From 4afba5fe7acc09d3f9d695edbb04b3572ff0aa09 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 27 Jul 2016 11:57:24 +0100
Subject: [PATCH] JAL-2156 resolve and add complementary views for
 saveAlignment

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 9861697..b027246 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -635,9 +635,15 @@ public class Jalview2XML
       JarOutputStream jout = new JarOutputStream(fos);
       List<AlignFrame> frames = new ArrayList<AlignFrame>();
 
+      // resolve splitframes
+      if (af.getViewport().getCodingComplement() != null)
       {
+        frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
       }
+      else
+      {
         frames.add(af);
+      }
       saveAllFrames(frames, jout);
       try
       {
-- 
1.7.10.2