Output groups in annotation file

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1c2605c..74460f7 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -673,7 +673,8 @@ public void itemStateChanged(ItemEvent evt)
   public String outputAnnotations(boolean displayTextbox)\r
   {\r
     String annotation = new AnnotationFile().printAnnotations(\r
-      viewport.alignment.getAlignmentAnnotation() );\r
+      viewport.alignment.getAlignmentAnnotation(),\r
+       viewport.alignment.getGroups() );\r
 \r
     if(displayTextbox)\r
     {\r