JAL-564 (annotation panel height adjustment) and alignment annotation popup menu...

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

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 6bf1dc7..d424367 100755 (executable)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -41,6 +41,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
   TreeCanvas treeCanvas;
 
   NJTree tree;
+  AlignmentPanel ap;
 
   AlignViewport av;
 
@@ -65,7 +66,7 @@ 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 +77,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
       ex.printStackTrace();
     }
 
-    initTreePanel(av, type, pwtype, null);
+    initTreePanel(ap, type, pwtype, null);
   }
 
   /**
@@ -93,7 +94,7 @@ 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 +106,19 @@ 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 +282,8 @@ 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);