import jalview.analysis.AlignmentSorter;
import jalview.analysis.Conservation;
+import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
import jalview.api.SequenceStructureBinding;
import jalview.bin.JalviewLite;
import java.util.Vector;
public class AlignFrame extends EmbmenuFrame implements ActionListener,
- ItemListener, KeyListener
+ ItemListener, KeyListener, AlignViewControllerGuiI
{
public AlignViewControllerI avc;
public AlignmentPanel alignPanel;
{
ex.printStackTrace();
}
-
+ // need to get window geometry before we calculate alignment layout
+ if (applet != null)
+ {
+ String param;
+ try
+ {
+ param = applet.getParameter("windowWidth");
+ if (param != null)
+ {
+ int width = Integer.parseInt(param);
+ DEFAULT_WIDTH = width;
+ }
+ param = applet.getParameter("windowHeight");
+ if (param != null)
+ {
+ int height = Integer.parseInt(param);
+ DEFAULT_HEIGHT = height;
+ }
+ } catch (Exception ex)
+ {
+ }
+ }
viewport = new AlignViewport(al, applet);
alignPanel = new AlignmentPanel(this, viewport);
- avc = new jalview.controller.AlignViewController(viewport, alignPanel);
+ avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
centreColumnLabelFlag.setState(true);
centreColumnLabelFlag_stateChanged();
}
- try
- {
- param = applet.getParameter("windowWidth");
- if (param != null)
- {
- int width = Integer.parseInt(param);
- DEFAULT_WIDTH = width;
- }
- param = applet.getParameter("windowHeight");
- if (param != null)
- {
- int height = Integer.parseInt(param);
- DEFAULT_HEIGHT = height;
- }
- } catch (Exception ex)
- {
- }
}
if (viewport.getAlignment().isNucleotide())
}
+
+ public void setStatus(String string) {
+ statusBar.setText(string);
+ };
+
MenuItem featureSettings = new MenuItem();
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();