JAL-1641 fixed broken functionalities after refactor

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index d3d4d6e..3b81e89 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());
 
@@ -597,6 +597,7 @@ public class AppletFormatAdapter
       {
         throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
       }
+
       afile.setNewlineString(newline);
       afile.addJVSuffix(jvsuffix);