- // old way:
- // PDBEntry[] pdbsForFile = getUniquePdbFiles(pdbs);
-
- // new way:
- Map<PDBEntry, SequenceI[]> seqsForPdb = getSequencesForPdbs(pdbs,
- seqsForPdbs);
- PDBEntry[] pdbsForFile = seqsForPdb.keySet().toArray(
- new PDBEntry[seqsForPdb.size()]);
- SequenceI[][] theSeqs = seqsForPdb.values().toArray(
- new SequenceI[seqsForPdb.size()][]);
- JalviewStructureDisplayI sview = null;
+ Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
+ seqs);
+ PDBEntry[] pdbsForFile = seqsForPdbs.keySet()
+ .toArray(new PDBEntry[seqsForPdbs.size()]);
+ SequenceI[][] theSeqs = seqsForPdbs.values()
+ .toArray(new SequenceI[seqsForPdbs.size()][]);
+ if (sview != null)
+ {
+ sview.setAlignAddedStructures(superposeAdded);
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+
+ for (int pdbep = 0; pdbep < pdbsForFile.length; pdbep++)
+ {
+ PDBEntry pdb = pdbsForFile[pdbep];
+ if (!sview.addAlreadyLoadedFile(theSeqs[pdbep], null, ap,
+ pdb.getId()))
+ {
+ sview.addToExistingViewer(pdb, theSeqs[pdbep], null, ap,
+ pdb.getId());
+ }
+ }
+
+ sview.updateTitleAndMenus();
+ }
+ }).start();
+ return sview;
+ }
+