JAL-1988 JAVA 11 enabled version with Quit, Preferences and About handlers enabled...

[jalview.git] / src / jalview / gui / TreePanel.java

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index c07648d..2727db1 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -155,7 +155,10 @@ public class TreePanel extends GTreePanel
       @Override
       public void internalFrameClosed(InternalFrameEvent evt)
       {
-        av.removePropertyChangeListener(listener);
+        if (av != null)
+        {
+          av.removePropertyChangeListener(listener);
+        }
       }
     });
 
@@ -519,7 +522,7 @@ public class TreePanel extends GTreePanel
 
     if (treeCanvas.applyToAllViews)
     {
-      final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+      final ArrayList<CommandI> commands = new ArrayList<>();
       for (AlignmentPanel ap : PaintRefresher
               .getAssociatedPanels(av.getSequenceSetId()))
       {
@@ -576,13 +579,14 @@ public class TreePanel extends GTreePanel
 
   public CommandI sortAlignmentIn(AlignmentPanel ap)
   {
+    // TODO: move to alignment view controller
     AlignmentViewport viewport = ap.av;
     SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
     AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
     CommandI undo;
     undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
 
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, false);
     return undo;
   }