Merge branch 'develop' into features/JAL-653_gffalignments

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index ba620ca..de9e6bd 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,6 +20,10 @@
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.InputStream;
+import java.util.List;
+
 import jalview.api.AlignViewportI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -28,10 +32,6 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
 
-import java.io.File;
-import java.io.InputStream;
-import java.util.List;
-
 /**
  * A low level class for alignment and feature IO with alignment formatting
  * methods used by both applet and application for generating flat alignment
@@ -293,6 +293,7 @@ public class AppletFormatAdapter
         {
           al.addGroup(sg);
         }
+
         return al;
       }
       else if (format.equals(HtmlFile.FILE_DESC))
@@ -444,7 +445,6 @@ public class AppletFormatAdapter
       else if (format.equals(JSONFile.FILE_DESC))
       {
         alignFile = new JSONFile(source);
-        // ((JSONFile) afile).setViewport(viewport);
         al = new Alignment(alignFile.getSeqsAsArray());
         alignFile.addAnnotations(al);
         alignFile.addSeqGroups(al);