From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 27 Jul 2016 10:57:24 +0000 (+0100)
Subject: JAL-2156 resolve and add complementary views for saveAlignment
X-Git-Tag: Release_2_10_0~125^2~4^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=4afba5fe7acc09d3f9d695edbb04b3572ff0aa09;p=jalview.git

JAL-2156 resolve and add complementary views for saveAlignment
---

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
       {