/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*/
package jalview.appletgui;
-import java.awt.Container;
-import java.util.BitSet;
-
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.Container;
+import java.util.BitSet;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolViewer;
-import org.jmol.applet.AppletConsole;
import org.jmol.popup.JmolPopup;
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
*/
private AppletJmol appletJmolBinding;
- public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry,
+ public AppletJmolBinding(AppletJmol appletJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
SequenceI[][] seq, String[][] chains, String protocol)
{
- super(pdbentry, seq, chains, protocol);
+ super(sSm, pdbentry, seq, chains, protocol);
appletJmolBinding = appletJmol;
}
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
+ AlignmentPanel ap = (AlignmentPanel)alignment;
if (appletJmolBinding.ap.av.showSequenceFeatures)
{
if (appletJmolBinding.fr == null)
return appletJmolBinding.fr;
}
- public jalview.api.SequenceRenderer getSequenceRenderer()
+ public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- return new SequenceRenderer(appletJmolBinding.ap.av);
+ return new SequenceRenderer(((AlignmentPanel)alignment).av);
}
public void sendConsoleEcho(String strEcho)
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ colourBySequence(ap.av.getShowSequenceFeatures(), ap);
}
public void showUrl(String url)
boolean asPopup)
{
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
+ jmolpopup = new JmolPopup();
+ jmolpopup.initialize(viewer, translateLocale, menuName,
asPopup);
}
protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
Container consolePanel, String buttonsToShow)
{
- return new AppletConsole(viewer2, consolePanel);
+ //return new org.jmol.console.AppletConsole(viewer2, consolePanel);
+ JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole().getAppConsole(viewer2);
+ return appc;
}
@Override
}
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ }
+ @Override
+ public void resizeInnerPanel(String data)
+ {
+ // TODO Auto-generated method stub
+
+ }
}