Dont export annotations if not visible

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 74460f7..061cf0d 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