src/jalview/io/vamsas/Sequencefeature.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   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
  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 java.util.Enumeration;
  24 import java.util.Vector;
  25
  26 import uk.ac.vamsas.objects.core.DataSetAnnotations;
  27 import uk.ac.vamsas.objects.core.Link;
  28 import uk.ac.vamsas.objects.core.Property;
  29 import uk.ac.vamsas.objects.core.Provenance;
  30 import uk.ac.vamsas.objects.core.RangeAnnotation;
  31 import uk.ac.vamsas.objects.core.Score;
  32 import uk.ac.vamsas.objects.core.Seg;
  33 import uk.ac.vamsas.objects.utils.Properties;
  34 import jalview.bin.Cache;
  35 import jalview.datamodel.SequenceFeature;
  36 import jalview.datamodel.SequenceI;
  37 import jalview.io.VamsasAppDatastore;
  38 import jalview.util.UrlLink;
  39
  40 /**
  41  * @author JimP
  42  *
  43  */
  44 public class Sequencefeature extends Rangetype
  45 {
  46
  47   uk.ac.vamsas.objects.core.DataSet dataset;
  48
  49   uk.ac.vamsas.objects.core.Sequence sequence;
  50
  51   private SequenceI dsSeq;
  52
  53   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  54           SequenceFeature sequenceFeature,
  55           uk.ac.vamsas.objects.core.DataSet dataset,
  56           uk.ac.vamsas.objects.core.Sequence sequence)
  57   {
  58     super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);
  59     this.dataset = dataset;
  60     this.sequence = sequence;
  61     doSync();
  62   }
  63
  64   public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
  65           DataSetAnnotations dseta, SequenceI dsSeq)
  66   {
  67     super(vamsasAppDatastore, dseta,
  68             jalview.datamodel.SequenceFeature.class);
  69     this.dsSeq = dsSeq;
  70     doJvUpdate();
  71   }
  72
  73   public void addToDocument()
  74   {
  75     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  76     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
  77     dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
  78             new DataSetAnnotations(), feature);
  79     if (dsa.getProvenance() == null)
  80     {
  81       dsa.setProvenance(new Provenance());
  82     }
  83     addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
  84     // to update
  85     dsa.addSeqRef(sequence); // we have just created this annotation
  86     // - so safe to use this
  87     bindjvvobj(feature, dsa);
  88     dataset.addDataSetAnnotations(dsa);
  89   }
  90
  91   public void addFromDocument()
  92   {
  93     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
  94     if (dsa.getSeqRefCount() != 1)
  95     {
  96       Cache.log
  97               .warn("Not binding "
  98                       + dsa.getVorbaId()
  99                       + " to Sequence Feature - has multiple dataset sequence references.");
 100       return;
 101     }
 102     jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
 103     dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
 104     jvobj = sf;
 105     bindjvvobj(sf, dsa);
 106   }
 107
 108   public void conflict()
 109   {
 110     log.warn("Untested sequencefeature conflict code");
 111     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 112     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 113     jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
 114     replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
 115                                       // to newly created feature
 116     dsSeq.addSequenceFeature(sf); // add new imported feature
 117     addToDocument(); // and create a new feature in the document
 118   }
 119
 120   public void updateToDoc()
 121   {
 122     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 123     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 124     if (dsa.getSeqRefCount() != 1)
 125     {
 126       replaceJvObjMapping(feature, null);
 127       Cache.log
 128               .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
 129       doSync(); // re-verify bindings.
 130     }
 131     else
 132     {
 133       // Sync the features from Jalview
 134       long oldref = dsa.get__last_hash();
 135       getDSAnnotationFromJalview(dsa, feature);
 136       if (oldref != dsa.hashCode())
 137       {
 138         Cache.log
 139                 .debug("Updated dataset sequence annotation from feature.");
 140         addProvenance(dsa.getProvenance(), "modified");
 141       }
 142     }
 143
 144   }
 145
 146   public void updateFromDoc()
 147   {
 148     DataSetAnnotations dsa = (DataSetAnnotations) vobj;
 149     jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
 150     if (dsa.getSeqRefCount() != 1)
 151     {
 152       // conflicting update from document - we cannot map this feature anymore.
 153       replaceJvObjMapping(feature, null);
 154       Cache.log
 155               .warn("annotation ("
 156                       + dsa.getVorbaId()
 157                       + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
 158       // - consider deleting the feature ?
 159       dsSeq.deleteFeature(feature);
 160       // doSync();
 161     }
 162     else
 163     {
 164       // Sync the features to Jalview - easiest to delete and add the feature
 165       // again
 166       jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
 167       dsSeq.deleteFeature(feature);
 168       replaceJvObjMapping(feature, newsf);
 169       dsSeq.addSequenceFeature(newsf);
 170       if (feature.otherDetails != null)
 171       {
 172         // TODO later: leave this to finalise method ?
 173         feature.otherDetails.clear();
 174       }
 175     }
 176   }
 177
 178   /**
 179    * correctly create/update a RangeAnnotation from a jalview sequence feature
 180    * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
 181    *
 182    * @param dsa
 183    *          (typically DataSetAnnotations or AlignmentSequenceAnnotation)
 184    * @param feature
 185    *          (the feature to be mapped from)
 186    * @return
 187    */
 188   private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
 189           jalview.datamodel.SequenceFeature feature)
 190   {
 191     dsa.setType(feature.getType());
 192     Seg vSeg = new Seg();
 193     vSeg.setStart(feature.getBegin());
 194     vSeg.setEnd(feature.getEnd());
 195     vSeg.setInclusive(true);
 196     if (dsa.getSegCount() > 1)
 197     {
 198       Cache.log
 199               .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
 200                       + dsa.getVorbaId() + ")");
 201     }
 202     dsa.setSeg(new Seg[]
 203     { 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 = (String) 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 (feature.getScore() != Float.NaN)
 224     {
 225       Score fscore = new Score();
 226       dsa.setScore(new Score[]
 227       { fscore });
 228       fscore.setContent(feature.getScore());
 229       fscore.setName(feature.getType());
 230     }
 231     if (feature.otherDetails != null)
 232     {
 233       Enumeration iter = feature.otherDetails.keys();
 234       Vector props = dsa.getPropertyAsReference();
 235       while (iter.hasMoreElements())
 236       {
 237         String key = (String) iter.nextElement();
 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(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
 255           }
 256           else if (vlu instanceof Float)
 257           {
 258             nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);
 259             valid = true;
 260           }
 261           if (valid)
 262           {
 263             if (props != null)
 264             {
 265               uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,
 266                       nprop);
 267             }
 268             else
 269             {
 270               dsa.addProperty(nprop);
 271             }
 272           }
 273         }
 274       }
 275     }
 276     return dsa;
 277   }
 278
 279   private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
 280   {
 281     int[] se = getBounds(dseta);
 282     SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 283             dseta.getType(), dseta.getDescription(), dseta.getStatus(),
 284             se[0], se[1], dseta.getGroup());
 285     if (dseta.getLinkCount() > 0)
 286     {
 287       Link[] links = dseta.getLink();
 288       for (int i = 0; i < links.length; i++)
 289       {
 290         // TODO: use URLLink parsing/validation here.
 291         sf.addLink(links[i].getContent() + "|" + links[i].getHref());
 292       }
 293     }
 294     if (dseta.getScoreCount() > 0)
 295     {
 296       Enumeration scr = dseta.enumerateScore();
 297       while (scr.hasMoreElements())
 298       {
 299         Score score = (Score) scr.nextElement();
 300         if (score.getName().equals(sf.getType()))
 301         {
 302           sf.setScore(score.getContent());
 303         }
 304         else
 305         {
 306           sf.setValue(score.getName(), "" + score.getContent());
 307         }
 308       }
 309     }
 310     // other details
 311     Enumeration props = dseta.enumerateProperty();
 312     while (props.hasMoreElements())
 313     {
 314       Property p = (Property) props.nextElement();
 315       Object val = null;
 316       if (Properties.isValid(p))
 317       {
 318         if (Properties.isString(p))
 319         {
 320           val = p.getContent();
 321         }
 322         if (Properties.isBoolean(p))
 323         {
 324           try
 325           {
 326             val = new Boolean(p.getContent());
 327           } catch (Exception e)
 328           {
 329           }
 330         }
 331         if (Properties.isFloat(p))
 332         {
 333           try
 334           {
 335             val = new Float(p.getContent());
 336
 337           } catch (Exception e)
 338           {
 339           }
 340         }
 341         if (Properties.isInteger(p))
 342         {
 343           try
 344           {
 345             val = new Integer(p.getContent());
 346           } catch (Exception e)
 347           {
 348           }
 349         }
 350         if (val != null)
 351         {
 352           sf.setValue(p.getName(), val);
 353         }
 354       }
 355     }
 356
 357     return sf;
 358   }
 359
 360 }