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.datamodel.AlignedCodonFrame;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.DBRefEntry;
26 import jalview.datamodel.Mapping;
27 import jalview.datamodel.SequenceI;
28 import jalview.gui.Desktop;
29 import jalview.io.VamsasAppDatastore;
31 import java.util.ArrayList;
32 import java.util.List;
33 import java.util.Vector;
35 import uk.ac.vamsas.objects.core.AlignmentSequence;
36 import uk.ac.vamsas.objects.core.DataSet;
37 import uk.ac.vamsas.objects.core.Sequence;
38 import uk.ac.vamsas.objects.core.SequenceMapping;
39 import uk.ac.vamsas.objects.core.SequenceType;
42 * binds a vamsas sequence mapping object from the vamsas document to a maplist
43 * object associated with a mapping in the Jalview model. We use the maplist
44 * object because these are referred to both in the Mapping object associated
45 * with a jalview.datamodel.DBRefEntry and in the array of
46 * jalview.datamodel.AlCodonFrame objects that Jalview uses to propagate
47 * sequence mapping position highlighting across the views.
52 public class Sequencemapping extends Rangetype
54 public Sequencemapping(VamsasAppDatastore datastore,
55 SequenceMapping sequenceMapping)
57 super(datastore, sequenceMapping, jalview.util.MapList.class);
61 private SequenceType from;
65 private Mapping mjvmapping;
68 * create or update a vamsas sequence mapping corresponding to a jalview
69 * Mapping between two dataset sequences
76 public Sequencemapping(VamsasAppDatastore datastore,
77 jalview.datamodel.Mapping mjvmapping,
78 uk.ac.vamsas.objects.core.SequenceType from,
79 uk.ac.vamsas.objects.core.DataSet ds)
81 super(datastore, mjvmapping.getMap(), SequenceMapping.class);
84 this.mjvmapping = mjvmapping;
90 * local check that extant mapping context is valid
92 public void validate()
95 SequenceMapping sequenceMapping = (SequenceMapping) vobj;
96 if (sequenceMapping == null)
100 if (from != null && sequenceMapping.getLoc() != from)
102 jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
103 + " doesn't match the local mapping sequence.");
105 if (ds != null && sequenceMapping.is__stored_in_document()
106 && sequenceMapping.getV_parent() != ds)
108 jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + ds
109 + " doesn't match the parent of the bound sequence mapping object.");
114 public void addToDocument()
116 add(mjvmapping, from, ds);
120 public void addFromDocument()
122 add((SequenceMapping) vobj);
126 public void conflict()
128 conflict(mjvmapping, (SequenceMapping) vobj);
133 public void updateToDoc()
135 update(mjvmapping, (SequenceMapping) vobj);
139 public void updateFromDoc()
141 update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj);
144 private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
146 System.err.println("Conflict in update of sequenceMapping "
147 + sequenceMapping.getVorbaId());
150 private void add(Mapping mjvmapping,
151 uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
153 SequenceI jvto = mjvmapping.getTo();
154 while (jvto.getDatasetSequence() != null)
156 jvto = jvto.getDatasetSequence();
158 SequenceType to = (SequenceType) getjv2vObj(jvto);
161 jalview.bin.Cache.log.warn(
162 "FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
165 SequenceMapping sequenceMapping = new SequenceMapping();
166 sequenceMapping.setLoc(from);
167 sequenceMapping.setMap(to);
168 boolean dnaToProt = false, sense = false;
169 // ensure that we create a mapping with the correct sense
170 if (((Sequence) sequenceMapping.getLoc()).getDictionary().equals(
171 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
173 if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
174 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
182 if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
183 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
192 jalview.bin.Cache.log.warn(
193 "Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
198 // locate dataset for storage of SequenceMapping
201 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
202 .getLoc()).getV_parent();
206 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
207 .getMap()).getV_parent();
212 this.initMapType(sequenceMapping, mjvmapping.getMap(), true);
216 this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(),
219 ds.addSequenceMapping(sequenceMapping);
220 sequenceMapping.setProvenance(
221 this.dummyProvenance("user defined coding region translation")); // TODO:
230 bindjvvobj(mjvmapping.getMap(), sequenceMapping);
232 jalview.bin.Cache.log.debug(
233 "Successfully created mapping " + sequenceMapping.getVorbaId());
236 // private void update(jalview.util.MapList mjvmapping,
237 // SequenceMapping sequenceMapping)
239 jalview.bin.Cache.log
240 .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
243 private void update(SequenceMapping sequenceMapping,
244 jalview.datamodel.Mapping mjvmapping)
246 jalview.bin.Cache.log
247 .error("Not implemented: Update DBRef Mapping from Jalview");
250 private void update(jalview.datamodel.Mapping mjvmapping,
251 SequenceMapping sequenceMapping)
253 jalview.bin.Cache.log.error(
254 "Not implemented: Jalview Update Sequence DBRef Mapping");
258 * bind a SequenceMapping to a live AlCodonFrame element limitations:
259 * Currently, jalview only deals with mappings between dataset sequences, and
260 * even then, only between those that map from DNA to Protein.
262 * @param sequenceMapping
264 private void add(SequenceMapping sequenceMapping)
267 SequenceI from = null, to = null;
268 boolean dnaToProt = false, sense = false;
269 Sequence sdloc = null, sdmap = null;
270 if (sequenceMapping.getLoc() instanceof AlignmentSequence)
272 sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc())
277 sdloc = ((Sequence) sequenceMapping.getLoc());
279 if (sequenceMapping.getMap() instanceof AlignmentSequence)
281 sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap())
286 sdmap = ((Sequence) sequenceMapping.getMap());
288 if (sdloc == null || sdmap == null)
290 jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
293 mobj = this.getvObj2jv(sdloc);
294 if (mobj instanceof SequenceI)
296 from = (SequenceI) mobj;
298 mobj = this.getvObj2jv(sdmap);
299 if (mobj instanceof SequenceI)
301 to = (SequenceI) mobj;
303 if (from == null || to == null)
306 jalview.bin.Cache.log.error(
307 "Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
311 if (sdloc.getDictionary().equals(
312 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
314 if (sdmap.getDictionary().equals(
315 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
326 if (sdmap.getDictionary().equals(
327 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
333 // create mapping storage object and make each dataset alignment reference
335 AlignmentI dsLoc = (AlignmentI) getvObj2jv(sdloc.getV_parent());
336 AlignmentI dsMap = (AlignmentI) getvObj2jv(sdmap.getV_parent());
337 AlignedCodonFrame acf = new AlignedCodonFrame();
339 if (dsLoc != null && dsLoc != dsMap)
341 dsLoc.addCodonFrame(acf);
345 dsMap.addCodonFrame(acf);
347 // create and add the new mapping to (each) dataset's codonFrame
349 jalview.util.MapList mapping = null;
354 mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
355 mapping = new jalview.util.MapList(mapping.getToRanges(),
356 mapping.getFromRanges(), mapping.getToRatio(),
357 mapping.getFromRatio());
358 acf.addMap(to, from, mapping);
362 mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
363 acf.addMap(from, to, mapping);
368 mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
369 acf.addMap(from, to, mapping);
371 bindjvvobj(mapping, sequenceMapping);
372 Desktop.getInstance().getStructureSelectionManager()
373 .registerMapping(acf);
374 // Try to link up any conjugate database references in the two sequences
375 // matchConjugateDBRefs(from, to, mapping);
376 // Try to propagate any dbrefs across this mapping.
381 * Complete any 'to' references in jalview.datamodel.Mapping objects
382 * associated with conjugate DBRefEntry under given mapping
385 * sequence corresponding to from reference for sequence mapping
387 * sequence correspondeing to to reference for sequence mapping
389 * maplist parsed in same sense as from and to
391 private void matchConjugateDBRefs(SequenceI from, SequenceI to,
392 jalview.util.MapList smap)
394 if (from.getDBRefs() == null && to.getDBRefs() == null)
396 if (jalview.bin.Cache.log.isDebugEnabled())
398 jalview.bin.Cache.log.debug("Not matching conjugate refs for "
399 + from.getName() + " and " + to.getName());
403 if (jalview.bin.Cache.log.isDebugEnabled())
405 jalview.bin.Cache.log.debug("Matching conjugate refs for "
406 + from.getName() + " and " + to.getName());
408 List<DBRefEntry> fdb = from.getDBRefs();
409 List<DBRefEntry> tdb = new ArrayList<>(to.getDBRefs());
410 int tdblen = to.getDBRefs().size();
415 // System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
420 Vector matched = new Vector();
421 jalview.util.MapList smapI = smap.getInverse();
422 for (int f = 0, fn = fdb.size(); f < fn; f++)
424 jalview.datamodel.DBRefEntry fe = fdb.get(f);
425 jalview.datamodel.Mapping fmp = fe.getMap();
426 boolean fmpnnl = (fmp != null);
427 // if (fmpnnl && fmp.getTo()!=null)
429 // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
433 // smap from maps from fe.local to fe.map
434 boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap())
436 // smap from maps from fe.map to fe.local.
437 boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap())
439 for (int t = 0; t < tdblen; t++)
441 jalview.datamodel.DBRefEntry te = tdb.get(t);
444 if (fe.getSource().equals(te.getSource())
445 && fe.getAccessionId().equals(te.getAccessionId()))
447 jalview.datamodel.Mapping tmp = te.getMap();
448 boolean tmpnnl = tmp != null;
449 if (tmpnnl && tmp.getTo() != null)
453 // smap to maps from te.local to te.map
454 boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap())
456 // smap to maps from te.map to te.local
457 boolean smaptotemap2local = (tmpnnl)
458 ? smapI.equals(fmp.getMap())
460 if (smapfromlocal2fe && smaptotemap2local)
462 // smap implies mapping from to to from
466 else if (smapfromfemap2local && smaptolocal2tm)