Look for pairwiseAlignpanel

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index e6200d9..af96ee8 100755 (executable)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -575,7 +575,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     void reorderAssociatedWindows(boolean minimize)
     {
       JInternalFrame[] frames = desktop.getAllFrames();
-      if (frames == null)
+      if (frames == null || frames.length<1)
         return;
 
       AlignViewport source = null, target = null;
@@ -585,6 +585,9 @@ public class Desktop extends jalview.jbgui.GDesktop
         source = ( (TreePanel) frames[0]).getViewPort();
       else if (frames[0] instanceof PCAPanel)
         source = ( (PCAPanel) frames[0]).av;
+      else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
+        source = ((PairwiseAlignPanel)frames[0].getContentPane()).av;
+
 
       if (source != null)
         for (int i = 0; i < frames.length; i++)
@@ -596,6 +599,8 @@ public class Desktop extends jalview.jbgui.GDesktop
             target = ( (TreePanel) frames[i]).getViewPort();
           else if (frames[i] instanceof PCAPanel)
             target = ( (PCAPanel) frames[i]).av;
+          else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
+            target = ( (PairwiseAlignPanel) frames[i].getContentPane()).av;
 
           if (source == target)
           {