Merge branch 'JAL-1378_jb2.1cli' into RNAalifold

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 24b6c61..6f07b69 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -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
             {