X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=90400f421547f8ca45e8b20134c1b28e2c06e1f5;hb=ff2d6b48be7f17742defac9c965c70d7944d773b;hp=d3d4d6e49ad81c26d9ac1aac38e116a00a92229d;hpb=65a810f2dd78c44eef0f06bc0afbe3ad3e891848;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d3d4d6e..90400f4 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -483,7 +483,7 @@ public class AppletFormatAdapter
   private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
   {
     // Standard boilerplate for creating alignment from parser
-    alignFile.configureForView(viewpanel);
+    // alignFile.configureForView(viewpanel);
 
     AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
 
@@ -519,7 +519,7 @@ public class AppletFormatAdapter
         aselview.addAnnotation(aa);
       }
     }
-
+    viewpanel = ap;
     return formatSequences(format, aselview, jvsuffix);
   }
 
@@ -597,11 +597,10 @@ public class AppletFormatAdapter
       {
         throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
       }
+
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);
-
       afile.setExportSettings(exportSettings);
-
       afile.configureForView(viewpanel);
 
       // check whether we were given a specific alignment to export, rather than