X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=7595a50cc71832fc0cb1625ce439577f52a99f7b;hb=de69fbf90655974ac954c4acb1dcd74fa581ef4c;hp=92dcde4360bf693cbeadf506639a7ed993d00318;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
old mode 100755
new mode 100644
index 92dcde4..7595a50
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -41,6 +41,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
   TreeCanvas treeCanvas;
 
   NJTree tree;
+  AlignmentPanel ap;
 
   AlignViewport av;
 
@@ -48,6 +49,12 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
   {
     return tree;
   }
+  
+  public void finalize() throws Throwable {
+    ap=null;
+    av=null;
+    super.finalize();
+  }
 
   /**
    * Creates a new TreePanel object.
@@ -65,7 +72,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
    * @param e
    *          DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, String type, String pwtype)
+  public TreePanel(AlignmentPanel ap, String type, String pwtype)
   {
     try
     {
@@ -76,7 +83,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       ex.printStackTrace();
     }
 
-    initTreePanel(av, type, pwtype, null);
+    initTreePanel(ap, type, pwtype, null);
   }
 
   /**
@@ -93,7 +100,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
    * @param pwtype
    *          DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, String type, String pwtype,
+  public TreePanel(AlignmentPanel ap, String type, String pwtype,
           NewickFile newtree)
   {
     try
@@ -105,18 +112,19 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       e.printStackTrace();
     }
 
-    initTreePanel(av, type, pwtype, newtree);
+    initTreePanel(ap, type, pwtype, newtree);
   }
 
-  void initTreePanel(AlignViewport av, String type, String pwtype,
+  void initTreePanel(AlignmentPanel ap, String type, String pwtype,
           NewickFile newTree)
   {
 
-    this.av = av;
+    this.ap = ap;
+    this.av = ap.av;
     this.type = type;
     this.pwtype = pwtype;
 
-    treeCanvas = new TreeCanvas(av, scrollPane);
+    treeCanvas = new TreeCanvas(ap, scrollPane);
     TreeLoader tl = new TreeLoader(newTree);
     tl.start();
     embedMenuIfNeeded(treeCanvas);
@@ -280,8 +288,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
 
   public void newickOutput_actionPerformed()
   {
-    jalview.io.NewickFile fout = new jalview.io.NewickFile(tree
-            .getTopNode());
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(
+            tree.getTopNode());
     String output = fout.print(false, true);
     CutAndPasteTransfer cap = new CutAndPasteTransfer(false, null);
     cap.setText(output);