X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;fp=src%2Fjalview%2Fgui%2FAlignViewport.java;h=9eaee2051ff5c66f109944304a1af846ad369f9c;hb=ae21643b1d2aa912f1de8b7b0ce3e388860a5493;hp=cf82bfe47ffff71daa1493799770ab08f4317c76;hpb=330763451812f4422e4027a8ee7dc81ab52b269d;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index cf82bfe..9eaee20 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -909,6 +909,7 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (openSplitPane)
     {
+      al.alignAs(thisAlignment);
       protein = openSplitFrame(newAlignFrame, thisAlignment,
               protein.getCodonFrames());
     }