Merge branch 'Release_2_8_2_Branch' into features/JAL-1333

diff --combined src/jalview/gui/PopupMenu.java
index e256b33,ace4762..44860a1
--- 1/src/jalview/gui/PopupMenu.java
--- 2/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@@ -256,12 -256,9 +256,12 @@@ public class PopupMenu extends JPopupMe
              {
                // TODO re JAL-860: optionally open dialog or provide a menu entry
                // allowing user to open just one structure per sequence
 -              new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 -              { pdb })[0], null, ap);
 -              // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
 +              //new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
 +              //{ pdb })[0], null, ap);
 +              new StructureViewer(ap.getStructureSelectionManager())
 +                      .viewStructures(pdb,
 +                              ap.av.collateForPDB(new PDBEntry[]
 +                              { pdb })[0], null, ap);
              }
  
            });
@@@ -561,7 -558,7 +561,7 @@@
            @Override
            public void actionPerformed(ActionEvent e)
            {
 -            new AppJmol(ap, pe, ap.av.collateForPDB(pe));
 +            new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pe, ap.av.collateForPDB(pe));
            }
          });
          if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
@@@ -579,7 -576,7 +579,7 @@@
              @Override
              public void actionPerformed(ActionEvent e)
              {
 -              new AppJmol(ap, pr, ap.av.collateForPDB(pr));
 +              new StructureViewer(ap.getStructureSelectionManager()).viewStructures(ap, pr, ap.av.collateForPDB(pr));
              }
            });
          }
@@@ -2100,7 -2097,7 +2100,7 @@@
              { sequence.getDisplayId(false) }));
      chooser.setToolTipText(MessageManager.formatMessage(
              "label.load_pdb_file_associate_with_sequence", new String[]
-             { new Integer(sequence.getDisplayId(false)).toString() }));
+             { sequence.getDisplayId(false) }));
  
      int value = chooser.showOpenDialog(null);