- long progressId = sequences.hashCode();
- setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"), progressId);
- final StructureViewer sViewer = new StructureViewer(ssm);
- setProgressBar(null, progressId);
-
- if (SiftsSettings.isMapWithSifts())
- {
- List<SequenceI> seqsWithoutSourceDBRef = new ArrayList<>();
- 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();
- setProgressBar(MessageManager.formatMessage(
- "status.fetching_dbrefs_for_sequences_without_valid_refs",
- y), progressId);
- SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
- int x = 0;
- for (SequenceI fSeq : seqsWithoutSourceDBRef)
- {
- seqWithoutSrcDBRef[x++] = fSeq;
- }