import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import org.openscience.jmol.app.jmolpanel.console.AppConsole;
public class AppJmolBinding extends JalviewJmolBinding
import org.openscience.jmol.app.jmolpanel.console.AppConsole;
public class AppJmolBinding extends JalviewJmolBinding
private FeatureRenderer fr = null;
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
private FeatureRenderer fr = null;
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
- super(sSm, pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, protocol);
- AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
- : (AlignmentPanel) alignment;
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow
+ .getAlignmentPanel() : (AlignmentPanel) alignment;
- jmolpopup = new JmolAwtPopup();
- jmolpopup.jpiInitialize((viewer), menuName);
+ // jmolpopup = new JmolAwtPopup();
+ // jmolpopup.jpiInitialize((viewer), menuName);