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 (file)
--- 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
       {