1 package jalview.io.vamsas;
3 import java.util.Vector;
5 import jalview.datamodel.AlignedCodonFrame;
6 import jalview.datamodel.Mapping;
7 import jalview.datamodel.SequenceI;
8 import jalview.io.VamsasAppDatastore;
9 import uk.ac.vamsas.client.Vobject;
10 import uk.ac.vamsas.objects.core.AlignmentSequence;
11 import uk.ac.vamsas.objects.core.DataSet;
12 import uk.ac.vamsas.objects.core.Local;
13 import uk.ac.vamsas.objects.core.RangeType;
14 import uk.ac.vamsas.objects.core.Seg;
15 import uk.ac.vamsas.objects.core.Sequence;
16 import uk.ac.vamsas.objects.core.SequenceMapping;
17 import uk.ac.vamsas.objects.core.SequenceType;
19 public class Sequencemapping extends Rangetype
21 public Sequencemapping(VamsasAppDatastore datastore, SequenceMapping sequenceMapping)
24 Object mjvmapping = getvObj2jv(sequenceMapping);
29 if (sequenceMapping.isUpdated())
31 update((jalview.util.MapList) mjvmapping, sequenceMapping);
36 * create or update a vamsas sequence mapping corresponding to a jalview
37 * Mapping between two dataset sequences
44 public Sequencemapping(VamsasAppDatastore datastore, jalview.datamodel.Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, uk.ac.vamsas.objects.core.DataSet ds)
47 SequenceMapping sequenceMapping = (SequenceMapping) getjv2vObj(mjvmapping);
48 if (sequenceMapping==null)
50 add(mjvmapping, from, ds);
52 if (from!=null && sequenceMapping.getLoc()!=from)
54 jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+from+" doesn't match the local mapping sequence.");
56 if (ds!=null && sequenceMapping.is__stored_in_document() && sequenceMapping.getV_parent()!=ds)
58 jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+ds+" doesn't match the parent of the bound sequence mapping object.");
60 if (sequenceMapping.isUpdated())
62 conflict(mjvmapping, sequenceMapping);
64 update(mjvmapping, sequenceMapping);
68 private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
70 System.err.println("Conflict in update of sequenceMapping "+sequenceMapping.getVorbaId());
72 private void add(Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
74 SequenceI jvto = mjvmapping.getTo();
75 while (jvto.getDatasetSequence()!=null)
77 jvto = jvto.getDatasetSequence();
79 SequenceType to = (SequenceType) getjv2vObj(jvto);
82 jalview.bin.Cache.log.warn("NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
85 SequenceMapping sequenceMapping = new SequenceMapping();
86 sequenceMapping.setLoc(from);
87 sequenceMapping.setMap(to);
88 boolean dnaToProt=false,sense=false;
89 // ensure that we create a mapping with the correct sense
90 if (((Sequence) sequenceMapping.getLoc())
92 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
94 if (((Sequence) sequenceMapping.getMap())
96 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
102 if (((Sequence) sequenceMapping.getMap())
104 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
113 jalview.bin.Cache.log.warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
118 // locate dataset for storage of SequenceMapping
121 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getLoc()).getV_parent();
123 ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getMap()).getV_parent();
128 this.initMapType(sequenceMapping, mjvmapping.getMap(), true);
130 this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(), true);
132 ds.addSequenceMapping(sequenceMapping);
133 sequenceMapping.setProvenance(this.dummyProvenance("user defined coding region translation")); // TODO:
142 bindjvvobj(mjvmapping, sequenceMapping);
144 jalview.bin.Cache.log.debug("Successfully created mapping "+sequenceMapping.getVorbaId());
146 private void update(jalview.util.MapList mjvmapping, SequenceMapping sequenceMapping)
148 jalview.bin.Cache.log.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
150 private void update(jalview.datamodel.Mapping mjvmapping, SequenceMapping sequenceMapping)
152 jalview.bin.Cache.log.error("Not implemented: Jalview Update Sequence DBRef Mapping");
155 * limitations: Currently, jalview only deals with mappings between dataset
156 * sequences, and even then, only between those that map from DNA to Protein.
158 * @param sequenceMapping
160 private void add(SequenceMapping sequenceMapping)
163 SequenceI from=null,to=null;
164 boolean dnaToProt=false,sense=false;
165 Sequence sdloc=null, sdmap=null;
166 if (sequenceMapping.getLoc() instanceof AlignmentSequence)
168 sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc()).getRefid();
170 sdloc = ((Sequence) sequenceMapping.getLoc());
172 if (sequenceMapping.getMap() instanceof AlignmentSequence)
174 sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap()).getRefid();
176 sdmap = ((Sequence) sequenceMapping.getMap());
178 if (sdloc==null || sdmap == null)
180 jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
183 mobj = this.getvObj2jv((Vobject) sdloc);
184 if (mobj instanceof SequenceI)
186 from = (SequenceI) mobj;
188 mobj = this.getvObj2jv((Vobject) sdmap);
189 if (mobj instanceof SequenceI)
191 to = (SequenceI) mobj;
193 if (from == null || to == null)
196 jalview.bin.Cache.log.error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
200 if (sdloc.getDictionary()
201 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
203 if (sdmap.getDictionary()
204 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
213 if (sdmap.getDictionary()
214 .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
220 // create mapping storage object and make each dataset alignment reference
222 jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc.getV_parent());
223 jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap.getV_parent());
224 AlignedCodonFrame afc = new AlignedCodonFrame(0);
226 if (dsLoc!=null && dsLoc!=dsMap)
228 dsLoc.addCodonFrame(afc);
232 dsMap.addCodonFrame(afc);
234 // create and add the new mapping to (each) dataset's codonFrame
236 jalview.util.MapList mapping = null;
239 mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
240 mapping = new jalview.util.MapList(mapping.getToRanges(), mapping.getFromRanges(), mapping.getToRatio(), mapping.getFromRatio());
241 afc.addMap(to, from, mapping);
243 mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
244 afc.addMap(from, to, mapping);
246 bindjvvobj(mapping, sequenceMapping);
247 jalview.structure.StructureSelectionManager.getStructureSelectionManager().addMappings(new AlignedCodonFrame[] { afc });
248 // Try to link up any conjugate database references in the two sequences
249 // matchConjugateDBRefs(from, to, mapping);
250 // Try to propagate any dbrefs across this mapping.
254 * Complete any 'to' references in jalview.datamodel.Mapping objects associated with conjugate DBRefEntry under given mapping
255 * @param from sequence corresponding to from reference for sequence mapping
256 * @param to sequence correspondeing to to reference for sequence mapping
257 * @param smap maplist parsed in same sense as from and to
259 private void matchConjugateDBRefs(SequenceI from, SequenceI to,
260 jalview.util.MapList smap)
262 if (from.getDBRef()==null && to.getDBRef()==null)
264 if (jalview.bin.Cache.log.isDebugEnabled())
266 jalview.bin.Cache.log.debug("Not matching conjugate refs for "+from.getName()+" and "+to.getName());
270 if (jalview.bin.Cache.log.isDebugEnabled())
272 jalview.bin.Cache.log.debug("Matching conjugate refs for "+from.getName()+" and "+to.getName());
274 jalview.datamodel.DBRefEntry[] fdb = from.getDBRef();
275 jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to.getDBRef().length];
276 int tdblen = to.getDBRef().length;
277 System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
278 Vector matched = new Vector();
279 jalview.util.MapList smapI = smap.getInverse();
280 for (int f=0;f<fdb.length; f++)
282 jalview.datamodel.DBRefEntry fe = fdb[f];
283 jalview.datamodel.Mapping fmp = fe.getMap();
284 boolean fmpnnl = fmp!=null;
285 // if (fmpnnl && fmp.getTo()!=null)
287 // jalview.bin.Cache.log.debug("Not overwriting existing To reference in "+fe);
290 // smap from maps from fe.local to fe.map
291 boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap()) : false;
292 // smap from maps from fe.map to fe.local.
293 boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap()) : false;
294 for (int t=0; t<tdblen; t++)
296 jalview.datamodel.DBRefEntry te = tdb[t];
299 if (fe.getSource().equals(te.getSource())
300 && fe.getAccessionId().equals(te.getAccessionId()))
302 jalview.datamodel.Mapping tmp = te.getMap();
303 boolean tmpnnl = tmp!=null;
304 if (tmpnnl && tmp.getTo()!=null)
308 // smap to maps from te.local to te.map
309 boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap()) : false;
310 // smap to maps from te.map to te.local
311 boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp.getMap()) : false;
312 if (smapfromlocal2fe && smaptotemap2local)
314 // smap implies mapping from to to from
318 if (smapfromfemap2local && smaptolocal2tm) {