src/jalview/io/vamsas/Sequencefeature.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.io.vamsas;
  19
  20 import java.util.Enumeration;
  21 import java.util.Vector;
  22
  23 import uk.ac.vamsas.objects.core.DataSet;
  24 import uk.ac.vamsas.objects.core.DataSetAnnotations;
  25 import uk.ac.vamsas.objects.core.Link;
  26 import uk.ac.vamsas.objects.core.Property;
  27 import uk.ac.vamsas.objects.core.Provenance;
  28 import uk.ac.vamsas.objects.core.RangeAnnotation;
  29 import uk.ac.vamsas.objects.core.Score;
  30 import uk.ac.vamsas.objects.core.Seg;
  31 import uk.ac.vamsas.objects.core.Sequence;
  32 import uk.ac.vamsas.objects.utils.Properties;
  33 import jalview.bin.Cache;
  34 import jalview.datamodel.SequenceFeature;
  35 import jalview.datamodel.SequenceI;
  36 import jalview.io.VamsasAppDatastore;
  37 import jalview.util.UrlLink;
  38
  39 /**
  40  * @author JimP
  41  *
  42  */
  43 public class Sequencefeature extends Rangetype
  44 {
  45
  46   uk.ac.vamsas.objects.core.DataSet dataset;
  47
  48   uk.ac.vamsas.objects.core.Sequence sequence;
  49
  50   private SequenceI dsSeq;
  51
  52   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  53           SequenceFeature sequenceFeature,
  54           uk.ac.vamsas.objects.core.DataSet dataset,
  55           uk.ac.vamsas.objects.core.Sequence sequence)
  56   {
  57     super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);
  58     this.dataset = dataset;
  59     this.sequence = sequence;
  60     doSync();
  61   }
  62
  63   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  64           DataSetAnnotations dseta, SequenceI dsSeq)
  65   {
  66     super(vamsasAppDatastore, dseta,
  67             jalview.datamodel.SequenceFeature.class);
  68     this.dsSeq = dsSeq;
  69     doJvUpdate();
  70   }
  71
  72   public void addToDocument()
  73   {
  74     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  75     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
  76     dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
  77             new DataSetAnnotations(), feature);
  78     if (dsa.getProvenance() == null)
  79     {
  80       dsa.setProvenance(new Provenance());
  81     }
  82     addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
  83     // to update
  84     dsa.addSeqRef(sequence); // we have just created this annotation
  85     // - so safe to use this
  86     bindjvvobj(feature, dsa);
  87     dataset.addDataSetAnnotations(dsa);
  88   }
  89
  90   public void addFromDocument()
  91   {
  92     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  93     if (dsa.getSeqRefCount() != 1)
  94     {
  95       Cache.log
  96               .warn("Not binding "
  97                       + dsa.getVorbaId()
  98                       + " to Sequence Feature - has multiple dataset sequence references.");
  99       return;
 100     }
 101     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
 102     dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
 103     jvobj = sf;
 104     bindjvvobj(sf, dsa);
 105   }
 106
 107   public void conflict()
 108   {
 109     log.warn("Untested sequencefeature conflict code");
 110     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 111     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 112     jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
 113     replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
 114                                       // to newly created feature
 115     dsSeq.addSequenceFeature(sf); // add new imported feature
 116     addToDocument(); // and create a new feature in the document
 117   }
 118
 119   public void updateToDoc()
 120   {
 121     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 122     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 123     if (dsa.getSeqRefCount() != 1)
 124     {
 125       replaceJvObjMapping(feature, null);
 126       Cache.log
 127               .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
 128       doSync(); // re-verify bindings.
 129     }
 130     else
 131     {
 132       // Sync the features from Jalview
 133       long oldref = dsa.get__last_hash();
 134       getDSAnnotationFromJalview(dsa, feature);
 135       if (oldref != dsa.hashCode())
 136       {
 137         Cache.log
 138                 .debug("Updated dataset sequence annotation from feature.");
 139         addProvenance(dsa.getProvenance(), "modified");
 140       }
 141     }
 142
 143   }
 144
 145   public void updateFromDoc()
 146   {
 147     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 148     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 149     if (dsa.getSeqRefCount() != 1)
 150     {
 151       // conflicting update from document - we cannot map this feature anymore.
 152       replaceJvObjMapping(feature, null);
 153       Cache.log
 154               .warn("annotation ("
 155                       + dsa.getVorbaId()
 156                       + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
 157       // - consider deleting the feature ?
 158       dsSeq.deleteFeature(feature);
 159       // doSync();
 160     }
 161     else
 162     {
 163       // Sync the features to Jalview - easiest to delete and add the feature
 164       // again
 165       jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
 166       dsSeq.deleteFeature(feature);
 167       replaceJvObjMapping(feature, newsf);
 168       dsSeq.addSequenceFeature(newsf);
 169       if (feature.otherDetails != null)
 170       {
 171         // TODO later: leave this to finalise method ?
 172         feature.otherDetails.clear();
 173       }
 174     }
 175   }
 176
 177   /**
 178    * correctly create/update a RangeAnnotation from a jalview sequence feature
 179    * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
 180    *
 181    * @param dsa
 182    *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
 183    * @param feature
 184    *          (the feature to be mapped from)
 185    * @return
 186    */
 187   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
 188           jalview.datamodel.SequenceFeature feature)
 189   {
 190     dsa.setType(feature.getType());
 191     Seg vSeg = new Seg();
 192     vSeg.setStart(feature.getBegin());
 193     vSeg.setEnd(feature.getEnd());
 194     vSeg.setInclusive(true);
 195     if (dsa.getSegCount() > 1)
 196     {
 197       Cache.log
 198               .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
 199                       + dsa.getVorbaId() + ")");
 200     }
 201     dsa.setSeg(new Seg[]
 202     { vSeg });
 203     dsa.setDescription(feature.getDescription());
 204     dsa.setStatus(feature.getStatus());
 205     if (feature.links != null && feature.links.size() > 0)
 206     {
 207       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
 208       {
 209         String link = (String) feature.links.elementAt(i);
 210         UrlLink ulink = new UrlLink(link);
 211         if (ulink.isValid())
 212         {
 213           // We only add static links to the document.
 214           Link vLink = new Link();
 215           vLink.setContent(ulink.getLabel());
 216           vLink.setHref(ulink.getTarget());
 217           dsa.addLink(vLink);
 218         }
 219       }
 220     }
 221     dsa.setGroup(feature.getFeatureGroup());
 222     if (feature.getScore() != Float.NaN)
 223     {
 224       Score fscore = new Score();
 225       dsa.setScore(new Score[]
 226       { 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 }