+ ssm.setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"));
+ final StructureViewer sViewer = new StructureViewer(ssm);
+
+ if (SiftsSettings.isMapWithSifts())
+ {
+ List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ int p = 0;
+ // TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
+ // real PDB ID. For moment, we can also safely do this if there is already
+ // a known mapping between the PDBEntry and the sequence.
+ for (SequenceI seq : sequences)
+ {
+ PDBEntry pdbe = pdbEntriesToView[p++];
+ if (pdbe != null && pdbe.getFile() != null)
+ {
+ StructureMapping[] smm = ssm.getMapping(pdbe.getFile());
+ if (smm != null && smm.length > 0)
+ {
+ for (StructureMapping sm : smm)
+ {
+ if (sm.getSequence() == seq)
+ {
+ continue;
+ }
+ }
+ }
+ }
+ if (seq.getPrimaryDBRefs().size() == 0)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
+ }
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ int y = seqsWithoutSourceDBRef.size();
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_dbrefs_for_sequences_without_valid_refs",
+ y));
+ SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
+ int x = 0;
+ for (SequenceI fSeq : seqsWithoutSourceDBRef)
+ {
+ seqWithoutSrcDBRef[x++] = fSeq;
+ }
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
+ dbRefFetcher.fetchDBRefs(true);
+ }
+ }