+ }
+ }).start();
+ }
+
+ private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+ {
+ Objects.requireNonNull(id);
+ Objects.requireNonNull(pdbEntries);
+ PDBEntry foundEntry = null;
+ for (PDBEntry entry : pdbEntries)
+ {
+ if (entry.getId().equalsIgnoreCase(id))
+ {
+ return entry;
+ }
+ }
+ return foundEntry;
+ }
+
+ private void launchStructureViewer(StructureSelectionManager ssm,
+ final PDBEntry[] pdbEntriesToView,
+ final AlignmentPanel alignPanel, SequenceI[] sequences)
+ {
+ ssm.setProgressBar("Launching PDB structure viewer..");
+ final StructureViewer sViewer = new StructureViewer(ssm);
+
+ if (SiftsSettings.isMapWithSifts())
+ {
+ ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
+ for (SequenceI seq : sequences)
+ {
+ if (seq.getSourceDBRef() == null)
+ {
+ if (seq.getDBRefs() == null)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
+ for (DBRefEntry dbRef : seq.getDBRefs())
+ {
+ if (dbRef.getSource().equalsIgnoreCase("uniprot"))
+ {
+ seq.setSourceDBRef(dbRef);
+ break;
+ }
+ }
+ for (DBRefEntry dbRef : seq.getDBRefs())
+ {
+ if (dbRef.getSource().equalsIgnoreCase("pdb"))
+ {
+ seq.setSourceDBRef(dbRef);
+ break;
+ }
+ }
+ if (seq.getSourceDBRef() == null)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ }
+ }
+ }
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ int y = seqsWithoutSourceDBRef.size();
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(">>>>> Fetching Database refs for " + y
+ + " sequence" + (y > 1 ? "s" : "")
+ + " with no valid uniprot or pdb ref for SIFTS mapping");
+ System.out.println(">>>>> Fetching Database refs for " + y
+ + " sequence" + (y > 1 ? "s" : "")
+ + " with no valid uniprot or pdb ref 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);
+ }