import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.gui.IProgressIndicator;
+import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
import java.awt.Container;
import java.util.Map;
-import javajs.awt.Dimension;
-
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.console.AppletConsole;
import org.jmol.java.BS;
-import org.jmol.popup.JmolAwtPopup;
class AppletJmolBinding extends JalviewJmolBinding
{
public AppletJmolBinding(AppletJmol appletJmol,
StructureSelectionManager sSm, PDBEntry[] pdbentry,
- SequenceI[][] seq, String[][] chains, String protocol)
+ SequenceI[][] seq, DataSourceType protocol)
{
- super(sSm, pdbentry, seq, chains, protocol);
+ super(sSm, pdbentry, seq, protocol);
appletJmolBinding = appletJmol;
}
public jalview.api.FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (appletJmolBinding.ap.av.isShowSequenceFeatures())
- {
- if (appletJmolBinding.fr == null)
- {
- appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(
- appletJmolBinding.ap.av);
- }
-
- appletJmolBinding.fr
- .transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
- }
-
- return appletJmolBinding.fr;
+ return appletJmolBinding.ap.getFeatureRenderer();
}
@Override
appletJmolBinding.showConsole(true);
}
- appletJmolBinding.history.append("\n" + strEcho);
+ appletJmolBinding.addToHistory(strEcho);
}
@Override
if (appletJmolBinding.history != null && strStatus != null
&& !strStatus.equals("Script completed"))
{
- appletJmolBinding.history.append("\n" + strStatus);
+ appletJmolBinding.addToHistory(strStatus);
}
}
appletJmolBinding.updateTitleAndMenus();
}
+ @Override
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ colourBySequence(ap);
}
+ @Override
public void showUrl(String url)
{
try
{
- appletJmolBinding.ap.av.applet.getAppletContext().showDocument(
- new java.net.URL(url), "jmol");
+ appletJmolBinding.ap.av.applet.getAppletContext()
+ .showDocument(new java.net.URL(url), "jmol");
} catch (java.net.MalformedURLException ex)
{
}
public void newJmolPopup(boolean translateLocale, String menuName,
boolean asPopup)
{
- jmolpopup = new JmolAwtPopup(); // is this used?
- jmolpopup.jpiInitialize((viewer), menuName);
-
+ // jmolpopup = new JmolAwtPopup(); // is this used?
+ // jmolpopup.jpiInitialize((viewer), menuName);
}
@Override
// do nothing.
}
+ @Override
public void selectionChanged(BS arg0)
{
// TODO Auto-generated method stub
}
@Override
- public Dimension resizeInnerPanel(String data)
+ public int[] resizeInnerPanel(String data)
{
// TODO Auto-generated method stub
return null;
// TODO Auto-generated method stub
return null;
}
+
+ @Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ // no progress indicators on the applet
+ return null;
+ }
}