Only output visible annotations

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 12a659d..4f21875 100644 (file)
--- a/src/jalview/io/AMSAFile.java
+++ b/src/jalview/io/AMSAFile.java
@@ -47,7 +47,7 @@ public class AMSAFile extends jalview.io.FastaFile
         for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
         {\r
           aa = al.getAlignmentAnnotation()[i];\r
-          if (aa.autoCalculated)\r
+          if (aa.autoCalculated || !aa.visible)\r
             continue;\r
 \r
           out.append(">#_" + aa.label);\r