JAL-381 Desktop.addInternalFrame cannot be called in headless mode

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 975a1a3..6f07b69 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -322,9 +322,14 @@ public class FileLoader implements Runnable
 
             if (!protocol.equals(AppletFormatAdapter.PASTE))
               alignFrame.setFileName(file, format);
-
-            Desktop.addInternalFrame(alignFrame, title,
-                    AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            if (raiseGUI)
+            {
+              // add the window to the GUI
+              // note - this actually should happen regardless of raiseGUI status in Jalview 3
+              // TODO: define 'virtual desktop' for benefit of headless scripts that perform queries to find the 'current working alignment'
+              Desktop.addInternalFrame(alignFrame, title,
+                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            }
 
             try
             {