src/jalview/io/vamsas/Sequencefeature.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.io.vamsas;
  22
  23 import jalview.bin.Cache;
  24 import jalview.datamodel.SequenceFeature;
  25 import jalview.datamodel.SequenceI;
  26 import jalview.io.VamsasAppDatastore;
  27 import jalview.util.UrlLink;
  28
  29 import java.util.Enumeration;
  30 import java.util.Iterator;
  31 import java.util.Vector;
  32
  33 import uk.ac.vamsas.objects.core.DataSetAnnotations;
  34 import uk.ac.vamsas.objects.core.Link;
  35 import uk.ac.vamsas.objects.core.Property;
  36 import uk.ac.vamsas.objects.core.Provenance;
  37 import uk.ac.vamsas.objects.core.RangeAnnotation;
  38 import uk.ac.vamsas.objects.core.Score;
  39 import uk.ac.vamsas.objects.core.Seg;
  40 import uk.ac.vamsas.objects.utils.Properties;
  41
  42 /**
  43  * @author JimP
  44  *
  45  */
  46 public class Sequencefeature extends Rangetype
  47 {
  48
  49   uk.ac.vamsas.objects.core.DataSet dataset;
  50
  51   uk.ac.vamsas.objects.core.Sequence sequence;
  52
  53   private SequenceI dsSeq;
  54
  55   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  56           SequenceFeature sequenceFeature,
  57           uk.ac.vamsas.objects.core.DataSet dataset,
  58           uk.ac.vamsas.objects.core.Sequence sequence)
  59   {
  60     super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);
  61     this.dataset = dataset;
  62     this.sequence = sequence;
  63     doSync();
  64   }
  65
  66   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  67           DataSetAnnotations dseta, SequenceI dsSeq)
  68   {
  69     super(vamsasAppDatastore, dseta,
  70             jalview.datamodel.SequenceFeature.class);
  71     this.dsSeq = dsSeq;
  72     doJvUpdate();
  73   }
  74
  75   @Override
  76   public void addToDocument()
  77   {
  78     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  79     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
  80     dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
  81             new DataSetAnnotations(), feature);
  82     if (dsa.getProvenance() == null)
  83     {
  84       dsa.setProvenance(new Provenance());
  85     }
  86     addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
  87     // to update
  88     dsa.addSeqRef(sequence); // we have just created this annotation
  89     // - so safe to use this
  90     bindjvvobj(feature, dsa);
  91     dataset.addDataSetAnnotations(dsa);
  92   }
  93
  94   @Override
  95   public void addFromDocument()
  96   {
  97     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  98     if (dsa.getSeqRefCount() != 1)
  99     {
 100       Cache.log
 101               .warn("Not binding "
 102                       + dsa.getVorbaId()
 103                       + " to Sequence Feature - has multiple dataset sequence references.");
 104       return;
 105     }
 106     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
 107     dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
 108     jvobj = sf;
 109     bindjvvobj(sf, dsa);
 110   }
 111
 112   @Override
 113   public void conflict()
 114   {
 115     log.warn("Untested sequencefeature conflict code");
 116     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 117     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 118     jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
 119     replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
 120                                       // to newly created feature
 121     dsSeq.addSequenceFeature(sf); // add new imported feature
 122     addToDocument(); // and create a new feature in the document
 123   }
 124
 125   @Override
 126   public void updateToDoc()
 127   {
 128     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 129     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 130     if (dsa.getSeqRefCount() != 1)
 131     {
 132       replaceJvObjMapping(feature, null);
 133       Cache.log
 134               .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
 135       doSync(); // re-verify bindings.
 136     }
 137     else
 138     {
 139       // Sync the features from Jalview
 140       long oldref = dsa.get__last_hash();
 141       getDSAnnotationFromJalview(dsa, feature);
 142       if (oldref != dsa.hashCode())
 143       {
 144         Cache.log
 145                 .debug("Updated dataset sequence annotation from feature.");
 146         addProvenance(dsa.getProvenance(), "modified");
 147       }
 148     }
 149
 150   }
 151
 152   @Override
 153   public void updateFromDoc()
 154   {
 155     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 156     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 157     if (dsa.getSeqRefCount() != 1)
 158     {
 159       // conflicting update from document - we cannot map this feature anymore.
 160       replaceJvObjMapping(feature, null);
 161       Cache.log
 162               .warn("annotation ("
 163                       + dsa.getVorbaId()
 164                       + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
 165       // - consider deleting the feature ?
 166       dsSeq.deleteFeature(feature);
 167       // doSync();
 168     }
 169     else
 170     {
 171       // Sync the features to Jalview - easiest to delete and add the feature
 172       // again
 173       jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
 174       dsSeq.deleteFeature(feature);
 175       replaceJvObjMapping(feature, newsf);
 176       dsSeq.addSequenceFeature(newsf);
 177       if (feature.otherDetails != null)
 178       {
 179         // TODO later: leave this to finalise method ?
 180         feature.otherDetails.clear();
 181       }
 182     }
 183   }
 184
 185   /**
 186    * correctly create/update a RangeAnnotation from a jalview sequence feature
 187    * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
 188    *
 189    * @param dsa
 190    *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
 191    * @param feature
 192    *          (the feature to be mapped from)
 193    * @return
 194    */
 195   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
 196           jalview.datamodel.SequenceFeature feature)
 197   {
 198     dsa.setType(feature.getType());
 199     Seg vSeg = new Seg();
 200     vSeg.setStart(feature.getBegin());
 201     vSeg.setEnd(feature.getEnd());
 202     vSeg.setInclusive(true);
 203     if (dsa.getSegCount() > 1)
 204     {
 205       Cache.log
 206               .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
 207                       + dsa.getVorbaId() + ")");
 208     }
 209     dsa.setSeg(new Seg[] { vSeg });
 210     dsa.setDescription(feature.getDescription());
 211     dsa.setStatus(feature.getStatus());
 212     if (feature.links != null && feature.links.size() > 0)
 213     {
 214       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
 215       {
 216         String link = feature.links.elementAt(i);
 217         UrlLink ulink = new UrlLink(link);
 218         if (ulink.isValid())
 219         {
 220           // We only add static links to the document.
 221           Link vLink = new Link();
 222           vLink.setContent(ulink.getLabel());
 223           vLink.setHref(ulink.getTarget());
 224           dsa.addLink(vLink);
 225         }
 226       }
 227     }
 228     dsa.setGroup(feature.getFeatureGroup());
 229     if (!Float.isNaN(feature.getScore()))
 230     {
 231       Score fscore = new Score();
 232       dsa.setScore(new Score[] { fscore });
 233       fscore.setContent(feature.getScore());
 234       fscore.setName(feature.getType());
 235     }
 236     if (feature.otherDetails != null)
 237     {
 238       Iterator<String> iter = feature.otherDetails.keySet().iterator();
 239       Vector props = dsa.getPropertyAsReference();
 240       while (iter.hasNext())
 241       {
 242         String key = iter.next();
 243         if (!key.equalsIgnoreCase("score")
 244                 && !key.equalsIgnoreCase("status"))
 245         {
 246           Property nprop = new Property();
 247           nprop.setName(key);
 248           Object vlu = feature.getValue(key);
 249           nprop.setContent(feature.getValue(key).toString());
 250           boolean valid = false;
 251           if (vlu instanceof String)
 252           {
 253             nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);
 254             valid = true;
 255           }
 256           else if (vlu instanceof Integer)
 257           {
 258             valid = true;
 259             nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
 260           }
 261           else if (vlu instanceof Float)
 262           {
 263             nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);
 264             valid = true;
 265           }
 266           if (valid)
 267           {
 268             if (props != null)
 269             {
 270               uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,
 271                       nprop);
 272             }
 273             else
 274             {
 275               dsa.addProperty(nprop);
 276             }
 277           }
 278         }
 279       }
 280     }
 281     return dsa;
 282   }
 283
 284   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
 285   {
 286     int[] se = getBounds(dseta);
 287     SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 288             dseta.getType(), dseta.getDescription(), dseta.getStatus(),
 289             se[0], se[1], dseta.getGroup());
 290     if (dseta.getLinkCount() > 0)
 291     {
 292       Link[] links = dseta.getLink();
 293       for (int i = 0; i < links.length; i++)
 294       {
 295         // TODO: use URLLink parsing/validation here.
 296         sf.addLink(links[i].getContent() + "|" + links[i].getHref());
 297       }
 298     }
 299     if (dseta.getScoreCount() > 0)
 300     {
 301       Enumeration scr = dseta.enumerateScore();
 302       while (scr.hasMoreElements())
 303       {
 304         Score score = (Score) scr.nextElement();
 305         if (score.getName().equals(sf.getType()))
 306         {
 307           sf.setScore(score.getContent());
 308         }
 309         else
 310         {
 311           sf.setValue(score.getName(), "" + score.getContent());
 312         }
 313       }
 314     }
 315     // other details
 316     Enumeration props = dseta.enumerateProperty();
 317     while (props.hasMoreElements())
 318     {
 319       Property p = (Property) props.nextElement();
 320       Object val = null;
 321       if (Properties.isValid(p))
 322       {
 323         if (Properties.isString(p))
 324         {
 325           val = p.getContent();
 326         }
 327         if (Properties.isBoolean(p))
 328         {
 329           try
 330           {
 331             val = new Boolean(p.getContent());
 332           } catch (Exception e)
 333           {
 334           }
 335         }
 336         if (Properties.isFloat(p))
 337         {
 338           try
 339           {
 340             val = new Float(p.getContent());
 341
 342           } catch (Exception e)
 343           {
 344           }
 345         }
 346         if (Properties.isInteger(p))
 347         {
 348           try
 349           {
 350             val = new Integer(p.getContent());
 351           } catch (Exception e)
 352           {
 353           }
 354         }
 355         if (val != null)
 356         {
 357           sf.setValue(p.getName(), val);
 358         }
 359       }
 360     }
 361
 362     return sf;
 363   }
 364
 365 }