import java.awt.Canvas;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
+import java.awt.FlowLayout;
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Frame;
import java.awt.Menu;
import java.awt.MenuBar;
import java.awt.MenuItem;
+import java.awt.Panel;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusEvent;
import java.util.StringTokenizer;
import java.util.Vector;
-import javax.swing.JOptionPane;
-
import org.jmol.viewer.Viewer;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
{
boolean showForAlignment = showAlignmentAnnotations.getState();
boolean showForSequences = showSequenceAnnotations.getState();
- for (AlignmentAnnotation aa : alignPanel.getAlignment()
+ if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : alignPanel.getAlignment()
.getAlignmentAnnotation())
{
boolean visible = (aa.sequenceRef == null ? showForAlignment
: showForSequences);
aa.visible = visible;
+ }
}
alignPanel.validateAnnotationDimensions(true);
validate();
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
- // TODO need to trigger a repaint of the complementary panel - how?
- // would prefer to handle in SplitFrame but it is not overriding key
- // listener chiz
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
}
}
/*
* If the cut affects all sequences, warn, remove highlighted columns
- */if (sg.getSize() == viewport.getAlignment().getHeight())
+ */
+ if (sg.getSize() == viewport.getAlignment().getHeight())
{
boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
.getAlignment().getWidth()) ? true : false;
if (isEntireAlignWidth)
{
- int confirm = JOptionPane.showConfirmDialog(this,
- MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
- MessageManager.getString("label.delete_all"), // $NON-NLS-1$
- JOptionPane.OK_CANCEL_OPTION);
-
- if (confirm == JOptionPane.CANCEL_OPTION
- || confirm == JOptionPane.CLOSED_OPTION)
+ String title = MessageManager.getString("label.delete_all");
+ Panel infoPanel = new Panel();
+ infoPanel.setLayout(new FlowLayout());
+ infoPanel
+ .add(new Label(MessageManager.getString("warn.delete_all")));
+
+ final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
+ dialog.setMainPanel(infoPanel);
+ dialog.ok.setLabel(MessageManager.getString("action.ok"));
+ dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
+ dialog.setVisible(true);
+
+ if (!dialog.accept)
{
return;
}
TrimRegionCommand trimRegion;
if (trimLeft)
{
- trimRegion = new TrimRegionCommand("Remove Left",
- TrimRegionCommand.TRIM_LEFT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
+ column, viewport.getAlignment());
viewport.setStartRes(0);
}
else
{
- trimRegion = new TrimRegionCommand("Remove Right",
- TrimRegionCommand.TRIM_RIGHT, seqs, column,
- viewport.getAlignment(), viewport.getColumnSelection(),
- viewport.getSelectionGroup());
+ trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
+ column, viewport.getAlignment());
}
statusBar.setText(MessageManager.formatMessage(
}
+ @Override
public void changeColour(ColourSchemeI cs)
{
this.add(statusBar, BorderLayout.SOUTH);
}
+ @Override
public void setStatus(String string)
{
statusBar.setText(string);