From 6378890a3881c82f7899386a6890655e758826e5 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 25 Jan 2007 16:02:36 +0000
Subject: [PATCH] Only output visible annotations

---
 src/jalview/io/AMSAFile.java |    2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/jalview/io/AMSAFile.java b/src/jalview/io/AMSAFile.java
index 12a659d..4f21875 100644
--- 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++)
         {
           aa = al.getAlignmentAnnotation()[i];
-          if (aa.autoCalculated)
+          if (aa.autoCalculated || !aa.visible)
             continue;
 
           out.append(">#_" + aa.label);
-- 
1.7.10.2