X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=aa76da599eb073f84dc9bcd530b8351694145b5e;hb=b005d2429ec2b467aaf18318336842dc4c292b76;hp=9ccde9e2968b9ca3bc1f4893eba6ea03d8b36fe2;hpb=e2d6753e8cf3c5eaf8bccf34f4f5e9d651e9cb8e;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9ccde9e..aa76da5 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -348,11 +348,11 @@ public class FileLoader implements Runnable
             }
             if (source instanceof HtmlFile)
             {
-              ((HtmlFile) source).LoadAlignmentFeatures(alignFrame);
+              ((HtmlFile) source).applySettingsToAlignFrame(alignFrame);
             }
             else if (source instanceof JSONFile)
             {
-              ((JSONFile) source).LoadAlignmentFeatures(alignFrame);
+              ((JSONFile) source).applySettingsToAlignFrame(alignFrame);
             }
 
             if (raiseGUI)
@@ -384,7 +384,9 @@ public class FileLoader implements Runnable
 
           final String errorMessage = "Couldn't load file " + title + "\n"
                   + error;
-          if (raiseGUI)
+          // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
+          // bits ?
+          if (raiseGUI && Desktop.desktop != null)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {