X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=5795a9fc90249b1499ed420a763a0ccf8fd914d0;hb=d43e766fa05058226c417d214e0b8d83294ec6e2;hp=c07648d6199e705b725621f72f50fd3fd463c45b;hpb=4ed094c1b9defe721d27e5c52b467dc49032f5ed;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index c07648d..5795a9f 100755
--- 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);
+        }
       }
     });
 
@@ -387,6 +390,7 @@ public class TreePanel extends GTreePanel
   @Override
   public void saveAsNewick_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 save newick file for Jalview-JS
     JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
@@ -519,7 +523,7 @@ 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 +580,14 @@ 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;
   }
 
@@ -692,6 +697,7 @@ public class TreePanel extends GTreePanel
 
     try
     {
+      // TODO: JAL-3048 not needed for Jalview-JS - Requires EpsGraphics2D dependency
       JalviewFileChooser chooser = new JalviewFileChooser(
               ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
       chooser.setFileView(new JalviewFileView());
@@ -735,6 +741,7 @@ public class TreePanel extends GTreePanel
   @Override
   public void pngTree_actionPerformed(ActionEvent e)
   {
+    // TODO: JAL-3048 image export supported in JalviewJS ?
     int width = treeCanvas.getWidth();
     int height = treeCanvas.getHeight();