- if (SiftsSettings.isMapWithSifts())
- {
- ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
- for (SequenceI seq : sequences)
- {
- if (seq.getSourceDBRef() == null && seq.getDBRefs() == null)
- {
- seqsWithoutSourceDBRef.add(seq);
- continue;
- }
- }
- if (!seqsWithoutSourceDBRef.isEmpty())
- {
- int y = seqsWithoutSourceDBRef.size();
- ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching db refs for " + y
- + " sequence" + (y > 1 ? "s" : "")
- + " without valid db ref required for SIFTS mapping");
- SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
- int x = 0;
- for (SequenceI fSeq : seqsWithoutSourceDBRef)
- {
- seqWithoutSrcDBRef[x++] = fSeq;
- }
- new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
- }
- }
- if (pdbEntriesToView.length > 1)
- {
- ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
- for (SequenceI seq : sequences)
- {
- seqsMap.add(new SequenceI[] { seq });
- }
- SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
- ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching PDB Structures for selected entries..");
- sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
- }
- else
- {
- ssm.setProgressBar(null);
- ssm.setProgressBar("Fetching PDB Structure for "
- + pdbEntriesToView[0].getId());
- sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
+ return sv == null ? new StructureViewer(ssm) : (StructureViewer) sv;
+ }
+
+ /**
+ * Adds PDB structures to a new or existing structure viewer
+ *
+ * @param ap
+ * @param pdbEntriesToView
+ * @param sequences
+ * @param superimpose
+ * @return viewer
+ */
+ protected StructureViewer launchStructureViewer(
+ AlignmentPanel ap, PDBEntry[] pdbEntriesToView,
+ SequenceI[] selectedSeqs)
+ {
+ boolean superimpose = chk_superpose.isSelected();
+ /*
+ * remember user's choice of superimpose or not
+ */
+ Cache.setProperty(AUTOSUPERIMPOSE,
+ Boolean.valueOf(superimpose).toString());
+ return StructureViewer.launchStructureViewer(ap, pdbEntriesToView, selectedSeqs,
+ superimpose, getTargetedStructureViewer(), progressBar);