X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=6f07b693f3f382e1ab6f5d7e63d4d942d2f37ed4;hb=ef0377ec8e57164363e74c33d6ede31f85e8ccf7;hp=cbdfc6ffae9a3ffdfe80e920441194187d794276;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index cbdfc6f..6f07b69 100755
--- 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, 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 
@@ -303,6 +303,7 @@ public class FileLoader implements Runnable
         {
           if (viewport != null)
           {
+            // TODO: create undo object for this JAL-1101
             for (int i = 0; i < al.getHeight(); i++)
             {
               viewport.getAlignment().addSequence(al.getSequenceAt(i));
@@ -321,9 +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
             {