2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.io.vamsas;
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;
29 import java.util.Enumeration;
30 import java.util.Iterator;
31 import java.util.Vector;
33 import uk.ac.vamsas.objects.core.DataSetAnnotations;
34 import uk.ac.vamsas.objects.core.Link;
35 import uk.ac.vamsas.objects.core.Property;
36 import uk.ac.vamsas.objects.core.Provenance;
37 import uk.ac.vamsas.objects.core.RangeAnnotation;
38 import uk.ac.vamsas.objects.core.Score;
39 import uk.ac.vamsas.objects.core.Seg;
40 import uk.ac.vamsas.objects.utils.Properties;
46 public class Sequencefeature extends Rangetype
49 uk.ac.vamsas.objects.core.DataSet dataset;
51 uk.ac.vamsas.objects.core.Sequence sequence;
53 private SequenceI dsSeq;
55 public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
56 SequenceFeature sequenceFeature,
57 uk.ac.vamsas.objects.core.DataSet dataset,
58 uk.ac.vamsas.objects.core.Sequence sequence)
60 super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);
61 this.dataset = dataset;
62 this.sequence = sequence;
66 public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
67 DataSetAnnotations dseta, SequenceI dsSeq)
69 super(vamsasAppDatastore, dseta,
70 jalview.datamodel.SequenceFeature.class);
76 public void addToDocument()
78 DataSetAnnotations dsa = (DataSetAnnotations) vobj;
79 jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
80 dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
81 new DataSetAnnotations(), feature);
82 if (dsa.getProvenance() == null)
84 dsa.setProvenance(new Provenance());
86 addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
88 dsa.addSeqRef(sequence); // we have just created this annotation
89 // - so safe to use this
90 bindjvvobj(feature, dsa);
91 dataset.addDataSetAnnotations(dsa);
95 public void addFromDocument()
97 DataSetAnnotations dsa = (DataSetAnnotations) vobj;
98 if (dsa.getSeqRefCount() != 1)
103 + " to Sequence Feature - has multiple dataset sequence references.");
106 jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
107 dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
113 public void conflict()
115 log.warn("Untested sequencefeature conflict code");
116 DataSetAnnotations dsa = (DataSetAnnotations) vobj;
117 jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
118 jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
119 replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
120 // to newly created feature
121 dsSeq.addSequenceFeature(sf); // add new imported feature
122 addToDocument(); // and create a new feature in the document
126 public void updateToDoc()
128 DataSetAnnotations dsa = (DataSetAnnotations) vobj;
129 jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
130 if (dsa.getSeqRefCount() != 1)
132 replaceJvObjMapping(feature, null);
134 .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
135 doSync(); // re-verify bindings.
139 // Sync the features from Jalview
140 long oldref = dsa.get__last_hash();
141 getDSAnnotationFromJalview(dsa, feature);
142 if (oldref != dsa.hashCode())
145 .debug("Updated dataset sequence annotation from feature.");
146 addProvenance(dsa.getProvenance(), "modified");
153 public void updateFromDoc()
155 DataSetAnnotations dsa = (DataSetAnnotations) vobj;
156 jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
157 if (dsa.getSeqRefCount() != 1)
159 // conflicting update from document - we cannot map this feature anymore.
160 replaceJvObjMapping(feature, null);
164 + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
165 // - consider deleting the feature ?
166 dsSeq.deleteFeature(feature);
171 // Sync the features to Jalview - easiest to delete and add the feature
173 jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
174 dsSeq.deleteFeature(feature);
175 replaceJvObjMapping(feature, newsf);
176 dsSeq.addSequenceFeature(newsf);
177 if (feature.otherDetails != null)
179 // TODO later: leave this to finalise method ?
180 feature.otherDetails.clear();
186 * correctly create/update a RangeAnnotation from a jalview sequence feature
187 * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
190 * (typically DataSetAnnotations or AlignmentSequenceAnnotation)
192 * (the feature to be mapped from)
195 private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
196 jalview.datamodel.SequenceFeature feature)
198 dsa.setType(feature.getType());
199 Seg vSeg = new Seg();
200 vSeg.setStart(feature.getBegin());
201 vSeg.setEnd(feature.getEnd());
202 vSeg.setInclusive(true);
203 if (dsa.getSegCount() > 1)
206 .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
207 + dsa.getVorbaId() + ")");
209 dsa.setSeg(new Seg[] { vSeg });
210 dsa.setDescription(feature.getDescription());
211 dsa.setStatus(feature.getStatus());
212 if (feature.links != null && feature.links.size() > 0)
214 for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
216 String link = feature.links.elementAt(i);
217 UrlLink ulink = new UrlLink(link);
220 // We only add static links to the document.
221 Link vLink = new Link();
222 vLink.setContent(ulink.getLabel());
223 vLink.setHref(ulink.getTarget());
228 dsa.setGroup(feature.getFeatureGroup());
229 if (!Float.isNaN(feature.getScore()))
231 Score fscore = new Score();
232 dsa.setScore(new Score[] { fscore });
233 fscore.setContent(feature.getScore());
234 fscore.setName(feature.getType());
236 if (feature.otherDetails != null)
238 Iterator<String> iter = feature.otherDetails.keySet().iterator();
239 Vector props = dsa.getPropertyAsReference();
240 while (iter.hasNext())
242 String key = iter.next();
243 if (!key.equalsIgnoreCase("score")
244 && !key.equalsIgnoreCase("status"))
246 Property nprop = new Property();
248 Object vlu = feature.getValue(key);
249 nprop.setContent(feature.getValue(key).toString());
250 boolean valid = false;
251 if (vlu instanceof String)
253 nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);
256 else if (vlu instanceof Integer)
259 nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
261 else if (vlu instanceof Float)
263 nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);
270 uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,
275 dsa.addProperty(nprop);
284 private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
286 int[] se = getBounds(dseta);
289 * try to identify feature score
291 boolean scoreFound = false;
293 String featureType = dseta.getType();
294 if (dseta.getScoreCount() > 0)
296 Enumeration scr = dseta.enumerateScore();
297 while (scr.hasMoreElements())
299 Score score = (Score) scr.nextElement();
300 if (score.getName().equals(featureType))
302 theScore = score.getContent();
308 SequenceFeature sf = null;
311 sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
312 se[1], theScore, dseta.getGroup());
316 sf = new SequenceFeature(featureType, dseta.getDescription(), se[0],
317 se[1], dseta.getGroup());
319 sf.setStatus(dseta.getStatus());
320 if (dseta.getLinkCount() > 0)
322 Link[] links = dseta.getLink();
323 for (int i = 0; i < links.length; i++)
325 // TODO: use URLLink parsing/validation here.
326 sf.addLink(links[i].getContent() + "|" + links[i].getHref());
329 if (dseta.getScoreCount() > 0)
331 Enumeration scr = dseta.enumerateScore();
332 while (scr.hasMoreElements())
334 Score score = (Score) scr.nextElement();
335 if (!score.getName().equals(sf.getType()))
337 sf.setValue(score.getName(), "" + score.getContent());
342 Enumeration props = dseta.enumerateProperty();
343 while (props.hasMoreElements())
345 Property p = (Property) props.nextElement();
347 if (Properties.isValid(p))
349 if (Properties.isString(p))
351 val = p.getContent();
353 if (Properties.isBoolean(p))
357 val = new Boolean(p.getContent());
358 } catch (Exception e)
362 if (Properties.isFloat(p))
366 val = new Float(p.getContent());
368 } catch (Exception e)
372 if (Properties.isInteger(p))
376 val = new Integer(p.getContent());
377 } catch (Exception e)
383 sf.setValue(p.getName(), val);