- Object sv = targetView.getSelectedItem();
-
- return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
- }
-
- /**
- * Adds PDB structures to a new or existing structure viewer
- *
- * @param ssm
- * @param pdbEntriesToView
- * @param alignPanel
- * @param sequences
- * @return
- */
- private StructureViewer launchStructureViewer(
- StructureSelectionManager ssm,
- final PDBEntry[] pdbEntriesToView,
- final AlignmentPanel alignPanel, SequenceI[] sequences)
- {
- long progressId = sequences.hashCode();
- setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"), progressId);
- final StructureViewer theViewer = getTargetedStructureViewer(ssm);
- boolean superimpose = chk_superpose.isSelected();
- theViewer.setSuperpose(superimpose);
-
- /*
- * remember user's choice of superimpose or not
- */
- Cache.setProperty(AUTOSUPERIMPOSE,
- Boolean.valueOf(superimpose).toString());
-
- 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().isEmpty())
- {
- 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 = seqsWithoutSourceDBRef
- .toArray(new SequenceI[y]);
- DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
- dbRefFetcher.fetchDBRefs(true);
-
- setProgressBar("Fetch complete.", progressId); // todo i18n
- }
- }
- if (pdbEntriesToView.length > 1)
- {
- setProgressBar(MessageManager.getString(
- "status.fetching_3d_structures_for_selected_entries"),
- progressId);
- theViewer.viewStructures(pdbEntriesToView, sequences, alignPanel);
- }
- else
- {
- setProgressBar(MessageManager.formatMessage(
- "status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()),progressId);
- theViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
- setProgressBar(null, progressId);
- // remember the last viewer we used...
- lastTargetedView = theViewer;
- return theViewer;