From 266c4e2544701f88a8d21294b4a4f4cc42cf76cc Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 10 May 2007 08:10:03 +0000
Subject: [PATCH] visibility setting

---
 src/jalview/gui/Jalview2XML.java |    9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index aa1abb3..061dfca 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1345,10 +1345,13 @@ public class Jalview2XML
         if (an[i].getId() != null
             && annotationIds.containsKey(an[i].getId()))
         {
-          al.addAnnotation(
+          jalview.datamodel.AlignmentAnnotation jda =
               (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
-              getId())
-              );
+              getId());
+          if (an[i].hasVisible())
+            jda.visible = an[i].getVisible();
+
+          al.addAnnotation(jda);
 
           continue;
         }
-- 
1.7.10.2