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