*/
public void saveAlignment(String file, FileFormatI format)
{
- saveAlignment(file, format, false);
+ saveAlignment(file, format, false, false);
}
- public void saveAlignment(String file, FileFormatI format, boolean stdout)
+ public void saveAlignment(String file, FileFormatI format, boolean stdout,
+ boolean forceBackup)
{
lastSaveSuccessful = true;
if (!stdout)
else
{
// create backupfiles object and get new temp filename destination
- boolean doBackup = BackupFiles.getEnabled() && !stdout;
+ boolean doBackup = forceBackup
+ || (BackupFiles.getEnabled() && !stdout);
BackupFiles backupfiles = null;
if (doBackup)
{
*/
public void createPNG(File f) throws ImageOutputException
{
- createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing());
+ createPNG(f, null, BitmapImageSizing.defaultBitmapImageSizing());
}
public void createPNG(File f, String renderer, BitmapImageSizing userBis)
closeAllTabs = true;
}
+ Desktop.closeModal(this);
+
try
{
if (alignPanels != null)
featureSettings.close();
featureSettings = null;
}
+
/*
* this will raise an INTERNAL_FRAME_CLOSED event and this method will
* be called recursively, with the frame now in 'closed' state
*
* @return alignment objects for all views
*/
- AlignmentI[] getViewAlignments()
+ public AlignmentI[] getViewAlignments()
{
if (alignPanels != null)
{
}
JInternalFrame frame = new JInternalFrame();
-
+ frame.setFrameIcon(null);
frame.getContentPane().add(new JScrollPane(pane));
Desktop.addInternalFrame(frame, MessageManager
return alignPanel.overviewPanel;
}
JInternalFrame frame = new JInternalFrame();
+ frame.setFrameIcon(null);
final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
showHidden);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
frame.getHeight(), true, true);
- frame.setFrameIcon(null);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
final AlignmentPanel thePanel = this.alignPanel;
else
{
JInternalFrame frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(new PairwiseAlignPanel(viewport));
Desktop.addInternalFrame(frame,
MessageManager.getString("action.pairwise_alignment"), 600,