import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
import java.awt.Container;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.console.AppletConsole;
-import org.jmol.java.BS;
+import javajs.util.BS;
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;
}
@Override
- 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;
- }
-
- @Override
public jalview.api.SequenceRenderer getSequenceRenderer(
AlignmentViewPanel alignment)
{
{
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)
{
}
Container consolePanel, String buttonsToShow)
{
JmolAppConsoleInterface appc = new AppletConsole();
- appc.start(viewer);
+ appc.start(jmolViewer);
return appc;
}
@Override
public int[] resizeInnerPanel(String data)
{
- // TODO Auto-generated method stub
return null;
}
@Override
public Map<String, Object> getJSpecViewProperty(String arg0)
{
- // TODO Auto-generated method stub
return null;
}
}