2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
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.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.io.vamsas;
20 import java.util.Vector;
22 import jalview.datamodel.AlignedCodonFrame;
23 import jalview.datamodel.Mapping;
24 import jalview.datamodel.SequenceI;
25 import jalview.gui.Desktop;
26 import jalview.io.VamsasAppDatastore;
27 import uk.ac.vamsas.client.Vobject;
28 import uk.ac.vamsas.objects.core.AlignmentSequence;
29 import uk.ac.vamsas.objects.core.DataSet;
30 import uk.ac.vamsas.objects.core.Sequence;
31 import uk.ac.vamsas.objects.core.SequenceMapping;
32 import uk.ac.vamsas.objects.core.SequenceType;
35 * binds a vamsas sequence mapping object from the vamsas document to a maplist
36 * object associated with a mapping in the Jalview model. We use the maplist
37 * object because these are referred to both in the Mapping object associated
38 * with a jalview.datamodel.DBRefEntry and in the array of
39 * jalview.datamodel.AlCodonFrame objects that Jalview uses to propagate
40 * sequence mapping position highlighting across the views.
45 public class Sequencemapping extends Rangetype
47 public Sequencemapping(VamsasAppDatastore datastore,
48 SequenceMapping sequenceMapping)
50 super(datastore, sequenceMapping, jalview.util.MapList.class);
54 private SequenceType from;
58 private Mapping mjvmapping;
61 * create or update a vamsas sequence mapping corresponding to a jalview
62 * Mapping between two dataset sequences
69 public Sequencemapping(VamsasAppDatastore datastore,
70 jalview.datamodel.Mapping mjvmapping,
71 uk.ac.vamsas.objects.core.SequenceType from,
72 uk.ac.vamsas.objects.core.DataSet ds)
74 super(datastore, mjvmapping.getMap(), SequenceMapping.class);
77 this.mjvmapping = mjvmapping;
83 * local check that extant mapping context is valid
85 public void validate()
88 SequenceMapping sequenceMapping = (SequenceMapping) vobj;
89 if (sequenceMapping == null)
93 if (from != null && sequenceMapping.getLoc() != from)
95 jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
96 + " doesn't match the local mapping sequence.");
98 if (ds != null && sequenceMapping.is__stored_in_document()
99 && sequenceMapping.getV_parent() != ds)
101 jalview.bin.Cache.log
102 .warn("Probable IMPLEMENTATION ERROR: "
104 + " doesn't match the parent of the bound sequence mapping object.");
108 public void addToDocument()
110 add(mjvmapping, from, ds);
113 public void addFromDocument()
115 add((SequenceMapping) vobj);
118 public void conflict()
120 conflict(mjvmapping, (SequenceMapping) vobj);
124 public void updateToDoc()
126 update(mjvmapping, (SequenceMapping) vobj);
129 public void updateFromDoc()
131 update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj);
134 private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
136 System.err.println("Conflict in update of sequenceMapping "
137 + sequenceMapping.getVorbaId());
140 private void add(Mapping mjvmapping,
141 uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
143 SequenceI jvto = mjvmapping.getTo();
144 while (jvto.getDatasetSequence() != null)
146 jvto = jvto.getDatasetSequence();
148 SequenceType to = (SequenceType) getjv2vObj(jvto);
151 jalview.bin.Cache.log
152 .warn("FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
155 SequenceMapping sequenceMapping = new SequenceMapping();
156 sequenceMapping.setLoc(from);
157 sequenceMapping.setMap(to);
158 boolean dnaToProt = false, sense = false;
159 // ensure that we create a mapping with the correct sense
160 if (((Sequence) sequenceMapping.getLoc()).getDictionary().equals(
161 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
163 if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
164 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
172 if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
173 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
182 jalview.bin.Cache.log
183 .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
188 // locate dataset for storage of SequenceMapping
191 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
192 .getLoc()).getV_parent();
196 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
197 .getMap()).getV_parent();
202 this.initMapType(sequenceMapping, mjvmapping.getMap(), true);
206 this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(),
209 ds.addSequenceMapping(sequenceMapping);
210 sequenceMapping.setProvenance(this
211 .dummyProvenance("user defined coding region translation")); // TODO:
220 bindjvvobj(mjvmapping.getMap(), sequenceMapping);
222 jalview.bin.Cache.log.debug("Successfully created mapping "
223 + sequenceMapping.getVorbaId());
226 // private void update(jalview.util.MapList mjvmapping,
227 // SequenceMapping sequenceMapping)
229 jalview.bin.Cache.log
230 .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
233 private void update(SequenceMapping sequenceMapping,
234 jalview.datamodel.Mapping mjvmapping)
236 jalview.bin.Cache.log
237 .error("Not implemented: Update DBRef Mapping from Jalview");
240 private void update(jalview.datamodel.Mapping mjvmapping,
241 SequenceMapping sequenceMapping)
243 jalview.bin.Cache.log
244 .error("Not implemented: Jalview Update Sequence DBRef Mapping");
248 * bind a SequenceMapping to a live AlCodonFrame element limitations:
249 * Currently, jalview only deals with mappings between dataset sequences, and
250 * even then, only between those that map from DNA to Protein.
252 * @param sequenceMapping
254 private void add(SequenceMapping sequenceMapping)
257 SequenceI from = null, to = null;
258 boolean dnaToProt = false, sense = false;
259 Sequence sdloc = null, sdmap = null;
260 if (sequenceMapping.getLoc() instanceof AlignmentSequence)
262 sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc())
267 sdloc = ((Sequence) sequenceMapping.getLoc());
269 if (sequenceMapping.getMap() instanceof AlignmentSequence)
271 sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap())
276 sdmap = ((Sequence) sequenceMapping.getMap());
278 if (sdloc == null || sdmap == null)
280 jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
283 mobj = this.getvObj2jv((Vobject) sdloc);
284 if (mobj instanceof SequenceI)
286 from = (SequenceI) mobj;
288 mobj = this.getvObj2jv((Vobject) sdmap);
289 if (mobj instanceof SequenceI)
291 to = (SequenceI) mobj;
293 if (from == null || to == null)
296 jalview.bin.Cache.log
297 .error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
301 if (sdloc.getDictionary().equals(
302 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
304 if (sdmap.getDictionary().equals(
305 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
316 if (sdmap.getDictionary().equals(
317 uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
323 // create mapping storage object and make each dataset alignment reference
325 jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc
327 jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap
329 AlignedCodonFrame afc = new AlignedCodonFrame(0);
331 if (dsLoc != null && dsLoc != dsMap)
333 dsLoc.addCodonFrame(afc);
337 dsMap.addCodonFrame(afc);
339 // create and add the new mapping to (each) dataset's codonFrame
341 jalview.util.MapList mapping = null;
346 mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
347 mapping = new jalview.util.MapList(mapping.getToRanges(),
348 mapping.getFromRanges(), mapping.getToRatio(),
349 mapping.getFromRatio());
350 afc.addMap(to, from, mapping);
354 mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
355 afc.addMap(from, to, mapping);
360 mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
361 afc.addMap(from, to, mapping);
363 bindjvvobj(mapping, sequenceMapping);
364 jalview.structure.StructureSelectionManager
365 .getStructureSelectionManager(Desktop.instance).addMappings(
366 new AlignedCodonFrame[]
368 // Try to link up any conjugate database references in the two sequences
369 // matchConjugateDBRefs(from, to, mapping);
370 // Try to propagate any dbrefs across this mapping.
375 * Complete any 'to' references in jalview.datamodel.Mapping objects
376 * associated with conjugate DBRefEntry under given mapping
379 * sequence corresponding to from reference for sequence mapping
381 * sequence correspondeing to to reference for sequence mapping
383 * maplist parsed in same sense as from and to
385 private void matchConjugateDBRefs(SequenceI from, SequenceI to,
386 jalview.util.MapList smap)
388 if (from.getDBRef() == null && to.getDBRef() == null)
390 if (jalview.bin.Cache.log.isDebugEnabled())
392 jalview.bin.Cache.log.debug("Not matching conjugate refs for "
393 + from.getName() + " and " + to.getName());
397 if (jalview.bin.Cache.log.isDebugEnabled())
399 jalview.bin.Cache.log.debug("Matching conjugate refs for "
400 + from.getName() + " and " + to.getName());
402 jalview.datamodel.DBRefEntry[] fdb = from.getDBRef();
403 jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
405 int tdblen = to.getDBRef().length;
406 System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
407 Vector matched = new Vector();
408 jalview.util.MapList smapI = smap.getInverse();
409 for (int f = 0; f < fdb.length; f++)
411 jalview.datamodel.DBRefEntry fe = fdb[f];
412 jalview.datamodel.Mapping fmp = fe.getMap();
413 boolean fmpnnl = fmp != null;
414 // if (fmpnnl && fmp.getTo()!=null)
416 // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
420 // smap from maps from fe.local to fe.map
421 boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap())
423 // smap from maps from fe.map to fe.local.
424 boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap())
426 for (int t = 0; t < tdblen; t++)
428 jalview.datamodel.DBRefEntry te = tdb[t];
431 if (fe.getSource().equals(te.getSource())
432 && fe.getAccessionId().equals(te.getAccessionId()))
434 jalview.datamodel.Mapping tmp = te.getMap();
435 boolean tmpnnl = tmp != null;
436 if (tmpnnl && tmp.getTo() != null)
440 // smap to maps from te.local to te.map
441 boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap())
443 // smap to maps from te.map to te.local
444 boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp
446 if (smapfromlocal2fe && smaptotemap2local)
448 // smap implies mapping from to to from
452 else if (smapfromfemap2local && smaptolocal2tm)