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.AlignedCodonFrame;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.DBRefEntry;
27 import jalview.datamodel.Mapping;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.Desktop;
30 import jalview.io.VamsasAppDatastore;
32 import java.util.ArrayList;
33 import java.util.List;
34 import java.util.Vector;
36 import uk.ac.vamsas.objects.core.AlignmentSequence;
37 import uk.ac.vamsas.objects.core.DataSet;
38 import uk.ac.vamsas.objects.core.Sequence;
39 import uk.ac.vamsas.objects.core.SequenceMapping;
40 import uk.ac.vamsas.objects.core.SequenceType;
43 * binds a vamsas sequence mapping object from the vamsas document to a maplist
44 * object associated with a mapping in the Jalview model. We use the maplist
45 * object because these are referred to both in the Mapping object associated
46 * with a jalview.datamodel.DBRefEntry and in the array of
47 * jalview.datamodel.AlCodonFrame objects that Jalview uses to propagate
48 * sequence mapping position highlighting across the views.
53 public class Sequencemapping extends Rangetype
55 public Sequencemapping(VamsasAppDatastore datastore,
56 SequenceMapping sequenceMapping)
58 super(datastore, sequenceMapping, jalview.util.MapList.class);
62 private SequenceType from;
66 private Mapping mjvmapping;
69 * create or update a vamsas sequence mapping corresponding to a jalview
70 * Mapping between two dataset sequences
77 public Sequencemapping(VamsasAppDatastore datastore,
78 jalview.datamodel.Mapping mjvmapping,
79 uk.ac.vamsas.objects.core.SequenceType from,
80 uk.ac.vamsas.objects.core.DataSet ds)
82 super(datastore, mjvmapping.getMap(), SequenceMapping.class);
85 this.mjvmapping = mjvmapping;
91 * local check that extant mapping context is valid
93 public void validate()
96 SequenceMapping sequenceMapping = (SequenceMapping) vobj;
97 if (sequenceMapping == null)
101 if (from != null && sequenceMapping.getLoc() != from)
103 Cache.warn("Probable IMPLEMENTATION ERROR: " + from
104 + " doesn't match the local mapping sequence.");
106 if (ds != null && sequenceMapping.is__stored_in_document()
107 && sequenceMapping.getV_parent() != ds)
109 Cache.warn("Probable IMPLEMENTATION ERROR: " + ds
110 + " doesn't match the parent of the bound sequence mapping object.");
114 public void addToDocument()
116 add(mjvmapping, from, ds);
119 public void addFromDocument()
121 add((SequenceMapping) vobj);
124 public void conflict()
126 conflict(mjvmapping, (SequenceMapping) vobj);
130 public void updateToDoc()
132 update(mjvmapping, (SequenceMapping) vobj);
135 public void updateFromDoc()
137 update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj);
140 private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
142 System.err.println("Conflict in update of sequenceMapping "
143 + sequenceMapping.getVorbaId());
146 private void add(Mapping mjvmapping,
147 uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
149 SequenceI jvto = mjvmapping.getTo();
150 while (jvto.getDatasetSequence() != null)
152 jvto = jvto.getDatasetSequence();
154 SequenceType to = (SequenceType) getjv2vObj(jvto);
158 "FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
161 SequenceMapping sequenceMapping = new SequenceMapping();
162 sequenceMapping.setLoc(from);
163 sequenceMapping.setMap(to);
164 boolean dnaToProt = false, sense = false;
165 // ensure that we create a mapping with the correct sense
166 if (((Sequence) sequenceMapping.getLoc()).getDictionary().equals(
167 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
169 if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
170 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
178 if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
179 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
189 "Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
194 // locate dataset for storage of SequenceMapping
197 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
198 .getLoc()).getV_parent();
202 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
203 .getMap()).getV_parent();
208 this.initMapType(sequenceMapping, mjvmapping.getMap(), true);
212 this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(),
215 ds.addSequenceMapping(sequenceMapping);
216 sequenceMapping.setProvenance(
217 this.dummyProvenance("user defined coding region translation")); // TODO:
226 bindjvvobj(mjvmapping.getMap(), sequenceMapping);
229 "Successfully created mapping " + sequenceMapping.getVorbaId());
232 // private void update(jalview.util.MapList mjvmapping,
233 // SequenceMapping sequenceMapping)
235 Cache.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
238 private void update(SequenceMapping sequenceMapping,
239 jalview.datamodel.Mapping mjvmapping)
241 Cache.error("Not implemented: Update DBRef Mapping from Jalview");
244 private void update(jalview.datamodel.Mapping mjvmapping,
245 SequenceMapping sequenceMapping)
248 "Not implemented: Jalview Update Sequence DBRef Mapping");
252 * bind a SequenceMapping to a live AlCodonFrame element limitations:
253 * Currently, jalview only deals with mappings between dataset sequences, and
254 * even then, only between those that map from DNA to Protein.
256 * @param sequenceMapping
258 private void add(SequenceMapping sequenceMapping)
261 SequenceI from = null, to = null;
262 boolean dnaToProt = false, sense = false;
263 Sequence sdloc = null, sdmap = null;
264 if (sequenceMapping.getLoc() instanceof AlignmentSequence)
266 sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc())
271 sdloc = ((Sequence) sequenceMapping.getLoc());
273 if (sequenceMapping.getMap() instanceof AlignmentSequence)
275 sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap())
280 sdmap = ((Sequence) sequenceMapping.getMap());
282 if (sdloc == null || sdmap == null)
284 Cache.info("Ignoring non sequence-sequence mapping");
287 mobj = this.getvObj2jv(sdloc);
288 if (mobj instanceof SequenceI)
290 from = (SequenceI) mobj;
292 mobj = this.getvObj2jv(sdmap);
293 if (mobj instanceof SequenceI)
295 to = (SequenceI) mobj;
297 if (from == null || to == null)
301 "Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
305 if (sdloc.getDictionary().equals(
306 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
308 if (sdmap.getDictionary().equals(
309 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
320 if (sdmap.getDictionary().equals(
321 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
327 // create mapping storage object and make each dataset alignment reference
329 AlignmentI dsLoc = (AlignmentI) getvObj2jv(sdloc.getV_parent());
330 AlignmentI dsMap = (AlignmentI) getvObj2jv(sdmap.getV_parent());
331 AlignedCodonFrame acf = new AlignedCodonFrame();
333 if (dsLoc != null && dsLoc != dsMap)
335 dsLoc.addCodonFrame(acf);
339 dsMap.addCodonFrame(acf);
341 // create and add the new mapping to (each) dataset's codonFrame
343 jalview.util.MapList mapping = null;
348 mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
349 mapping = new jalview.util.MapList(mapping.getToRanges(),
350 mapping.getFromRanges(), mapping.getToRatio(),
351 mapping.getFromRatio());
352 acf.addMap(to, from, mapping);
356 mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
357 acf.addMap(from, to, mapping);
362 mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
363 acf.addMap(from, to, mapping);
365 bindjvvobj(mapping, sequenceMapping);
366 jalview.structure.StructureSelectionManager
367 .getStructureSelectionManager(Desktop.instance)
368 .registerMapping(acf);
369 // Try to link up any conjugate database references in the two sequences
370 // matchConjugateDBRefs(from, to, mapping);
371 // Try to propagate any dbrefs across this mapping.
376 * Complete any 'to' references in jalview.datamodel.Mapping objects
377 * associated with conjugate DBRefEntry under given mapping
380 * sequence corresponding to from reference for sequence mapping
382 * sequence correspondeing to to reference for sequence mapping
384 * maplist parsed in same sense as from and to
386 private void matchConjugateDBRefs(SequenceI from, SequenceI to,
387 jalview.util.MapList smap)
389 if (from.getDBRefs() == null && to.getDBRefs() == null)
391 if (Cache.isDebugEnabled())
393 Cache.debug("Not matching conjugate refs for "
394 + from.getName() + " and " + to.getName());
398 if (Cache.isDebugEnabled())
400 Cache.debug("Matching conjugate refs for "
401 + from.getName() + " and " + to.getName());
403 List<DBRefEntry> fdb = from.getDBRefs();
404 List<DBRefEntry> tdb = new ArrayList<DBRefEntry>(to.getDBRefs());
405 int tdblen = to.getDBRefs().size();
410 // System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
415 Vector matched = new Vector();
416 jalview.util.MapList smapI = smap.getInverse();
417 for (int f = 0, fn = fdb.size(); f < fn; f++)
419 jalview.datamodel.DBRefEntry fe = fdb.get(f);
420 jalview.datamodel.Mapping fmp = fe.getMap();
421 boolean fmpnnl = (fmp != null);
422 // if (fmpnnl && fmp.getTo()!=null)
424 // Cache.debug("Not overwriting existing To reference in
428 // smap from maps from fe.local to fe.map
429 boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap())
431 // smap from maps from fe.map to fe.local.
432 boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap())
434 for (int t = 0; t < tdblen; t++)
436 jalview.datamodel.DBRefEntry te = tdb.get(t);
439 if (fe.getSource().equals(te.getSource())
440 && fe.getAccessionId().equals(te.getAccessionId()))
442 jalview.datamodel.Mapping tmp = te.getMap();
443 boolean tmpnnl = tmp != null;
444 if (tmpnnl && tmp.getTo() != null)
448 // smap to maps from te.local to te.map
449 boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap())
451 // smap to maps from te.map to te.local
452 boolean smaptotemap2local = (tmpnnl)
453 ? smapI.equals(fmp.getMap())
455 if (smapfromlocal2fe && smaptotemap2local)
457 // smap implies mapping from to to from
461 else if (smapfromfemap2local && smaptolocal2tm)