (feature.getScore() != Float.NaN)\r
 223     {\r
 224       Score fscore = new Score();\r
 225       dsa.setScore(new Score[]\r
 226       { fscore });\r
 227       fscore.setContent(feature.getScore());\r
 228       fscore.setName(feature.getType());\r
 229     }\r
 230     if (feature.otherDetails != null)\r
 231     {\r
 232       Enumeration iter = feature.otherDetails.keys();\r
 233       Vector props = dsa.getPropertyAsReference();\r
 234       while (iter.hasMoreElements())\r
 235       {\r
 236         String key = (String) iter.nextElement();\r
 237         if (!key.equalsIgnoreCase("score")\r
 238                 && !key.equalsIgnoreCase("status"))\r
 239         {\r
 240           Property nprop = new Property();\r
 241           nprop.setName(key);\r
 242           Object vlu = feature.getValue(key);\r
 243           nprop.setContent(feature.getValue(key).toString());\r
 244           boolean valid = false;\r
 245           if (vlu instanceof String)\r
 246           {\r
 247             nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);\r
 248             valid = true;\r
 249           }\r
 250           else if (vlu instanceof Integer)\r
 251           {\r
 252             valid = true;\r
 253             nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);\r
 254           }\r
 255           else if (vlu instanceof Float)\r
 256           {\r
 257             nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);\r
 258             valid = true;\r
 259           }\r
 260           if (valid)\r
 261           {\r
 262             if (props != null)\r
 263             {\r
 264               uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,\r
 265                       nprop);\r
 266             }\r
 267             else\r
 268             {\r
 269               dsa.addProperty(nprop);\r
 270             }\r
 271           }\r
 272         }\r
 273       }\r
 274     }\r
 275     return dsa;\r
 276   }\r
 277 \r
 278   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)\r
 279   {\r
 280     int[] se = getBounds(dseta);\r
 281     SequenceFeature sf = new jalview.datamodel.SequenceFeature(\r
 282             dseta.getType(), dseta.getDescription(), dseta.getStatus(),\r
 283             se[0], se[1], dseta.getGroup());\r
 284     if (dseta.getLinkCount() > 0)\r
 285     {\r
 286       Link[] links = dseta.getLink();\r
 287       for (int i = 0; i < links.length; i++)\r
 288       {\r
 289         // TODO: use URLLink parsing/validation here.\r
 290         sf.addLink(links[i].getContent() + "|" + links[i].getHref());\r
 291       }\r
 292     }\r
 293     if (dseta.getScoreCount() > 0)\r
 294     {\r
 295       Enumeration scr = dseta.enumerateScore();\r
 296       while (scr.hasMoreElements())\r
 297       {\r
 298         Score score = (Score) scr.nextElement();\r
 299         if (score.getName().equals(sf.getType()))\r
 300         {\r
 301           sf.setScore(score.getContent());\r
 302         }\r
 303         else\r
 304         {\r
 305           sf.setValue(score.getName(), "" + score.getContent());\r
 306         }\r
 307       }\r
 308     }\r
 309     // other details\r
 310     Enumeration props = dseta.enumerateProperty();\r
 311     while (props.hasMoreElements())\r
 312     {\r
 313       Property p = (Property) props.nextElement();\r
 314       Object val = null;\r
 315       if (Properties.isValid(p))\r
 316       {\r
 317         if (Properties.isString(p))\r
 318         {\r
 319           val = p.getContent();\r
 320         }\r
 321         if (Properties.isBoolean(p))\r
 322         {\r
 323           try\r
 324           {\r
 325             val = new Boolean(p.getContent());\r
 326           } catch (Exception e)\r
 327           {\r
 328           }\r
 329         }\r
 330         if (Properties.isFloat(p))\r
 331         {\r
 332           try\r
 333           {\r
 334             val = new Float(p.getContent());\r
 335 \r
 336           } catch (Exception e)\r
 337           {\r
 338           }\r
 339         }\r
 340         if (Properties.isInteger(p))\r
 341         {\r
 342           try\r
 343           {\r
 344             val = new Integer(p.getContent());\r
 345           } catch (Exception e)\r
 346           {\r
 347           }\r
 348         }\r
 349         if (val != null)\r
 350         {\r
 351           sf.setValue(p.getName(), val);\r
 352         }\r
 353       }\r
 354     }\r
 355 \r
 356     return sf;\r
 357   }\r
 358 \r
 359 }\r