src/jalview/io/vamsas/Sequencefeature.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   3  * Copyright (C) 2014 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 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  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.io.vamsas;
  20
  21 import java.util.Enumeration;
  22 import java.util.Vector;
  23
  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.utils.Properties;
  32 import jalview.bin.Cache;
  33 import jalview.datamodel.SequenceFeature;
  34 import jalview.datamodel.SequenceI;
  35 import jalview.io.VamsasAppDatastore;
  36 import jalview.util.UrlLink;
  37
  38 /**
  39  * @author JimP
  40  *
  41  */
  42 public class Sequencefeature extends Rangetype
  43 {
  44
  45   uk.ac.vamsas.objects.core.DataSet dataset;
  46
  47   uk.ac.vamsas.objects.core.Sequence sequence;
  48
  49   private SequenceI dsSeq;
  50
  51   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  52           SequenceFeature sequenceFeature,
  53           uk.ac.vamsas.objects.core.DataSet dataset,
  54           uk.ac.vamsas.objects.core.Sequence sequence)
  55   {
  56     super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);
  57     this.dataset = dataset;
  58     this.sequence = sequence;
  59     doSync();
  60   }
  61
  62   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  63           DataSetAnnotations dseta, SequenceI dsSeq)
  64   {
  65     super(vamsasAppDatastore, dseta,
  66             jalview.datamodel.SequenceFeature.class);
  67     this.dsSeq = dsSeq;
  68     doJvUpdate();
  69   }
  70
  71   public void addToDocument()
  72   {
  73     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  74     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
  75     dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
  76             new DataSetAnnotations(), feature);
  77     if (dsa.getProvenance() == null)
  78     {
  79       dsa.setProvenance(new Provenance());
  80     }
  81     addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
  82     // to update
  83     dsa.addSeqRef(sequence); // we have just created this annotation
  84     // - so safe to use this
  85     bindjvvobj(feature, dsa);
  86     dataset.addDataSetAnnotations(dsa);
  87   }
  88
  89   public void addFromDocument()
  90   {
  91     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  92     if (dsa.getSeqRefCount() != 1)
  93     {
  94       Cache.log
  95               .warn("Not binding "
  96                       + dsa.getVorbaId()
  97                       + " to Sequence Feature - has multiple dataset sequence references.");
  98       return;
  99     }
 100     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
 101     dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
 102     jvobj = sf;
 103     bindjvvobj(sf, dsa);
 104   }
 105
 106   public void conflict()
 107   {
 108     log.warn("Untested sequencefeature conflict code");
 109     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 110     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 111     jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
 112     replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
 113                                       // to newly created feature
 114     dsSeq.addSequenceFeature(sf); // add new imported feature
 115     addToDocument(); // and create a new feature in the document
 116   }
 117
 118   public void updateToDoc()
 119   {
 120     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 121     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 122     if (dsa.getSeqRefCount() != 1)
 123     {
 124       replaceJvObjMapping(feature, null);
 125       Cache.log
 126               .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
 127       doSync(); // re-verify bindings.
 128     }
 129     else
 130     {
 131       // Sync the features from Jalview
 132       long oldref = dsa.get__last_hash();
 133       getDSAnnotationFromJalview(dsa, feature);
 134       if (oldref != dsa.hashCode())
 135       {
 136         Cache.log
 137                 .debug("Updated dataset sequence annotation from feature.");
 138         addProvenance(dsa.getProvenance(), "modified");
 139       }
 140     }
 141
 142   }
 143
 144   public void updateFromDoc()
 145   {
 146     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 147     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 148     if (dsa.getSeqRefCount() != 1)
 149     {
 150       // conflicting update from document - we cannot map this feature anymore.
 151       replaceJvObjMapping(feature, null);
 152       Cache.log
 153               .warn("annotation ("
 154                       + dsa.getVorbaId()
 155                       + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
 156       // - consider deleting the feature ?
 157       dsSeq.deleteFeature(feature);
 158       // doSync();
 159     }
 160     else
 161     {
 162       // Sync the features to Jalview - easiest to delete and add the feature
 163       // again
 164       jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
 165       dsSeq.deleteFeature(feature);
 166       replaceJvObjMapping(feature, newsf);
 167       dsSeq.addSequenceFeature(newsf);
 168       if (feature.otherDetails != null)
 169       {
 170         // TODO later: leave this to finalise method ?
 171         feature.otherDetails.clear();
 172       }
 173     }
 174   }
 175
 176   /**
 177    * correctly create/update a RangeAnnotation from a jalview sequence feature
 178    * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
 179    *
 180    * @param dsa
 181    *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
 182    * @param feature
 183    *          (the feature to be mapped from)
 184    * @return
 185    */
 186   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
 187           jalview.datamodel.SequenceFeature feature)
 188   {
 189     dsa.setType(feature.getType());
 190     Seg vSeg = new Seg();
 191     vSeg.setStart(feature.getBegin());
 192     vSeg.setEnd(feature.getEnd());
 193     vSeg.setInclusive(true);
 194     if (dsa.getSegCount() > 1)
 195     {
 196       Cache.log
 197               .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
 198                       + dsa.getVorbaId() + ")");
 199     }
 200     dsa.setSeg(new Seg[]
 201     { vSeg });
 202     dsa.setDescription(feature.getDescription());
 203     dsa.setStatus(feature.getStatus());
 204     if (feature.links != null && feature.links.size() > 0)
 205     {
 206       for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
 207       {
 208         String link = (String) feature.links.elementAt(i);
 209         UrlLink ulink = new UrlLink(link);
 210         if (ulink.isValid())
 211         {
 212           // We only add static links to the document.
 213           Link vLink = new Link();
 214           vLink.setContent(ulink.getLabel());
 215           vLink.setHref(ulink.getTarget());
 216           dsa.addLink(vLink);
 217         }
 218       }
 219     }
 220     dsa.setGroup(feature.getFeatureGroup());
 221     if (feature.getScore() != Float.NaN)
 222     {
 223       Score fscore = new Score();
 224       dsa.setScore(new Score[]
 225       { fscore });
 226       fscore.setContent(feature.getScore());
 227       fscore.setName(feature.getType());
 228     }
 229     if (feature.otherDetails != null)
 230     {
 231       Enumeration iter = feature.otherDetails.keys();
 232       Vector props = dsa.getPropertyAsReference();
 233       while (iter.hasMoreElements())
 234       {
 235         String key = (String) iter.nextElement();
 236         if (!key.equalsIgnoreCase("score")
 237                 && !key.equalsIgnoreCase("status"))
 238         {
 239           Property nprop = new Property();
 240           nprop.setName(key);
 241           Object vlu = feature.getValue(key);
 242           nprop.setContent(feature.getValue(key).toString());
 243           boolean valid = false;
 244           if (vlu instanceof String)
 245           {
 246             nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);
 247             valid = true;
 248           }
 249           else if (vlu instanceof Integer)
 250           {
 251             valid = true;
 252             nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
 253           }
 254           else if (vlu instanceof Float)
 255           {
 256             nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);
 257             valid = true;
 258           }
 259           if (valid)
 260           {
 261             if (props != null)
 262             {
 263               uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,
 264                       nprop);
 265             }
 266             else
 267             {
 268               dsa.addProperty(nprop);
 269             }
 270           }
 271         }
 272       }
 273     }
 274     return dsa;
 275   }
 276
 277   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
 278   {
 279     int[] se = getBounds(dseta);
 280     SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 281             dseta.getType(), dseta.getDescription(), dseta.getStatus(),
 282             se[0], se[1], dseta.getGroup());
 283     if (dseta.getLinkCount() > 0)
 284     {
 285       Link[] links = dseta.getLink();
 286       for (int i = 0; i < links.length; i++)
 287       {
 288         // TODO: use URLLink parsing/validation here.
 289         sf.addLink(links[i].getContent() + "|" + links[i].getHref());
 290       }
 291     }
 292     if (dseta.getScoreCount() > 0)
 293     {
 294       Enumeration scr = dseta.enumerateScore();
 295       while (scr.hasMoreElements())
 296       {
 297         Score score = (Score) scr.nextElement();
 298         if (score.getName().equals(sf.getType()))
 299         {
 300           sf.setScore(score.getContent());
 301         }
 302         else
 303         {
 304           sf.setValue(score.getName(), "" + score.getContent());
 305         }
 306       }
 307     }
 308     // other details
 309     Enumeration props = dseta.enumerateProperty();
 310     while (props.hasMoreElements())
 311     {
 312       Property p = (Property) props.nextElement();
 313       Object val = null;
 314       if (Properties.isValid(p))
 315       {
 316         if (Properties.isString(p))
 317         {
 318           val = p.getContent();
 319         }
 320         if (Properties.isBoolean(p))
 321         {
 322           try
 323           {
 324             val = new Boolean(p.getContent());
 325           } catch (Exception e)
 326           {
 327           }
 328         }
 329         if (Properties.isFloat(p))
 330         {
 331           try
 332           {
 333             val = new Float(p.getContent());
 334
 335           } catch (Exception e)
 336           {
 337           }
 338         }
 339         if (Properties.isInteger(p))
 340         {
 341           try
 342           {
 343             val = new Integer(p.getContent());
 344           } catch (Exception e)
 345           {
 346           }
 347         }
 348         if (val != null)
 349         {
 350           sf.setValue(p.getName(), val);
 351         }
 352       }
 353     }
 354
 355     return sf;
 356   }
 357
 358 }