added default ClustalWS or MuscleWS to remove gaps.

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 83ee1c3..343ca2b 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1187,7 +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);
         }
   }
 
@@ -1273,7 +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) {