src/jalview/io/vamsas/Sequencefeature.java

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