X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=c18c989dce5b5299d1c0f9d8698695310099ebea;hb=7a1a7eea9501cd9e3841e996f4926cf1686be76a;hp=b27518607159c03661be36f5cea17bbb4b8245d4;hpb=c9df5bd6e95c23c9b560c0a59003d1f4043f8055;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b275186..c18c989 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());
     }
@@ -1027,13 +1028,13 @@ public class AlignViewport extends AlignmentViewport implements
      * is found, the result will be empty.
      */
     SearchResults sr = new SearchResults();
-    int seqOffset = findComplementScrollTarget(sr);
+    int verticalOffset = findComplementScrollTarget(sr);
     if (!sr.isEmpty())
     {
       // TODO would like next line without cast but needs more refactoring...
       final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()).getAlignPanel();
       complementPanel.setFollowingComplementScroll(true);
-      complementPanel.scrollToCentre(sr, seqOffset);
+      complementPanel.scrollToCentre(sr, verticalOffset);
     }
   }