From d7c94f1d531ef43bbabb7d1951c8e34c1366eeb2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 1 Sep 2005 13:43:26 +0000
Subject: [PATCH] Need reference to mainApplet

---
 src/jalview/appletgui/APopupMenu.java       |    2 +-
 src/jalview/appletgui/AlignFrame.java       |    4 ++--
 src/jalview/appletgui/AnnotationLabels.java |    2 +-
 src/jalview/appletgui/TreePanel.java        |    9 +++++----
 4 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 80006c2..68960f4 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -467,7 +467,7 @@ public class APopupMenu
 
   protected void analyze_actionPerformed(ActionEvent e)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
     Frame frame = new Frame();
     frame.add(cap);
     jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 5641846..7289fc4 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1161,13 +1161,13 @@ public class AlignFrame
     if (viewport.getSelectionGroup() != null &&
         viewport.getSelectionGroup().getSize() > 3)
     {
-      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,
+      tp = new TreePanel(alignPanel, viewport.getSelectionGroup().sequences, type,
                          pwType,
                          0, viewport.alignment.getWidth());
     }
     else
     {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
+      tp = new TreePanel(alignPanel, viewport.getAlignment().getSequences(),
                          type, pwType, 0, viewport.alignment.getWidth());
     }
 
diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index ca5fe23..82b97a5 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -75,7 +75,7 @@ public class AnnotationLabels
     }
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))
     {
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
       Frame frame = new Frame();
       frame.add(cap);
       jalview.bin.JalviewLite.addFrame(frame,
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 58da074..1785961 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -34,7 +34,7 @@ public class TreePanel
   SequenceI[] seq;
   String type;
   String pwtype;
-  AlignViewport av;
+  AlignmentPanel ap;
   int start;
   int end;
   TreeCanvas treeCanvas;
@@ -45,11 +45,12 @@ public class TreePanel
     return tree;
   }
 
-  public TreePanel(AlignViewport av, Vector seqVector, String type,
+  public TreePanel(AlignmentPanel ap, Vector seqVector, String type,
                    String pwtype, int s, int e)
   {
     super();
 
+    this.ap = ap;
     this.type = type;
     this.pwtype = pwtype;
 
@@ -69,7 +70,7 @@ public class TreePanel
 
     tree = new NJTree(seq, type, pwtype, start, end);
 
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);
+    treeCanvas = new TreeCanvas(ap.av, tree, scrollPane, longestName);
 
     tree.reCount(tree.getTopNode());
     tree.findHeight(tree.getTopNode());
@@ -142,7 +143,7 @@ public class TreePanel
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
     String output = fout.print(false, true);
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
     cap.setText(output);
     java.awt.Frame frame = new java.awt.Frame();
     frame.add(cap);
-- 
1.7.10.2