From 55356b1071b5352edd68ce25a5d3dc3c60dcdc2d Mon Sep 17 00:00:00 2001
From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Mon, 8 Dec 2014 09:45:44 +0000
Subject: [PATCH] Added annotation export configuration for Html export option

---
 .classpath                   |    1 +
 src/jalview/bin/Jalview.java |    4 ++++
 2 files changed, 5 insertions(+)

diff --git a/.classpath b/.classpath
index 4c39421..b75a654 100644
--- a/.classpath
+++ b/.classpath
@@ -55,5 +55,6 @@
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/Plugin.jar"/>
 	<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.launching.macosx.MacOSXType/Java SE 6 [1.6.0_65-b14-462]"/>
 	<classpathentry kind="output" path="classes"/>
 </classpath>
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 17c2472..50e3559 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -398,6 +398,10 @@ public class Jalview
         {
           af.getViewport().setSortByTree(true);
         }
+        if (aparser.contains("no-annotation"))
+        {
+          af.getViewport().setShowAnnotation(false);
+        }
         if (aparser.contains("nosortbytree"))
         {
           af.getViewport().setSortByTree(false);
-- 
1.7.10.2