JAL-1641 round trip test/refactoring

[jalview.git] / src / jalview / io / AppletFormatAdapter.java

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d3d4d6e..90400f4 100755 (executable)
--- 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