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.warn("Not binding " + dsa.getVorbaId()
 101               + " to Sequence Feature - has multiple dataset sequence references.");
 102       return;
 103     }
 104     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
 105     dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
 106     jvobj = sf;
 107     bindjvvobj(sf, dsa);
 108   }
 109
 110   @Override
 111   public void conflict()
 112   {
 113     log.warn("Untested sequencefeature conflict code");
 114     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 115     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 116     jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
 117     replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
 118                                       // to newly created feature
 119     dsSeq.addSequenceFeature(sf); // add new imported feature
 120     addToDocument(); // and create a new feature in the document
 121   }
 122
 123   @Override
 124   public void updateToDoc()
 125   {
 126     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 127     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 128     if (dsa.getSeqRefCount() != 1)
 129     {
 130       replaceJvObjMapping(feature, null);
 131       Cache.log.warn(
 132               "Binding of annotation to jalview feature has changed. Removing binding and recreating.");
 133       doSync(); // re-verify bindings.
 134     }
 135     else
 136     {
 137       // Sync the features from Jalview
 138       long oldref = dsa.get__last_hash();
 139       getDSAnnotationFromJalview(dsa, feature);
 140       if (oldref != dsa.hashCode())
 141       {
 142         Cache.log
 143                 .debug("Updated dataset sequence annotation from feature.");
 144         addProvenance(dsa.getProvenance(), "modified");
 145       }
 146     }
 147
 148   }
 149
 150   @Override
 151   public void updateFromDoc()
 152   {
 153     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 154     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 155     if (dsa.getSeqRefCount() != 1)
 156     {
 157       // conflicting update from document - we cannot map this feature anymore.
 158       replaceJvObjMapping(feature, null);
 159       Cache.log.warn("annotation (" + dsa.getVorbaId()
 160               + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
 161       // - consider deleting the feature ?
 162       dsSeq.deleteFeature(feature);
 163       // doSync();
 164     }
 165     else
 166     {
 167       // Sync the features to Jalview - easiest to delete and add the feature
 168       // again
 169       jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
 170       dsSeq.deleteFeature(feature);
 171       replaceJvObjMapping(feature, newsf);
 172       dsSeq.addSequenceFeature(newsf);
 173       if (feature.otherDetails != null)
 174       {
 175         // TODO later: leave this to finalise method ?
 176         feature.otherDetails.clear();
 177       }
 178     }
 179   }
 180
 181   /**
 182    * correctly create/update a RangeAnnotation from a jalview sequence feature
 183    * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
 184    *
 185    * @param dsa
 186    *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
 187    * @param feature
 188    *          (the feature to be mapped from)
 189    * @return
 190    */
 191   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
 192           jalview.datamodel.SequenceFeature feature)
 193   {
 194     dsa.setType(feature.getType());
 195     Seg vSeg = new Seg();
 196     vSeg.setStart(feature.getBegin());
 197     vSeg.setEnd(feature.getEnd());
 198     vSeg.setInclusive(true);
 199     if (dsa.getSegCount() > 1)
 200     {
 201       Cache.log.debug(
 202               "About to destroy complex annotation in vamsas document mapped to sequence feature ("
 203                       + dsa.getVorbaId() + ")");
 204     }
 205     dsa.setSeg(new Seg[] { vSeg });
 206     dsa.setDescription(feature.getDescription());
 207     dsa.setStatus(feature.getStatus());
 208     if (feature.links != null && feature.links.size() > 0)
 209     {
 210       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
 211       {
 212         String link = feature.links.elementAt(i);
 213         UrlLink ulink = new UrlLink(link);
 214         if (ulink.isValid())
 215         {
 216           // We only add static links to the document.
 217           Link vLink = new Link();
 218           vLink.setContent(ulink.getLabel());
 219           vLink.setHref(ulink.getTarget());
 220           dsa.addLink(vLink);
 221         }
 222       }
 223     }
 224     dsa.setGroup(feature.getFeatureGroup());
 225     if (!Float.isNaN(feature.getScore()))
 226     {
 227       Score fscore = new Score();
 228       dsa.setScore(new Score[] { fscore });
 229       fscore.setContent(feature.getScore());
 230       fscore.setName(feature.getType());
 231     }
 232     if (feature.otherDetails != null)
 233     {
 234       Iterator<String> iter = feature.otherDetails.keySet().iterator();
 235       Vector props = dsa.getPropertyAsReference();
 236       while (iter.hasNext())
 237       {
 238         String key = iter.next();
 239         if (!key.equalsIgnoreCase("score")
 240                 && !key.equalsIgnoreCase("status"))
 241         {
 242           Property nprop = new Property();
 243           nprop.setName(key);
 244           Object vlu = feature.getValue(key);
 245           nprop.setContent(feature.getValue(key).toString());
 246           boolean valid = false;
 247           if (vlu instanceof String)
 248           {
 249             nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);
 250             valid = true;
 251           }
 252           else if (vlu instanceof Integer)
 253           {
 254             valid = true;
 255             nprop.setType(
 256                     uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
 257           }
 258           else if (vlu instanceof Float)
 259           {
 260             nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);
 261             valid = true;
 262           }
 263           if (valid)
 264           {
 265             if (props != null)
 266             {
 267               uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,
 268                       nprop);
 269             }
 270             else
 271             {
 272               dsa.addProperty(nprop);
 273             }
 274           }
 275         }
 276       }
 277     }
 278     return dsa;
 279   }
 280
 281   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
 282   {
 283     int[] se = getBounds(dseta);
 284
 285     /*
 286      * try to identify feature score
 287      */
 288     boolean scoreFound = false;
 289     float theScore = 0f;
 290     String featureType = dseta.getType();
 291     if (dseta.getScoreCount() > 0)
 292     {
 293       Enumeration scr = dseta.enumerateScore();
 294       while (scr.hasMoreElements())
 295       {
 296         Score score = (Score) scr.nextElement();
 297         if (score.getName().equals(featureType))
 298         {
 299           theScore = score.getContent();
 300           scoreFound = true;
 301         }
 302       }
 303     }
 304
 305     SequenceFeature sf = null;
 306     if (scoreFound)
 307     {
 308       sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
 309               se[1], theScore, dseta.getGroup());
 310     }
 311     else
 312     {
 313       sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
 314               se[1], dseta.getGroup());
 315     }
 316     sf.setStatus(dseta.getStatus());
 317     if (dseta.getLinkCount() > 0)
 318     {
 319       Link[] links = dseta.getLink();
 320       for (int i = 0; i < links.length; i++)
 321       {
 322         // TODO: use URLLink parsing/validation here.
 323         sf.addLink(links[i].getContent() + "|" + links[i].getHref());
 324       }
 325     }
 326     if (dseta.getScoreCount() > 0)
 327     {
 328       Enumeration scr = dseta.enumerateScore();
 329       while (scr.hasMoreElements())
 330       {
 331         Score score = (Score) scr.nextElement();
 332         if (!score.getName().equals(sf.getType()))
 333         {
 334           sf.setValue(score.getName(), "" + score.getContent());
 335         }
 336       }
 337     }
 338     // other details
 339     Enumeration props = dseta.enumerateProperty();
 340     while (props.hasMoreElements())
 341     {
 342       Property p = (Property) props.nextElement();
 343       Object val = null;
 344       if (Properties.isValid(p))
 345       {
 346         if (Properties.isString(p))
 347         {
 348           val = p.getContent();
 349         }
 350         if (Properties.isBoolean(p))
 351         {
 352           try
 353           {
 354             val = Boolean.valueOf(p.getContent());
 355           } catch (Exception e)
 356           {
 357           }
 358         }
 359         if (Properties.isFloat(p))
 360         {
 361           try
 362           {
 363             val = Float.valueOf(p.getContent());
 364
 365           } catch (Exception e)
 366           {
 367           }
 368         }
 369         if (Properties.isInteger(p))
 370         {
 371           try
 372           {
 373             val = Integer.valueOf(p.getContent());
 374           } catch (Exception e)
 375           {
 376           }
 377         }
 378         if (val != null)
 379         {
 380           sf.setValue(p.getName(), val);
 381         }
 382       }
 383     }
 384
 385     return sf;
 386   }
 387
 388 }