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