import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.java.BS;
-import org.jmol.popup.JmolAwtPopup;
import org.openscience.jmol.app.jmolpanel.console.AppConsole;
public class AppJmolBinding extends JalviewJmolBinding
private FeatureRenderer fr = null;
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
{
- super(sSm, pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, protocol);
appJmolWindow = appJmol;
}
@Override
- public FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
- : (AlignmentPanel) alignment;
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow
+ .getAlignmentPanel() : (AlignmentPanel) alignment;
if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
}
@Override
- public SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
// appJmolWindow.repaint();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
appJmolWindow.updateTitleAndMenus();
});
}
+ @Override
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source, topap;
+ AlignmentPanel ap = (AlignmentPanel) source;
// ignore events from panels not used to colour this view
if (!appJmolWindow.isUsedforcolourby(ap))
{
}
if (!isLoadingFromArchive())
{
- colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ colourBySequence(ap);
}
}
// msWalltime);
}
+ @Override
public void showUrl(String url)
{
showUrl(url, "jmol");
public void newJmolPopup(String menuName)
{
- jmolpopup = new JmolAwtPopup();
- jmolpopup.jpiInitialize((viewer), menuName);
+ // jmolpopup = new JmolAwtPopup();
+ // jmolpopup.jpiInitialize((viewer), menuName);
}
@Override