import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
- public void saveAlignment(String file, FileFormatI format, boolean stdout)
+ public void saveAlignment(String file, FileFormatI format, boolean stdout,
+ boolean forceBackup)
/*
* this will raise an INTERNAL_FRAME_CLOSED event and this method will
* be called recursively, with the frame now in 'closed' state
/*
* this will raise an INTERNAL_FRAME_CLOSED event and this method will
* be called recursively, with the frame now in 'closed' state
frame.getContentPane().add(new JScrollPane(pane));
Desktop.addInternalFrame(frame, MessageManager
frame.getContentPane().add(new JScrollPane(pane));
Desktop.addInternalFrame(frame, MessageManager
final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
showHidden);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
frame.getHeight(), true, true);
final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
showHidden);
frame.setContentPane(overview);
Desktop.addInternalFrame(frame, "", true, frame.getWidth(),
frame.getHeight(), true, true);
frame.setContentPane(new PairwiseAlignPanel(viewport));
Desktop.addInternalFrame(frame,
MessageManager.getString("action.pairwise_alignment"), 600,
frame.setContentPane(new PairwiseAlignPanel(viewport));
Desktop.addInternalFrame(frame,
MessageManager.getString("action.pairwise_alignment"), 600,
- Jalview.setCurrentAlignFrame(this);
- groovy.ui.Console console = Desktop.getGroovyConsole();
+ Jalview.getInstance().setCurrentAlignFrame(this);
+ groovy.console.ui.Console console = Desktop.getGroovyConsole();