Allow for frame insets

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 74460f7..de9da9f 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -673,12 +673,11 @@ public void itemStateChanged(ItemEvent evt)
   public String outputAnnotations(boolean displayTextbox)\r
   {\r
     String annotation = new AnnotationFile().printAnnotations(\r
-      viewport.alignment.getAlignmentAnnotation(),\r
-       viewport.alignment.getGroups() );\r
+        viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,\r
+        viewport.alignment.getGroups());\r
 \r
     if(displayTextbox)\r
     {\r
-\r
       CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
       Frame frame = new Frame();\r
       frame.add(cap);\r
@@ -1513,8 +1512,8 @@ public void itemStateChanged(ItemEvent evt)
     frame.add(overview);\r
     // +50 must allow for applet frame window\r
     jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
-                                     overview.preferredSize().width,\r
-                                     overview.preferredSize().height + 50);\r
+                                     overview.getPreferredSize().width,\r
+                                     overview.getPreferredSize().height + 50);\r
 \r
     frame.pack();\r
     frame.addWindowListener(new WindowAdapter()\r
@@ -2421,7 +2420,7 @@ public void itemStateChanged(ItemEvent evt)
     viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
     viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
 \r
-    alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height\r
+    alignPanel.setSize(viewport.applet.getSize().width, viewport.applet.getSize().height\r
                        - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
 \r
      viewport.applet.add(alignPanel, BorderLayout.CENTER);\r