X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=38033ff1a19542d495789270535d32b217483027;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=f22d93af948d4970aae034b779fa5e5538394d12;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index f22d93a..38033ff 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -152,6 +152,7 @@ public class FileLoader implements Runnable
   public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
   {
     this.source = source;
+
     file = source.getInFile();
     protocol = source.type;
     this.format = format;
@@ -276,7 +277,7 @@ public class FileLoader implements Runnable
                   .println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
           // We read the data anyway - it might make sense.
         }
-        alignFrame = new Jalview2XML(raiseGUI).LoadJalviewAlign(file);
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
       }
       else
       {
@@ -352,6 +353,11 @@ public class FileLoader implements Runnable
             {
               alignFrame.setFileName(file, format);
             }
+            if (source instanceof HtmlFile)
+            {
+              ((HtmlFile) source).LoadAlignmentFeatures(alignFrame);
+
+            }
             if (raiseGUI)
             {
               // add the window to the GUI