+
+ @Override
+ public void sortByTree_actionPerformed()
+ {
+
+ // if (applyToAllViews)
+
+ final ArrayList<CommandI> commands = new ArrayList<>();
+ for (AlignmentPanel ap : PaintRefresher
+ .getAssociatedPanels(parentAvport.getSequenceSetId()))
+ {
+ commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
+ ap.alignFrame.addHistoryItem(new CommandI()
+ {
+
+ @Override
+ public void undoCommand(AlignmentI[] views)
+ {
+ for (CommandI tsort : commands)
+ {
+ tsort.undoCommand(views);
+ }
+ }
+
+ @Override
+ public int getSize()
+ {
+ return commands.size();
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return "Tree Sort (many views)";
+ }
+
+ @Override
+ public void doCommand(AlignmentI[] views)
+ {
+
+ for (CommandI tsort : commands)
+ {
+ tsort.doCommand(views);
+ }
+ }
+ });
+
+ ap.alignFrame.updateEditMenuBar();
+ }
+ }
+ // else
+ // {
+ // alignPanel.alignFrame.addHistoryItem(sortAlignmentIn(alignPanel));
+ // }
+
+
+
+ @Override
+ public CommandI sortAlignmentIn(AlignmentPanel ap)
+ {
+ AlignmentViewport viewport = ap.av;
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ try
+ {
+ AlignmentSorter.sortByTree(viewport.getAlignment(),
+ nodesBoundToSequences,
+ treeView.getTree());
+ CommandI undo;
+ undo = new OrderCommand("Tree Sort", oldOrder,
+ viewport.getAlignment());
+
+ ap.paintAlignment(true, false);
+ return undo;
+
+ } catch (Exception e)
+ {
+ System.err.println(e.getMessage());
+ }
+ return null;