New view copies annotations across

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 36ee5da..1c2605c 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1426,6 +1426,17 @@ public void itemStateChanged(ItemEvent evt)
     else\r
       newal = new Alignment(viewport.alignment.getSequencesArray());\r
 \r
+    if(viewport.alignment.getAlignmentAnnotation()!=null)\r
+    {\r
+      for(int i=0; i<viewport.alignment.getAlignmentAnnotation().length; i++)\r
+      {\r
+        if(!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+        {\r
+          newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
+        }\r
+      }\r
+    }\r
+\r
     AlignFrame newaf = new AlignFrame(newal,\r
                                       viewport.applet,\r
                                       "",\r