/*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
{
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));
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
{