X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=343ca2b776cc5299843f4b4105b1c16d3ec4cab8;hb=abe6225acb5316fd1f8c20e56a58c26aeced0b0c;hp=b0eca3ebc3952f24a0ff3a67c25a99fbeecd52d5;hpb=965f716343378d40bcf2dc29d7cb2ec3d10e2767;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b0eca3e..343ca2b 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1004,7 +1004,8 @@ public class AlignFrame extends GAlignFrame
 
   public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
   {
-    if(viewport.getSelectionGroup().getSize()<2)
+    if((viewport.getSelectionGroup()==null) ||
+       viewport.getSelectionGroup().getSize()<2)
       JOptionPane.showInternalMessageDialog(this, "You must select at least 2 sequences.", "Invalid Selection", JOptionPane.WARNING_MESSAGE);
     else
     {
@@ -1186,7 +1187,7 @@ public class AlignFrame extends GAlignFrame
 
         }
         if (msa!=null) {
-          jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, true, true);
+          jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS", title, msa, false, true);
         }
   }
 
@@ -1272,7 +1273,7 @@ public class AlignFrame extends GAlignFrame
 
       }
       if (msa!=null) {
-        MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, true, true);
+        MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS",title, msa, false, true);
       }
   }
     protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {