X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=de9da9fa1f852b8194e0afb7caef44943b486f8e;hb=bad9b1c3e957e44c2fa5ad3a0717ea2a40c1bc12;hp=1c2605c5bf14ea70678d93288ad9cdcc8cd12cf9;hpb=bbc14e2d648fe667157c327043d9bbb238faf65e;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1c2605c..de9da9f 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -673,11 +673,11 @@ public void itemStateChanged(ItemEvent evt)
   public String outputAnnotations(boolean displayTextbox)
   {
     String annotation = new AnnotationFile().printAnnotations(
-      viewport.alignment.getAlignmentAnnotation() );
+        viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,
+        viewport.alignment.getGroups());
 
     if(displayTextbox)
     {
-
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
       Frame frame = new Frame();
       frame.add(cap);
@@ -1512,8 +1512,8 @@ public void itemStateChanged(ItemEvent evt)
     frame.add(overview);
     // +50 must allow for applet frame window
     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
-                                     overview.preferredSize().width,
-                                     overview.preferredSize().height + 50);
+                                     overview.getPreferredSize().width,
+                                     overview.getPreferredSize().height + 50);
 
     frame.pack();
     frame.addWindowListener(new WindowAdapter()
@@ -2420,7 +2420,7 @@ public void itemStateChanged(ItemEvent evt)
     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
     viewport.applet.add(statusBar, BorderLayout.SOUTH);
 
-    alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height
+    alignPanel.setSize(viewport.applet.getSize().width, viewport.applet.getSize().height
                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);
 
      viewport.applet.add(alignPanel, BorderLayout.CENTER);