src/jalview/io/vamsas/Sequencefeature.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 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.Vector;
  31
  32 import uk.ac.vamsas.objects.core.DataSetAnnotations;
  33 import uk.ac.vamsas.objects.core.Link;
  34 import uk.ac.vamsas.objects.core.Property;
  35 import uk.ac.vamsas.objects.core.Provenance;
  36 import uk.ac.vamsas.objects.core.RangeAnnotation;
  37 import uk.ac.vamsas.objects.core.Score;
  38 import uk.ac.vamsas.objects.core.Seg;
  39 import uk.ac.vamsas.objects.utils.Properties;
  40
  41 /**
  42  * @author JimP
  43  *
  44  */
  45 public class Sequencefeature extends Rangetype
  46 {
  47
  48   uk.ac.vamsas.objects.core.DataSet dataset;
  49
  50   uk.ac.vamsas.objects.core.Sequence sequence;
  51
  52   private SequenceI dsSeq;
  53
  54   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  55           SequenceFeature sequenceFeature,
  56           uk.ac.vamsas.objects.core.DataSet dataset,
  57           uk.ac.vamsas.objects.core.Sequence sequence)
  58   {
  59     super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);
  60     this.dataset = dataset;
  61     this.sequence = sequence;
  62     doSync();
  63   }
  64
  65   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  66           DataSetAnnotations dseta, SequenceI dsSeq)
  67   {
  68     super(vamsasAppDatastore, dseta,
  69             jalview.datamodel.SequenceFeature.class);
  70     this.dsSeq = dsSeq;
  71     doJvUpdate();
  72   }
  73
  74   public void addToDocument()
  75   {
  76     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  77     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
  78     dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
  79             new DataSetAnnotations(), feature);
  80     if (dsa.getProvenance() == null)
  81     {
  82       dsa.setProvenance(new Provenance());
  83     }
  84     addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
  85     // to update
  86     dsa.addSeqRef(sequence); // we have just created this annotation
  87     // - so safe to use this
  88     bindjvvobj(feature, dsa);
  89     dataset.addDataSetAnnotations(dsa);
  90   }
  91
  92   public void addFromDocument()
  93   {
  94     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  95     if (dsa.getSeqRefCount() != 1)
  96     {
  97       Cache.log
  98               .warn("Not binding "
  99                       + dsa.getVorbaId()
 100                       + " to Sequence Feature - has multiple dataset sequence references.");
 101       return;
 102     }
 103     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
 104     dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
 105     jvobj = sf;
 106     bindjvvobj(sf, dsa);
 107   }
 108
 109   public void conflict()
 110   {
 111     log.warn("Untested sequencefeature conflict code");
 112     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 113     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 114     jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
 115     replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
 116                                       // to newly created feature
 117     dsSeq.addSequenceFeature(sf); // add new imported feature
 118     addToDocument(); // and create a new feature in the document
 119   }
 120
 121   public void updateToDoc()
 122   {
 123     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 124     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 125     if (dsa.getSeqRefCount() != 1)
 126     {
 127       replaceJvObjMapping(feature, null);
 128       Cache.log
 129               .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
 130       doSync(); // re-verify bindings.
 131     }
 132     else
 133     {
 134       // Sync the features from Jalview
 135       long oldref = dsa.get__last_hash();
 136       getDSAnnotationFromJalview(dsa, feature);
 137       if (oldref != dsa.hashCode())
 138       {
 139         Cache.log
 140                 .debug("Updated dataset sequence annotation from feature.");
 141         addProvenance(dsa.getProvenance(), "modified");
 142       }
 143     }
 144
 145   }
 146
 147   public void updateFromDoc()
 148   {
 149     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 150     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 151     if (dsa.getSeqRefCount() != 1)
 152     {
 153       // conflicting update from document - we cannot map this feature anymore.
 154       replaceJvObjMapping(feature, null);
 155       Cache.log
 156               .warn("annotation ("
 157                       + dsa.getVorbaId()
 158                       + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
 159       // - consider deleting the feature ?
 160       dsSeq.deleteFeature(feature);
 161       // doSync();
 162     }
 163     else
 164     {
 165       // Sync the features to Jalview - easiest to delete and add the feature
 166       // again
 167       jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
 168       dsSeq.deleteFeature(feature);
 169       replaceJvObjMapping(feature, newsf);
 170       dsSeq.addSequenceFeature(newsf);
 171       if (feature.otherDetails != null)
 172       {
 173         // TODO later: leave this to finalise method ?
 174         feature.otherDetails.clear();
 175       }
 176     }
 177   }
 178
 179   /**
 180    * correctly create/update a RangeAnnotation from a jalview sequence feature
 181    * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
 182    *
 183    * @param dsa
 184    *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
 185    * @param feature
 186    *          (the feature to be mapped from)
 187    * @return
 188    */
 189   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
 190           jalview.datamodel.SequenceFeature feature)
 191   {
 192     dsa.setType(feature.getType());
 193     Seg vSeg = new Seg();
 194     vSeg.setStart(feature.getBegin());
 195     vSeg.setEnd(feature.getEnd());
 196     vSeg.setInclusive(true);
 197     if (dsa.getSegCount() > 1)
 198     {
 199       Cache.log
 200               .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
 201                       + dsa.getVorbaId() + ")");
 202     }
 203     dsa.setSeg(new Seg[] { vSeg });
 204     dsa.setDescription(feature.getDescription());
 205     dsa.setStatus(feature.getStatus());
 206     if (feature.links != null && feature.links.size() > 0)
 207     {
 208       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
 209       {
 210         String link = feature.links.elementAt(i);
 211         UrlLink ulink = new UrlLink(link);
 212         if (ulink.isValid())
 213         {
 214           // We only add static links to the document.
 215           Link vLink = new Link();
 216           vLink.setContent(ulink.getLabel());
 217           vLink.setHref(ulink.getTarget());
 218           dsa.addLink(vLink);
 219         }
 220       }
 221     }
 222     dsa.setGroup(feature.getFeatureGroup());
 223     if (!Float.isNaN(feature.getScore()))
 224     {
 225       Score fscore = new Score();
 226       dsa.setScore(new Score[] { fscore });
 227       fscore.setContent(feature.getScore());
 228       fscore.setName(feature.getType());
 229     }
 230     if (feature.otherDetails != null)
 231     {
 232       Enumeration iter = feature.otherDetails.keys();
 233       Vector props = dsa.getPropertyAsReference();
 234       while (iter.hasMoreElements())
 235       {
 236         String key = (String) iter.nextElement();
 237         if (!key.equalsIgnoreCase("score")
 238                 && !key.equalsIgnoreCase("status"))
 239         {
 240           Property nprop = new Property();
 241           nprop.setName(key);
 242           Object vlu = feature.getValue(key);
 243           nprop.setContent(feature.getValue(key).toString());
 244           boolean valid = false;
 245           if (vlu instanceof String)
 246           {
 247             nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);
 248             valid = true;
 249           }
 250           else if (vlu instanceof Integer)
 251           {
 252             valid = true;
 253             nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
 254           }
 255           else if (vlu instanceof Float)
 256           {
 257             nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);
 258             valid = true;
 259           }
 260           if (valid)
 261           {
 262             if (props != null)
 263             {
 264               uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,
 265                       nprop);
 266             }
 267             else
 268             {
 269               dsa.addProperty(nprop);
 270             }
 271           }
 272         }
 273       }
 274     }
 275     return dsa;
 276   }
 277
 278   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
 279   {
 280     int[] se = getBounds(dseta);
 281     SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 282             dseta.getType(), dseta.getDescription(), dseta.getStatus(),
 283             se[0], se[1], dseta.getGroup());
 284     if (dseta.getLinkCount() > 0)
 285     {
 286       Link[] links = dseta.getLink();
 287       for (int i = 0; i < links.length; i++)
 288       {
 289         // TODO: use URLLink parsing/validation here.
 290         sf.addLink(links[i].getContent() + "|" + links[i].getHref());
 291       }
 292     }
 293     if (dseta.getScoreCount() > 0)
 294     {
 295       Enumeration scr = dseta.enumerateScore();
 296       while (scr.hasMoreElements())
 297       {
 298         Score score = (Score) scr.nextElement();
 299         if (score.getName().equals(sf.getType()))
 300         {
 301           sf.setScore(score.getContent());
 302         }
 303         else
 304         {
 305           sf.setValue(score.getName(), "" + score.getContent());
 306         }
 307       }
 308     }
 309     // other details
 310     Enumeration props = dseta.enumerateProperty();
 311     while (props.hasMoreElements())
 312     {
 313       Property p = (Property) props.nextElement();
 314       Object val = null;
 315       if (Properties.isValid(p))
 316       {
 317         if (Properties.isString(p))
 318         {
 319           val = p.getContent();
 320         }
 321         if (Properties.isBoolean(p))
 322         {
 323           try
 324           {
 325             val = new Boolean(p.getContent());
 326           } catch (Exception e)
 327           {
 328           }
 329         }
 330         if (Properties.isFloat(p))
 331         {
 332           try
 333           {
 334             val = new Float(p.getContent());
 335
 336           } catch (Exception e)
 337           {
 338           }
 339         }
 340         if (Properties.isInteger(p))
 341         {
 342           try
 343           {
 344             val = new Integer(p.getContent());
 345           } catch (Exception e)
 346           {
 347           }
 348         }
 349         if (val != null)
 350         {
 351           sf.setValue(p.getName(), val);
 352         }
 353       }
 354     }
 355
 356     return sf;
 357   }
 358
 359 }