X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;fp=src%2Fjalview%2Fws%2Fjws2%2FMsaWSThread.java;h=d2c1b383d1dbf1373e14ddacbdac7add90fc76fd;hb=59c9459d9b84f5e980da09599f2f0067a639fa8b;hp=d0d0a6e5ef75a5f1330837e03038bbb34f484bdd;hpb=b418ccd95340c2d930e69c5f1033aa8eac7c7935;p=jalview.git

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index d0d0a6e..d2c1b38 100644
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -959,6 +959,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
     }
     else
     {
+      // TODO 2.9.x feature
       System.out.println("MERGE WITH OLD FRAME");
       // TODO: modify alignment in original frame, replacing old for new
       // alignment using the commands.EditCommand model to ensure the update can
@@ -987,17 +988,22 @@ class MsaWSThread extends AWS2Thread implements WSClientI
       addSortByMenuItems(af, alorders);
     }
 
+    // TODO: refactor retrieve and show as new splitFrame as Desktop method
+
     /*
      * If alignment was requested from one half of a SplitFrame, show in a
      * SplitFrame with the other pane similarly aligned.
      */
     AlignFrame requestedBy = getRequestingAlignFrame();
-    if (requestedBy != null && requestedBy.getSplitViewContainer() != null)
+    if (requestedBy != null && requestedBy.getSplitViewContainer() != null
+    		&& requestedBy.getSplitViewContainer().getComplement(requestedBy)!=null)
     {
       AlignmentI complement = requestedBy.getSplitViewContainer()
               .getComplement(requestedBy);
       String complementTitle = requestedBy.getSplitViewContainer()
               .getComplementTitle(requestedBy);
+      // becomes null if the alignment window was closed before the alignment
+      // job finished.
       AlignmentI copyComplement = new Alignment(complement);
       copyComplement.alignAs(al);
       if (copyComplement.getHeight() > 0)