Need reference to mainApplet

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 80006c2..68960f4 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -467,7 +467,7 @@ public class APopupMenu
 \r
   protected void analyze_actionPerformed(ActionEvent e)\r
   {\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
     Frame frame = new Frame();\r
     frame.add(cap);\r
     jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 5641846..7289fc4 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1161,13 +1161,13 @@ public class AlignFrame
     if (viewport.getSelectionGroup() != null &&\r
         viewport.getSelectionGroup().getSize() > 3)\r
     {\r
-      tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
+      tp = new TreePanel(alignPanel, viewport.getSelectionGroup().sequences, type,\r
                          pwType,\r
                          0, viewport.alignment.getWidth());\r
     }\r
     else\r
     {\r
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
+      tp = new TreePanel(alignPanel, viewport.getAlignment().getSequences(),\r
                          type, pwType, 0, viewport.alignment.getWidth());\r
     }\r
 \r

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index ca5fe23..82b97a5 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -75,7 +75,7 @@ public class AnnotationLabels
     }\r
     else if (evt.getActionCommand().equals(OUTPUT_TEXT))\r
     {\r
-      CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
       Frame frame = new Frame();\r
       frame.add(cap);\r
       jalview.bin.JalviewLite.addFrame(frame,\r

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 58da074..1785961 100755 (executable)
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -34,7 +34,7 @@ public class TreePanel
   SequenceI[] seq;\r
   String type;\r
   String pwtype;\r
-  AlignViewport av;\r
+  AlignmentPanel ap;\r
   int start;\r
   int end;\r
   TreeCanvas treeCanvas;\r
@@ -45,11 +45,12 @@ public class TreePanel
     return tree;\r
   }\r
 \r
-  public TreePanel(AlignViewport av, Vector seqVector, String type,\r
+  public TreePanel(AlignmentPanel ap, Vector seqVector, String type,\r
                    String pwtype, int s, int e)\r
   {\r
     super();\r
 \r
+    this.ap = ap;\r
     this.type = type;\r
     this.pwtype = pwtype;\r
 \r
@@ -69,7 +70,7 @@ public class TreePanel
 \r
     tree = new NJTree(seq, type, pwtype, start, end);\r
 \r
-    treeCanvas = new TreeCanvas(av, tree, scrollPane, longestName);\r
+    treeCanvas = new TreeCanvas(ap.av, tree, scrollPane, longestName);\r
 \r
     tree.reCount(tree.getTopNode());\r
     tree.findHeight(tree.getTopNode());\r
@@ -142,7 +143,7 @@ public class TreePanel
   {\r
     jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
     String output = fout.print(false, true);\r
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
     cap.setText(output);\r
     java.awt.Frame frame = new java.awt.Frame();\r
     frame.add(cap);\r