JAL-653 JAL-966 TODO and avoid NPE when desktop instance unavailable

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9ccde9e..aa76da5 100755 (executable)
--- 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()
             {