From bbc14e2d648fe667157c327043d9bbb238faf65e Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 29 Jan 2007 17:41:12 +0000
Subject: [PATCH] New view copies annotations across

---
 src/jalview/appletgui/AlignFrame.java |   11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 36ee5da..1c2605c 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1426,6 +1426,17 @@ public void itemStateChanged(ItemEvent evt)
     else
       newal = new Alignment(viewport.alignment.getSequencesArray());
 
+    if(viewport.alignment.getAlignmentAnnotation()!=null)
+    {
+      for(int i=0; i<viewport.alignment.getAlignmentAnnotation().length; i++)
+      {
+        if(!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)
+        {
+          newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);
+        }
+      }
+    }
+
     AlignFrame newaf = new AlignFrame(newal,
                                       viewport.applet,
                                       "",
-- 
1.7.10.2